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stringlengths 4
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stringclasses 28
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int64 31
5.38M
| score
float64 2.52
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listlengths 0
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stringclasses 2
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stringlengths 31
5.39M
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bool 1
class |
|---|---|---|---|---|---|---|---|---|---|---|---|
6a075f6f8438f51c12371e562c017539109833a8
|
Shell
|
mcamiano/grog
|
/grog/kshscripts/showm.sh
|
UTF-8
| 259
| 2.734375
| 3
|
[] |
no_license
|
# showm.sh: Show defined methods
#
# $1=Oracle username/password
# $2=class name
#
echo "Class: $2"
sqlplus -s $1 <<EOT | grep -v "^$"
set heading off
set feedback off
select methodtype, name from grogmethod where upper(classname) = upper('$2')
/
quit
/
EOT
| true
|
b3d2512bb9bab62ab100de37b5dba58b857b242c
|
Shell
|
talkersource/ncohafmuta
|
/bot/restart
|
UTF-8
| 516
| 3.546875
| 4
|
[] |
no_license
|
#!/bin/sh
# by Cygnus
# ncohafmuta@asteroid-b612.org
#
# The name of the storybot binary or program
BINARY="storybot"
# This next part copies over the log file to a backup,
if test -f "botlog"
then
echo "Coping bot log to backup file..."
cp botlog botlog.`/bin/date '+%m%d%y.%T'`
rm botlog
touch botlog
fi
if test -f "$BINARY"
then
echo -n "Starting the storybot..."
./$BINARY
echo "Done"
echo "See log file for details"
else
echo "Can't find the storybot program! Have you compiled it with ./compile?"
fi
| true
|
bf9e50c7531eb977628ced17e350713991a8faa6
|
Shell
|
nagabhushandevops/DevopsClass
|
/printnoto1.sh
|
UTF-8
| 73
| 3.15625
| 3
|
[] |
no_license
|
#!/bin/bash
n=$1
while [ $n -gt 0 ];
do
echo "$n"
n=`expr $n - 1`
done
| true
|
1315035b66bd858255e674f6476adc208f7956fb
|
Shell
|
infinitis/ci
|
/entrypoint.sh
|
UTF-8
| 2,714
| 3.4375
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
set -euo pipefail
# verify that variables used only in sourced files are set
# so exit/failure will happen appropriately
# ( source returns 0 if no commands are run which happen with bash strict mode )
REMOTE=$REMOTE_LOCATION
REPOS=$REPOSITORY_NAMES
# setup ssh
runuser -u git -- mkdir -p /home/git/.ssh
echo "$HOST_FINGERPRINT" >> /home/git/.ssh/known_hosts
cat > /home/git/.ssh/config << EOF
Host github.com
IdentityFile ~/.ssh/keys/github
User git
StrictHostKeyChecking no
EOF
chown git:git /home/git/.ssh/known_hosts
chown git:git /home/git/.ssh/config
# clone repos
. /clone.sh
# setup fcgiwrap
echo "FCGI_CHILDREN=2" > /etc/default/fcgiwrap
service fcgiwrap start
# setup nginx
cat > /etc/nginx/nginx.conf << EOF
user www-data www-data;
events { }
http {
include mime.types;
server {
listen 80;
root /usr/share/gitweb;
# static repo files for cloning over https
location ~ ^.*\.git/objects/([0-9a-f]+/[0-9a-f]+|pack/pack-[0-9a-f]+.(pack|idx))$ {
root /repos/;
}
# requests that need to go to git-http-backend
location ~ ^.*\.git/(HEAD|info/refs|objects/info/.*|git-(upload|receive)-pack)$ {
root /repos/;
fastcgi_pass unix:/var/run/fcgiwrap.socket;
fastcgi_param SCRIPT_FILENAME /usr/lib/git-core/git-http-backend;
fastcgi_param PATH_INFO \$uri;
fastcgi_param GIT_PROJECT_ROOT \$document_root;
fastcgi_param GIT_HTTP_EXPORT_ALL "";
fastcgi_param REMOTE_USER \$remote_user;
include fastcgi_params;
}
# Remove all conf beyond if you don't want Gitweb
try_files \$uri @gitweb;
location @gitweb {
fastcgi_pass unix:/var/run/fcgiwrap.socket;
fastcgi_param SCRIPT_FILENAME /usr/share/gitweb/gitweb.cgi;
fastcgi_param PATH_INFO \$uri;
fastcgi_param GITWEB_CONFIG /etc/gitweb.conf;
include fastcgi_params;
}
}
}
EOF
# setup gitweb
cat > /etc/gitweb.conf << EOF
\$projectroot = "/repos";
\$git_temp = "/tmp";
\$site_name = "$SITE_NAME";
\$base_url = "/";
EOF
# setup push.sh script for cron
cat > /push.sh << EOF
#!/usr/bin/env bash
set -euo pipefail
while IFS= read -r repo
do
if [[ -n "\$repo" ]]; then
cd "/repos/\$repo.git"
if [[ -z "\`git remote | grep github\`" ]]; then
git remote add github "git@github.com:$GITHUB_USERNAME/\$repo.git"
fi
git push --all -f github
fi
done < <(echo "$REPOSITORY_NAMES")
EOF
chmod +x /push.sh
# setup fetch.sh script for cron
cat > /fetch.sh << EOF
#!/usr/bin/env bash
set -euo pipefail
while IFS= read -r repo
do
if [[ -n "\$repo" ]]; then
cd "/repos/\$repo.git"
git fetch --prune --prune-tags
fi
done < <(echo "$REPOSITORY_NAMES")
EOF
chmod +x /fetch.sh
# setup cron
service cron start
# start nginx
nginx -g 'daemon off;'
| true
|
630298c7202b870a6571ed059960739af4f2b925
|
Shell
|
satheeshkumark/NLP
|
/Sentiment_Analysis/step1_ParseJSONTweets.sh
|
UTF-8
| 1,403
| 3.4375
| 3
|
[] |
no_license
|
inputJSONFile=$1
outputParseFile=$2
script_path='scripts/'
enDataPath='data/'
esDataPath='data1/'
ruDataPath='data2/'
faDataPath='data3/'
keywordPath='keywords/'
parseScript=$script_path'step0_jsonparser.py'
dbScript=$script_path'step0_InsertRecords.py'
enkeyWordFile=$enDataPath$keywordPath'en-keywords.txt'
eskeyWordFile=$esDataPath$keywordPath'es-keywords.txt'
rukeyWordFile=$ruDataPath$keywordPath'ru-keywords.txt'
fakeyWordFile=$faDataPath$keywordPath'fa-keywords.txt'
#################################
#### Input : Input JSON File containing Twitter data
#### Output : Parsed File containing tweets and their meta data
echo $outputParseFile
python $parseScript $inputJSONFile $outputParseFile
#################################
#### Input : Output of previous step. Parsed metdata file from twitter
#### Output : Inserts data in the database
#### Requirement : Have to configure the database settings within the step0_InsertRecords.py program
#### This code needs to be modified if any new language is going to be added
#python $dbScript $outputParseFile
################ Push the tweetmetadata into db depending on language and retrieve the tweets of required language.
################ The above script pushes the tweet metadata to db. NOTE : db is needed to be configured accordingly
################ The script filteringTweets.py pulls and processes tweets depending on the language
| true
|
e5e94a93711a931656c5dea33f1ad341f045a392
|
Shell
|
kitwtnb/dotfiles
|
/bin/adbss
|
UTF-8
| 382
| 3.0625
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
set -ue -o pipefail
export LC_ALL=C
DEVICE_NAME=`adb devices | sed -e '1d' | cut -f 1 | peco`
echo "Capturing $DEVICE_NAME"
SAVE_PATH="$HOME/Downloads/capture.png"
adb -s $DEVICE_NAME shell screencap -p /sdcard/screen.png
adb -s $DEVICE_NAME pull /sdcard/screen.png $SAVE_PATH
adb -s $DEVICE_NAME shell rm /sdcard/screen.png
echo "Saved image to $SAVE_PATH"
| true
|
2eaa91610673a6b9c9a9ce233207194ee82c2410
|
Shell
|
matthewfallshaw/dotfiles
|
/oh-my-zsh/cds.zsh
|
UTF-8
| 144
| 3.125
| 3
|
[] |
no_license
|
# cd into source dir
function cds {
if [ -z "$1" ]; then
cd ~/source
else
cd ~/source/$1
fi
}
compdef '_files -/ -W ~/source' cds
| true
|
97403a2c7ff4b4e3c6a192808a56ad50581226d9
|
Shell
|
swvanderlaan/HerculesToolKit
|
/_archived/check_mich_imp.sh
|
UTF-8
| 30,498
| 3.46875
| 3
|
[
"MIT"
] |
permissive
|
#!/bin/bash
#
#$ -S /bin/bash # the type of BASH you'd like to use
#$ -N IMPUTE_HRC # the name of this script
# -hold_jid some_other_basic_bash_script # the current script (basic_bash_script) will hold until some_other_basic_bash_script has finished
#$ -o /hpc/dhl_ec/svanderlaan/projects/impute_hrc/impute_hrc.v2.3.1.v20190117.log # the log file of this job
#$ -e /hpc/dhl_ec/svanderlaan/projects/impute_hrc/impute_hrc.v2.3.1.v20190117.errors # the error file of this job
#$ -l h_rt=00:15:00 # h_rt=[max time, e.g. 02:02:01] - this is the time you think the script will take
#$ -l h_vmem=8G # h_vmem=[max. mem, e.g. 45G] - this is the amount of memory you think your script will use
# -l tmpspace=64G # this is the amount of temporary space you think your script will use
#$ -M s.w.vanderlaan-2@umcutrecht.nl # you can send yourself emails when the job is done; "-M" and "-m" go hand in hand
#$ -m beas # you can choose: b=begin of job; e=end of job; a=abort of job; s=suspended job; n=no mail is send
#$ -cwd # set the job start to the current directory - so all the things in this script are relative to the current directory!!!
#
# You can use the variables above (indicated by "#$") to set some things for the submission system.
# Another useful tip: you can set a job to run after another has finished. Name the job
# with "-N SOMENAME" and hold the other job with -hold_jid SOMENAME".
# Further instructions: https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/HowToS#Run_a_job_after_your_other_jobs
#
# It is good practice to properly name and annotate your script for future reference for
# yourself and others. Trust me, you'll forget why and how you made this!!!
### Creating display functions
### Setting colouring
NONE='\033[00m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
BOLD='\033[1m'
ITALIC='\033[3m'
UNDERLINE='\033[4m'
STRIKETHROUGH='\033[9m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 1979-${THISYEAR} Sander W. van der Laan +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror "- Argument #1 -- Project name, could be 'Athero-ExpressGenomicsStudy1' ."
echoerror "- Argument #2 -- Dataset name to create directories and intermediate files, could be 'AEGS1'."
echoerror "- Argument #3 -- File name of input file, could be 'aegs1_snp5brlmmp_b37_QCwithChrX'."
echoerror "- Argument #4 -- complete/path_to where the original data resides, could be '/hpc/dhl_ec/data/_ae_originals'."
echoerror "- Argument #5 -- complete/path_to where the project directory is, could be '/hpc/dhl_ec/svanderlaan/projects/impute_hrc'."
echoerror "- Argument #6 -- set the script mode, could be [PREP/CHECK]."
echoerror ""
echoerror "An example command would be: impute_hrc.sh [arg1: Athero-ExpressGenomicsStudy1] [arg2: AEGS1] [arg3: aegs1_snp5brlmmp_b37_QCwithChrX ] [arg4: /hpc/dhl_ec/data/_ae_originals] [arg5: /hpc/dhl_ec/svanderlaan/projects/impute_hrc] [arg6: PREP/CHECK]"
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
script_arguments_error_mode() {
echoerror "$1"
echoerror ""
echoerror " *** ERROR *** ERROR --- $(basename "${0}") --- ERROR *** ERROR ***"
echoerror ""
echoerror " You must supply the correct argument:"
echoerror " * [PREP] -- set the PREPARATOR mode, meaning the cohort data will be prepared for use on the Imputation-server."
echoerror " * [CHECK] -- set the CHECK mode, meaning we will check the output of the PREPARATOR mode."
echoerror ""
echoerror " Please refer to instruction above."
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " MICHIGAN IMPUTATION DATA STATISTICS"
echo ""
echoitalic "* Written by : Sander W. van der Laan"
echoitalic "* E-mail : s.w.vanderlaan-2@umcutrecht.nl"
echoitalic "* Last update : 2019-02-14"
echoitalic "* Version : 1.0.0"
echo ""
echoitalic "* Description : This script will calculate some SNP and sample based "
echoitalic " statistics for a study after imputation through the "
echoitalic " Michigan Imputation Server."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Today's: "$(date)
TODAY=$(date +"%Y%m%d")
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
if [[ $# -lt 6 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [6] correct arguments when running a *** MICHIGAN IMPUTATION SERVER PREPARATOR ***!"
else
# Set these as an argument for your study
PROJECTNAME="$1" # "Athero-Express Genomics Study 1"
DATASETNAME="$2" # "AEGS1"
FILENAME="$3" # "aegs1_snp5brlmmp_b37_QCwithChrX", i.e. the original-dataset name
ORIGINALS="$4" # "/hpc/dhl_ec/data/_ae_originals"
# Set this to your root
ROOTDIR="$5" # "/hpc/dhl_ec/svanderlaan/projects/impute_hrc"
# You needn't change this - this should all be present
if [ ! -d ${ROOTDIR}/PRE_IMP_CHECK/ ]; then
mkdir -v ${ROOTDIR}/PRE_IMP_CHECK/
fi
PROJECTDIR="${ROOTDIR}/PRE_IMP_CHECK"
# Set mode
MODE="$6"
echo ""
echobold "We have set the following project paths and (file)names:"
echo "Project name: ________________________________ [ ${PROJECTNAME} ]"
echo "Dataset output name: _________________________ [ ${DATASETNAME} ]"
echo "Dataset input filename (without path): _______ [ ${FILENAME} ]"
echo "Complete path to input dataset: ______________ [ ${ORIGINALS} ]"
echo "Complete path to the working directory _______ [ ${ROOTDIR} ]"
echoitalic "Note that all the data will be written to a subdirectory (PRE_IMP_CHECK) of the working directory."
# Software settings
SOFTWARE="/hpc/local/CentOS7/dhl_ec/software"
QCTOOL15="${SOFTWARE}/qctool_v1.5-linux-x86_64-static/qctool"
VCFTOOLS="${SOFTWARE}/vcftools-v0.1.14-10-g4491144/bin"
BCFTOOLS="${SOFTWARE}/bcftools_v1.6"
CHECKVCF="${SOFTWARE}/checkvcf/checkVCF.py"
VCFSORT="${SOFTWARE}/vcftools-v0.1.14-10-g4491144/bin/vcf-sort"
BGZIP16="${SOFTWARE}/bgzip_v1.6"
TABIX16="${SOFTWARE}/tabix_v1.6"
PLINK19="${SOFTWARE}/plink_v1.9"
echo ""
echobold "We will make use of the following software: "
echo "Software directory ___________________________ ${SOFTWARE}"
echo " - QCTOOL v1.5 _______________________________ ${QCTOOL15}"
echo " - VCFTools __________________________________ ${VCFTOOLS}"
echo " - BCFTools __________________________________ ${BCFTOOLS}"
echo " - CHECKVCF __________________________________ ${CHECKVCF}"
echo " - VCFsort ___________________________________ ${VCFSORT}"
echo " - BGZip _____________________________________ ${BGZIP16}"
echo " - Tabix _____________________________________ ${TABIX16}"
echo " - PLINK v1.09 (beta) ________________________ ${PLINK19}"
# QSUB settings
QSUBTIME="01:00:00"
QSUBMEM="8G"
QSUBCHECKTIME="02:00:00"
QSUBCHECKMEM="64G"
QSUBMAIL="s.w.vanderlaan-2@umcutrecht.nl"
QSUBMAILSETTING="a"
echo ""
echoitalic "Job-queue submission rules were set."
echo ""
if [[ ${MODE} = "PREP" ]]; then
echobold "The mode is [ ${MODE} ], hence we will prepare the cohort data for use on the Michigan Imputation Server."
elif [[ ${MODE} = "CHECK" ]]; then
echobold "The mode is [ ${MODE} ], hence we will check whether the preparation of the data was successful."
else
### If arguments are not met then this error message will be displayed
script_arguments_error_mode
fi
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Setting up the stage for the PLINK file checking."
echo ""
echobold "Making directories."
## Make directories for script if they do not exist yet (!!!PREREQUISITE!!!)
echo "* ${PROJECTNAME} [ ${DATASETNAME} ]"
# directories to collect all the post-imputation-check data
if [ ! -d ${PROJECTDIR}/${DATASETNAME}_HRC_r1_1_2016/ ]; then
mkdir -v ${PROJECTDIR}/${DATASETNAME}_HRC_r1_1_2016/
fi
IMPDATA_HRC=${PROJECTDIR}/${DATASETNAME}_HRC_r1_1_2016
if [ ! -d ${PROJECTDIR}/${DATASETNAME}_1000Gp3/ ]; then
mkdir -v ${PROJECTDIR}/${DATASETNAME}_1000Gp3/
fi
IMPDATA_1KGp3=${PROJECTDIR}/${DATASETNAME}_1000Gp3
echo ""
echobold "Installing tools & references."
echo "* Creating directories."
if [ ! -d ${SOFTWARE}/wrayner_tools/ ]; then
mkdir -v ${SOFTWARE}/wrayner_tools/
fi
WRAYNERTOOLS=${SOFTWARE}/wrayner_tools
if [ ! -d ${WRAYNERTOOLS}/HRC_r1_1_2016/ ]; then
mkdir -v ${WRAYNERTOOLS}/HRC_r1_1_2016/
fi
WRAYNERTOOLS_HRC=${WRAYNERTOOLS}/HRC_r1_1_2016
if [ ! -d ${WRAYNERTOOLS}/1000GP_Phase3/ ]; then
mkdir -v ${WRAYNERTOOLS}/1000GP_Phase3/
fi
WRAYNERTOOLS_1KGP3=${WRAYNERTOOLS}/1000GP_Phase3
### On our HPC this is already done. Note that I had gotten a custom version from Rayner with
### that works on our system ("${SOFTWARE}/wrayner_tools/HRC-1000G-check-bim.v4.2.9.pl")
echo "* Downloading tool -- do only once!!!"
### wget http://www.well.ox.ac.uk/~wrayner/tools/HRC-1000G-check-bim.v4.2.5.zip -O ${WRAYNERTOOLS}/HRC-1000G-check-bim.v4.2.5.zip
### wget http://www.well.ox.ac.uk/~wrayner/tools/HRC-1000G-check-bim-v4.2.6.zip -O ${WRAYNERTOOLS}/HRC-1000G-check-bim.v4.2.6.zip
### wget http://www.well.ox.ac.uk/~wrayner/tools/HRC-1000G-check-bim-v4.2.7.zip -O ${WRAYNERTOOLS}/HRC-1000G-check-bim.v4.2.7.zip
### echo "* unzipping tool"
### cd ${WRAYNERTOOLS}
### unzip -o ${WRAYNERTOOLS}/HRC-1000G-check-bim.v4.2.6.zip
### Just a sanity check: is it there?
ls -lh ${WRAYNERTOOLS}
# Setting Wrayner's CheckTool
HRC1000GCHECK="${SOFTWARE}/wrayner_tools/HRC-1000G-check-bim.v4.2.9.pl"
echo "* Downloading references -- do only once!!!"
echo " - Downloading HRC release 1.1 2016, b37."
### wget ftp://ngs.sanger.ac.uk/production/hrc/HRC.r1-1/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz -O ${WRAYNERTOOLS_HRC}/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz
### ${WRAYNERTOOLS_HRC}
### gunzip -v ${WRAYNERTOOLS_HRC}/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz
### Just a sanity check: is it there?
ls -lh ${WRAYNERTOOLS_HRC}
### On our HPC this is also already done.
echo " - Downloading 1000G phase 3 (combined), b37."
### wget http://www.well.ox.ac.uk/~wrayner/tools/1000GP_Phase3_combined.legend.gz -O ${WRAYNERTOOLS_1KGP3}/1000GP_Phase3_combined.legend.gz
### ${WRAYNERTOOLS_1KGP3}
### gunzip -v ${WRAYNERTOOLS_1KGP3}/1000GP_Phase3_combined.legend.gz
ls -lh ${WRAYNERTOOLS_1KGP3}
echobold "Installing checkVCF -- do only once!!!"
### RUN ONLY ONCE!!!
### On our HPC this is already done.
### cd ${SOFTWARE}
### mkdir -v checkvcf
### cd checkvcf/
### wget http://qbrc.swmed.edu/zhanxw/software/checkVCF/checkVCF-20140116.tar.gz
### tar -zxvf checkVCF-20140116.tar.gz
### rm -v checkVCF-20140116.tar.gz
### samtools_v1.3 faidx hs37d5.fa
### cd ..
### chmod -Rv a+xrw checkvcf/
if [[ ${MODE} = "PREP" ]]; then
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Calculating frequencies."
echo "* Frequencies in ${DATASETNAME}"
cp -fv ${ORIGINALS}/${FILENAME}.bed ${IMPDATA_HRC}/${DATASETNAME}.postQC.bed
cp -fv ${ORIGINALS}/${FILENAME}.bim ${IMPDATA_HRC}/${DATASETNAME}.postQC.bim
cp -fv ${ORIGINALS}/${FILENAME}.fam ${IMPDATA_HRC}/${DATASETNAME}.postQC.fam
cp -fv ${ORIGINALS}/${FILENAME}.bed ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.bed
cp -fv ${ORIGINALS}/${FILENAME}.bim ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.bim
cp -fv ${ORIGINALS}/${FILENAME}.fam ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.fam
echo "${PLINK19} --bfile ${IMPDATA_HRC}/${DATASETNAME}.postQC --freq --out ${IMPDATA_HRC}/${DATASETNAME}.postQC_FREQ " > ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.sh
qsub -S /bin/bash -N FREQ_HRC_MICHIMP -e ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.errors -o ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_HRC} ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.sh
echo "${PLINK19} --bfile ${IMPDATA_1KGp3}/${DATASETNAME}.postQC --freq --out ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_FREQ " > ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.sh
qsub -S /bin/bash -N FREQ_1kG_MICHIMP -e ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.errors -o ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_1KGp3} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.sh
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Checking PLINK files for [ ${DATASETNAME} ]."
### Usage:
### For HRC:
### perl HRC-1000G-check-bim-v4.2.7.pl -b <bim file> -f <Frequency file> -r <Reference panel> -h [-v -t <allele frequency threshold -n]
###
### For 1000G:
### perl HRC-1000G-check-bim-v4.2.7.pl -b <bim file> -f <Frequency file> -r <Reference panel> -g -p <population> [-v -t <allele frequency threshold -n]
###
###
### -b --bim bim file Plink format .bim file
### -f --frequency Frequency file Plink format .frq allele frequency file, from plink --freq command
### -r --ref Reference panel Reference Panel file, either 1000G or HRC
### -h --hrc Flag to indicate Reference panel file given is HRC
### -g --1000g Flag to indicate Reference panel file given is 1000G
### -p --pop Population Population to check frequency against, 1000G only. Default ALL, options ALL, EUR, AFR, AMR, SAS, EAS
### -v --verbose Optional flag to increase verbosity in the log file
### -t --threshold Freq threshold Frequency difference to use when checking allele frequency of data set versus reference; default: 0.2; range: 0-1
### -n --noexclude Optional flag to include all SNPs regardless of allele frequency differences, default is exclude based on -t threshold, overrides -t
echo ""
echo "* Checking for HRC imputation."
cd ${IMPDATA_HRC}
# old version: ${WRAYNERTOOLS}/HRC-1000G-check-bim.pl
echo "perl ${HRC1000GCHECK} -b ${IMPDATA_HRC}/${DATASETNAME}.postQC.bim -f ${IMPDATA_HRC}/${DATASETNAME}.postQC_FREQ.frq -r ${WRAYNERTOOLS_HRC}/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz -h -v " > ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.sh
qsub -S /bin/bash -N Check_HRC_MICHIMP -hold_jid FREQ_HRC_MICHIMP -e ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.errors -o ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.log -l h_rt=${QSUBCHECKTIME} -l h_vmem=${QSUBCHECKMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_HRC} ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.sh
echo ""
echo "* Checking for 1000G imputation."
cd ${IMPDATA_1KGp3}
# old version: ${WRAYNERTOOLS}/HRC-1000G-check-bim.pl
echo "perl ${HRC1000GCHECK} -b ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.bim -f ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_FREQ.frq -r ${WRAYNERTOOLS_1KGP3}/1000GP_Phase3_combined.legend.gz -g -p ALL -v " > ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.sh
qsub -S /bin/bash -N Check_1kG_MICHIMP -hold_jid FREQ_1kG_MICHIMP -e ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.errors -o ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.log -l h_rt=${QSUBCHECKTIME} -l h_vmem=${QSUBCHECKMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_1KGp3} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.sh
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Running PLINK-based corrections for [ ${DATASETNAME} ]."
echo ""
echo "* Correcting."
cd ${IMPDATA_HRC}
echo "bash ${IMPDATA_HRC}/Run-plink.sh \ " > ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.sh
qsub -S /bin/bash -N Corr_HRC_MICHIMP -hold_jid Check_HRC_MICHIMP -e ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.errors -o ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_HRC} ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.sh
cd ${IMPDATA_1KGp3}
echo "bash ${IMPDATA_1KGp3}/Run-plink.sh \ " > ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.sh
qsub -S /bin/bash -N Corr_1kG_MICHIMP -hold_jid Check_1kG_MICHIMP -e ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.errors -o ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_1KGp3} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.sh
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Generating VCF files for HRC imputation of [ ${DATASETNAME} ]."
echo ""
echo "* Making VCF."
cd ${IMPDATA_HRC}
for CHR in $(seq 1 23); do
echo ""
echo "- Converting"
echo "${PLINK19} --bfile ${IMPDATA_HRC}/${DATASETNAME}.postQC-updated-chr${CHR} --chr ${CHR} --output-chr MT --keep-allele-order --recode vcf-iid --out ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR} " > ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.sh
qsub -S /bin/bash -N Convert_HRC_MICHIMP -hold_jid Corr_HRC_MICHIMP -e ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.errors -o ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_HRC} ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.sh
echo ""
echo "- BGzipping and indexing"
echo "${VCFSORT} ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.vcf | ${BGZIP16} ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.vcf " > ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.sh
echo "${TABIX16} -p vcf ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.vcf.gz " >> ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.sh
qsub -S /bin/bash -N Index_HRC_MICHIMP -hold_jid Convert_HRC_MICHIMP -e ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.errors -o ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_HRC} ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.sh
done
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Generating VCF files for 1000G imputation of [ ${DATASETNAME} ]."
echo ""
echo "* Making VCF."
cd ${IMPDATA_1KGp3}
for CHR in $(seq 1 23); do
echo ""
echo "${PLINK19} --bfile ${IMPDATA_1KGp3}/${DATASETNAME}.postQC-updated-chr${CHR} --chr ${CHR} --output-chr MT --keep-allele-order --recode vcf-iid --out ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR} " > ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.sh
qsub -S /bin/bash -N Convert_1kG_MICHIMP -hold_jid Corr_1kG_MICHIMP -e ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.errors -o ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_1KGp3} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.sh
echo ""
echo "- BGzipping and indexing"
echo "${VCFSORT} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.vcf | ${BGZIP16} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.vcf " > ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.sh
echo "${TABIX16} -p vcf ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.vcf.gz " >> ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.sh
qsub -S /bin/bash -N Index_1kG_MICHIMP -hold_jid Convert_1kG_MICHIMP -e ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.errors -o ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.log -l h_rt=${QSUBTIME} -l h_vmem=${QSUBMEM} -M ${QSUBMAIL} -m ${QSUBMAILSETTING} -wd ${IMPDATA_1KGp3} ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.sh
done
elif [[ ${MODE} = "CHECK" ]]; then
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Checking outputs."
### NOT FINISHED YET
### - make it automatic
### - make it write a report
### - get in if-else statements regarding checks, if error > do not remove etc files
if [ ! -d ${IMPDATA_HRC}/_scripts_logs ]; then
mkdir -v ${IMPDATA_HRC}/_scripts_logs
fi
SCRIPTLOGDIR_HRC="${IMPDATA_HRC}/_scripts_logs"
if [ ! -d ${IMPDATA_1KGp3}/_scripts_logs ]; then
mkdir -v ${IMPDATA_1KGp3}/_scripts_logs
fi
SCRIPTLOGDIR_1KGp3="${IMPDATA_1KGp3}/_scripts_logs"
echo ""
echoitalic "Frequencies calculations"
cat ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.log | grep -e "--freq: Allele frequencies (founders only) written to"
mv -v ${IMPDATA_HRC}/${DATASETNAME}.postQC.freq.* ${SCRIPTLOGDIR_HRC}/
cat ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.log | grep -e "--freq: Allele frequencies (founders only) written to"
mv -v ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.freq.* ${SCRIPTLOGDIR_1KGp3}/
echo ""
echoitalic "Genotype checking"
tail -30 ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.log
cat ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.log | grep -e "people pass filters and QC."
mv -v ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcheck.* ${SCRIPTLOGDIR_HRC}/
mv -v ${IMPDATA_HRC}/${DATASETNAME}.postQC.HRCcorr.* ${SCRIPTLOGDIR_HRC}/
tail -30 ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.log
cat ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.log | grep -e "people pass filters and QC."
mv -v ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcheck.* ${SCRIPTLOGDIR_1KGp3}/
mv -v ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.1kGcorr.* ${SCRIPTLOGDIR_1KGp3}/
echo ""
echoitalic "PLINK corrections"
for CHR in $(seq 1 23); do
echo "checking updated files for chromosome ${CHR}"
cat ${IMPDATA_HRC}/${DATASETNAME}.postQC-updated-chr${CHR}.log | grep -e "Total genotyping rate is"
cat ${IMPDATA_1KGp3}/${DATASETNAME}.postQC-updated-chr${CHR}.log | grep -e "Total genotyping rate is"
done
echo ""
echoitalic "VCF conversion"
for CHR in $(seq 1 23) ; do
echo "checking conversion of chromosome $CHR"
cat ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.log | grep -e "pass filters and QC."
mv -v ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCconvert.* ${SCRIPTLOGDIR_HRC}/
cat ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.log | grep -e "pass filters and QC."
mv -v ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGconvert.* ${SCRIPTLOGDIR_1KGp3}/
done
echo ""
echoitalic "- VCF indexing and bzgipping"
for CHR in $(seq 1 23) ; do
echo "checking conversion of chromosome $CHR"
cat ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.log | grep -e "pass filters and QC."
mv -v ${IMPDATA_HRC}/${DATASETNAME}.postQC.chr${CHR}.HRCindexzip.* ${SCRIPTLOGDIR_HRC}/
cat ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.log | grep -e "pass filters and QC."
mv -v ${IMPDATA_1KGp3}/${DATASETNAME}.postQC.chr${CHR}.1kGindexzip.* ${SCRIPTLOGDIR_1KGp3}/
done
echo ""
echoitalic "- VCF files"
for CHR in $(seq 1 23) ; do
echo "checking chromosome $CHR files"
${CHECKVCF} -r ${SOFTWARE}/checkvcf/hs37d5.fa -o -out ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.vcf.gz
mv -v $(pwd)/-out.check.af ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.af
mv -v $(pwd)/-out.check.dup ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.dup
mv -v $(pwd)/-out.check.geno ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.geno
mv -v $(pwd)/-out.check.log ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.log
mv -v $(pwd)/-out.check.mono ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.mono
mv -v $(pwd)/-out.check.nonSnp ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.nonSnp
mv -v $(pwd)/-out.check.ref ${IMPDATA_HRC}/${DATASETNAME}.postQC_inHRCr11_chr${CHR}.check.ref
${CHECKVCF} -r ${SOFTWARE}/checkvcf/hs37d5.fa -o -out ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.vcf.gz
mv -v $(pwd)/-out.check.af ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.af
mv -v $(pwd)/-out.check.dup ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.dup
mv -v $(pwd)/-out.check.geno ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.geno
mv -v $(pwd)/-out.check.log ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.log
mv -v $(pwd)/-out.check.mono ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.mono
mv -v $(pwd)/-out.check.nonSnp ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.nonSnp
mv -v $(pwd)/-out.check.ref ${IMPDATA_1KGp3}/${DATASETNAME}.postQC_in1KGp3_chr${CHR}.check.ref
done
echo ""
echoitalic "- gzipping the txt-file-shizzle"
else
### If arguments are not met then this error message will be displayed
script_arguments_error_mode
fi
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Wow. I'm all done buddy. What a job! let's have a beer!"
date
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message
# TEMPORARY -- WILL BE REMOVED
# mich_imp_prep HELPFul_GSA HELPFul_GSA helpful.gsa.clean /hpc/dhl_ec/data/_helpful_originals/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep MYOMARKER_GSA MYOMARKER_GSA myomarker.gsa.clean /hpc/dhl_ec/data/_myomarker_originals/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep UCORBIO_GSA UCORBIO_GSA ucorbio.gsa.clean /hpc/dhl_ec/data/_ucorbio_originals/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep BIOSHIFTTRIUMPH_GSA BIOSHIFTTRIUMPH_GSA bioshifttriumph.gsa.clean /hpc/dhl_ec/data/_bioshift_triumph_originals/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep RIVM_GSA RIVM_GSA rivm.gsa.clean /hpc/dhl_ec/data/_rivm_originals/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep AEGS1_AFFYSNP5 AEGS1_AFFYSNP5 AEGS1.clean /hpc/dhl_ec/data/_ae_originals/AEGS1_AffySNP5/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep AEGS2_AFFYAXIOMCEU AEGS2_AFFYAXIOMCEU AEGS2.clean /hpc/dhl_ec/data/_ae_originals/AEGS2_AffyAxiomGWCEU1/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep AEGS3_GSA AEGS3_GSA aegs3.gsa.clean /hpc/dhl_ec/data/_ae_originals/AEGS3_GSA/GENOTYPES2018 /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# mich_imp_prep EPIC_NL_GSA EPIC_NL_GSA FINAL_GSA_SET /hpc/dhl_ec/data/_epic_nl/EPICNLGSA_QC /hpc/dhl_ec/svanderlaan/projects/impute_hrc
# for i in $(seq 1 22) ; do qctool_v2 -filetype vcf -g epicnl.1kgp3.chr${i}.dose.vcf.gz -vcf-genotype-field GP -snp-stats -osnp epicnl.1kgp3.chr${i}.dose.vcf.stats; done
| true
|
42970a189d73eb5a38bf810fca8e6bb609acb17d
|
Shell
|
thaddeusdiamond/Home
|
/.bash_aliases
|
UTF-8
| 6,057
| 3.703125
| 4
|
[] |
no_license
|
#####################################
# ALIASES FOR SCRIPTS #
#####################################
# Custom delete function
alias del='mv ${*} -t ~/TRASH'
# Suppress output
Quiet() { >/dev/null 2>&1 $* & }
# Find all usages of a given term in a specific directory
GetUsages() { SEARCH_TERM=$1; shift; grep -I -n -R "$SEARCH_TERM" $* | grep -v build/ | grep -v .hg/ | grep -v external-doc/; }
# remove .orig and .rej files kicking around repo
ClearOrigRej() { find . | grep -v .hg/ | grep '\.orig$' | xargs rm; find . | grep '\.rej$' | grep -v .hg/ | xargs rm; }
alias hg_qpatch="hg diff -r qparent > ~/workspace/patch.diff"
function hg_qseries() {
if [ $# -ne 0 ]; then
if [ $1 = "--help" ]; then
echo "Description: View patches in a given queue."
echo "Usage: hg_qseries [QUEUE_NAME]"
echo ""
echo " QUEUE_NAME The name of the patch queue. If omitted, the active queue is used."
return 1
fi
fi
QUEUE=""
if [ $# -eq 0 ]; then
QUEUE="`hg qqueue --active`"
else
QUEUE=$1
fi
PATCH_DIR="`hg root`/.hg/patches-$QUEUE"
if [ ! -d "$PATCH_DIR" ]; then
echo "Cannot find patch directory for specified queue: $PATCH_DIR"
echo ""
return 1
fi
cat $PATCH_DIR/series
}
function hg_qreorder() {
if [ $# -ne 0 ]; then
if [ $1 = "--help" ]; then
echo "Description: Edit the series file for a given mqueue, usually to reorder patches."
echo "Usage: hg_qreorder [QUEUE_NAME]"
echo " QUEUE_NAME The name of the patch queue. If omitted, the active queue "
echo " is used."
echo ""
return 1
fi
fi
QUEUE=""
if [ $# -eq 0 ]; then
QUEUE="`hg qqueue --active`"
if [ -n "`hg qapplied`" ]; then
echo "Patches applied; pop all patches first."
echo ""
return 1;
fi
else
QUEUE=$1
fi
PATCH_DIR="`hg root`/.hg/patches-$QUEUE"
if [ ! -d "$PATCH_DIR" ]; then
echo "Cannot find patch directory for specified queue: $PATCH_DIR"
echo ""
return 1
fi
vi $PATCH_DIR/series
}
function _hg_qcopy() {
ACTIVE_QUEUE="`hg qqueue --active`"
if [ $ACTIVE_QUEUE = $2 ]; then
if [ -n "`hg qapplied`" ]; then
echo "Patches applied; pop all patches first."
echo ""
return 1;
fi
fi
if [ $ACTIVE_QUEUE = $3 ]; then
if [ -n "`hg qapplied`" ]; then
echo "Patches applied; pop all patches first."
echo ""
return 1;
fi
fi
PATCH_DIR="`hg root`/.hg/patches"
PATCH_DIR_SRC="$PATCH_DIR-$2"
if [ ! -d "$PATCH_DIR_SRC" ]; then
echo "Cannot find patch directory for specified queue: $PATCH_DIR_SRC"
echo ""
return 1
fi
PATCH_DIR_DST="$PATCH_DIR-$3"
if [ ! -d "$PATCH_DIR_DST" ]; then
echo "Cannot find patch directory for specified queue: $PATCH_DIR_DST"
echo ""
return 1
fi
PATCH_FILENAME=$1
PATCH_PATH=$PATCH_DIR_SRC/$PATCH_FILENAME
if [ ! -f "$PATCH_PATH" ]; then
echo "Cannot find specified patch file: $PATCH_PATH"
echo ""
return 1
fi
PATCH_SERIES_DST=$PATCH_DIR_DST/series
echo $PATCH_FILENAME > $PATCH_SERIES_DST.tmp
cat $PATCH_SERIES_DST >> $PATCH_SERIES_DST.tmp
mv $PATCH_SERIES_DST.tmp $PATCH_SERIES_DST
cp $PATCH_PATH $PATCH_DIR_DST
}
function hg_qcopy() {
if [ $# -ne 3 ]; then
echo "Description: Copy a patch file from one queue to another. Note: This will also "
echo " update the series file in the destination queue."
echo "Usage: hg_qcopy PATCH_FILE SRC_QUEUE_NAME DST_QUEUE_NAME"
echo ""
return 1
fi
_hg_qcopy $1 $2 $3
}
function hg_qmove() {
if [ $# -ne 3 ]; then
echo "Description: Move a patch file from one queue to another. Note: This will also "
echo " update the series file in both queues."
echo "Usage: hg_qmove PATCH_FILE SRC_QUEUE_NAME DST_QUEUE_NAME"
echo ""
return 1
fi
_hg_qcopy $1 $2 $3
RETURN_CODE=$?
if [ $RETURN_CODE -ne 0 ]; then
return $RETURN_CODE
fi
PATCH_SERIES_SRC=$PATCH_DIR_SRC/series
sed "/`echo $PATCH_FILENAME`/d" $PATCH_SERIES_SRC > $PATCH_SERIES_SRC.tmp
mv $PATCH_SERIES_SRC.tmp $PATCH_SERIES_SRC
rm $PATCH_PATH $PATCH_DIR_DST
}
function hg_qexport() {
if [ $# -ne 3 ]; then
echo "Description: Export a patch file from a queue to the given directory."
echo "Usage: hg_qexport PATCH_FILE QUEUE_NAME DST_DIR"
echo ""
return 1
fi
PATCH_DIR="`hg root`/.hg/patches-$2"
if [ ! -d "$PATCH_DIR" ]; then
echo "Cannot find patch directory for specified queue: $PATCH_DIR"
echo ""
return 1
fi
DST_DIR=$3
if [ ! -d "$DST_DIR" ]; then
echo "Cannot find specified destination directory: $DST_DIR"
echo ""
return 1
fi
cp $PATCH_DIR/$1 $DST_DIR
}
function idea_repo_sync() {
if [ $# -ne 2 ]; then
echo "Description: Copy IntelliJ project settings from one local repo to another. "
echo " This will update any paths in the setting files as needed. "
echo ""
echo " Note: This assumes the repo is located at ~/workspace/REPO_NAME. "
echo ""
echo ""
echo "Usage: idea_repo_sync SRC_REPO_NAME DST_REPO_NAME"
echo ""
return 1
fi
SRC_REPO_NAME=$1
DST_REPO_NAME=$2
SRC_REPO_ROOT=~/workspace/$SRC_REPO_NAME
DST_REPO_ROOT=~/workspace/$DST_REPO_NAME
rm ${DST_REPO_ROOT}/*.iml
rm -r ${DST_REPO_ROOT}/.idea
scp ${SRC_REPO_ROOT}/*.iml ${DST_REPO_ROOT}
scp -r ${SRC_REPO_ROOT}/.idea ${DST_REPO_ROOT}
sed -i -e "s,$SRC_REPO_NAME,$DST_REPO_NAME,g" ${DST_REPO_ROOT}/.idea/.name
sed -i -e "s,$SRC_REPO_NAME,$DST_REPO_NAME,g" ${DST_REPO_ROOT}/.idea/*.xml
mv ${DST_REPO_ROOT}/${SRC_REPO_NAME}.iml ${DST_REPO_ROOT}/${DST_REPO_NAME}.iml
}
# Go into each subdirectory and print out the difference in git branch
git-recursive() {
for i in `ls`
do
cd $i
echo $i
echo =======
git "$@"
echo
cd ..
done
}
git-recursive-out() {
git-recursive out "$@"
}
git-recursive-stat() {
git-recursive stat "$@"
}
| true
|
d599047118c73fe7dcad7c7238413739d8aeaead
|
Shell
|
quelltextlich/gerrit-builder
|
/write_full_hierarchy_index_html_files.sh
|
UTF-8
| 3,905
| 4.15625
| 4
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
#---------------------------------------------------------------------
source "$(dirname "$0")/common.inc"
#---------------------------------------------------------------------
BASE_URL='http://builds.quelltextlich.at/'
print_help() {
cat <<EOF
$0 ARGUMENTS
Writes out index html files for folders
ARGUMENTS:
--base-url BASE_URL
-- The base url to fetch structure information from.
E.g.: http://build.quelltextlich.at/gerrit
EOF
}
while [ $# -gt 0 ]
do
ARGUMENT="$1"
shift
case "$ARGUMENT" in
"--help" | "-h" | "-?" )
print_help
exit 0
;;
"--base-url" )
[ $# -ge 1 ] || error "$ARGUMENT requires 1 more argument"
BASE_URL="$1"
shift || true
;;
* )
error "Unknown argument '$ARGUMENT'"
;;
esac
done
cat_url_file_entries() {
local URL="$1"
curl --silent --show-error "$URL" | grep '^<tr><td' | cut -f 4 -d '"'
}
write_base_index_html() {
local DIR_URL="$1"
local SHORT_TITLE="$2"
local TITLE="$3"
if [ -z "$TITLE" ]
then
TITLE="$SHORT_TITLE"
fi
if [ "${DIR_URL: -1}" != "/" ]
then
DIR_URL="$DIR_URL/"
fi
local FILE_RELS_PAD="$DIR_URL"
if [ ! -z "$FILE_RELS_PAD" ]
then
FILE_RELS_PAD="${FILE_RELS_PAD:0: -1}"
fi
FILE_RELS_PAD="${FILE_RELS_PAD////_}"
local FILE_RELS="index$FILE_RELS_PAD.html"
section "Writing index file for '$FILE_RELS'"
local SKIP_PARENT_LINK=no
if [ "$FILE_RELS" = "$INDEX_FILE_RELC" ]
then
SKIP_PARENT_LINK=yes
fi
set_target_html_file_abs "$FILE_RELS"
cat_html_header_target_html \
"$SHORT_TITLE" \
"$SHORT_TITLE" \
"" \
"$TITLE"
cat_target_html <<EOF
<table>
<tr>
<th>Entry</th>
<th>Description</th>
</tr>
EOF
cat_url_file_entries "$BASE_URL$DIR_URL" | while read LINE
do
SKIP=no
case "$LINE" in
"../" )
if [ -z "$FILE_RELS_PAD" ]
then
SKIP=yes
else
DESCRIPTION="Parent directory"
fi
;;
"favicon.ico" )
SKIP=yes
;;
"$INDEX_FILE_RELC" )
SKIP=yes
;;
"gerrit/" )
DESCRIPTION="Builds of Gerrit & plugins"
;;
"images/" )
SKIP=yes
;;
"nightly/" )
DESCRIPTION="Nightly builds of Gerrit & plugins"
;;
"LICENSE-Apache-2.0" )
DESCRIPTION="Default license for artifacts"
;;
"README.txt" )
DESCRIPTION="More information about the builds"
;;
"master/" | "stable-"*"/")
DESCRIPTION="Nightly builds of Gerrit & plugins for the ${LINE:0: -1} branch"
;;
"master-java_"*"/")
DESCRIPTION="Nightly builds of Gerrit & plugins for the master branch using Java ${LINE:12: -1}"
;;
* )
DESCRIPTION="$LINE"
;;
esac
if [ "$SKIP" = "no" ]
then
HREF="$LINE"
if [ "${HREF: -1}" = "/" ]
then
HREF="${HREF}${INDEX_FILE_RELC}"
fi
cat_target_html <<EOF
<tr>
<td><a href="$HREF">$LINE</a></td>
<td>$DESCRIPTION</td>
</tr>
EOF
fi
done
echo_target_html "</table>"
cat_html_footer_target_html
}
write_base_index_html "" "Automated builds"
write_base_index_html "/gerrit" "Gerrit builds" "Automated Gerrit builds"
write_base_index_html "/gerrit/nightly" "Nightly Gerrit builds"
finalize
| true
|
933c43b7efed903c794bc94b1b1ec5d7c8eff8a7
|
Shell
|
htugraz/abs
|
/x86_64/community/openntpd/PKGBUILD
|
UTF-8
| 1,696
| 2.765625
| 3
|
[] |
no_license
|
# $Id: PKGBUILD 143008 2015-10-05 14:02:15Z anatolik $
# Maintainer: Vesa Kaihlavirta <vegai@iki.fi>
# Contributor: Mark Rosenstand <mark@borkware.net>
# Contributor: Giorgio Lando <patroclo7@gmail.com> (adjtimex patch)
# Contributor: Alexander Rødseth <rodseth@gmail.com>
pkgname=openntpd
pkgver=5.7p4
pkgrel=1
pkgdesc='Free, easy to use implementation of the Network Time Protocol.'
url='http://www.openntpd.org/'
arch=('x86_64' 'i686')
license=('BSD')
depends=('openssl')
conflicts=('ntp')
backup=('etc/ntpd.conf')
install=$pkgname.install
source=("ftp://ftp.openbsd.org/pub/OpenBSD/OpenNTPD/$pkgname-$pkgver.tar.gz"
'openntpd.tmpfiles'
'openntpd.service')
sha256sums=('a993d95976e375acc0ab1a677fd268f55024477835633c8ae404895046bccb23'
'fe12841110c3c080519e248988c4b6334f54bd9646b015753c7e15de2a9600c5'
'3239fc6f69d661cd9233233da9e68bebdf7b12888febbc2f2d794742db2d8ed1')
build() {
cd $pkgname-$pkgver
autoreconf -fi
./configure \
--prefix=/usr \
--sysconfdir=/etc \
--sbindir=/usr/bin \
--with-privsep-user=ntp \
--with-privsep-path=/run/openntpd/ \
--with-adjtimex
make
}
package() {
cd "$srcdir/$pkgname-$pkgver"
make DESTDIR="$pkgdir" install
install -Dm644 "$srcdir/$pkgname-$pkgver/COPYING" \
"$pkgdir/usr/share/licenses/$pkgname/COPYING"
sed -i 's/\*/0.0.0.0/' "$pkgdir/etc/ntpd.conf"
install -d -m700 "$pkgdir/var/lib/ntp"
install -Dm644 "$srcdir/openntpd.tmpfiles" "$pkgdir/usr/lib/tmpfiles.d/openntpd.conf"
install -Dm644 "$srcdir/openntpd.service" "$pkgdir/usr/lib/systemd/system/openntpd.service"
install -dm755 "$pkgdir/usr/lib/systemd/ntp-units.d"
echo "$pkgname.service" > "$pkgdir/usr/lib/systemd/ntp-units.d/$pkgname.list"
}
# vim:set ts=2 sw=2 et:
| true
|
e606ac9d29b3ec5e2bcf3d85be86be4d6675e2c8
|
Shell
|
kerzol81/Bash-and-Python-scripts
|
/axis/syncroniser
|
UTF-8
| 2,573
| 4.46875
| 4
|
[] |
no_license
|
#!/bin/bash
# the script mounts the remote FTP folder, and syncronises and arranges the files into subfolders
set -x
AXIS_IP="$1"
USER="$2"
PASS="$3"
NAME="$4"
#
AXIS_PORT='21'
LOCAL_FOLDER="${HOME}"/"axis_remote_${NAME}_SD_DISK" # temporary mount point
ARRANGED_FOLDER="${HOME}"/"${NAME}" # the folder where the files will be arranged
EXTENSION='mkv' # the video file extensions
function check_args(){
if [ "$#" -eq 0 ] || [ "$#" -lt 4 ]; then
echo '[-] Pass args to the scipt!'
usage
exit 1
fi
}
function usage(){
readonly PROGNAME=`basename $0`
cat <<- EOF
usage:
--------------------------------------------
./$PROGNAME <IP> <USERNAME> <PASSWORD> <SITE NAME>
--------------------------------------------
crontab -e and append one of these examples:
run it in every minute:
*/1 * * * * /path/to/script/$PROGNAME <IP> <USERNAME> <PASSWORD> <SITE NAME>
run it in every 30 minutes from 20:00 until 04:00 o' clock:
*/30 20-23,0-4 * * * /path/to/script/$PROGNAME <IP> <USERNAME> <PASSWORD> <SITE NAME>
EOF
}
function check_hdd(){
local SPACE=$(df -h | tr -d "%" | awk '/sda/ { print $5 }')
local INT='^[0-9]+$'
local MAX='99'
if ! [[ "$SPACE" =~ $INT ]] ; then
echo "[-] something went wrong while figuring out disk space"
exit 3
fi
if [ "$SPACE" -ge $MAX ];then
exit 4
fi
}
function check_axis(){
if ! ping -c 1 "$AXIS_IP";then
echo "[-] The axis server is not available..."
exit 5
fi
}
function mountRemote(){
local AXIS_SD="/var/spool/storage/SD_DISK/"
if [ ! -d "$LOCAL_FOLDER" ];then
mkdir -p "$LOCAL_FOLDER"
fi
echo "[*] Mounting remote filesystem..."
if ! curlftpfs -v "${USER}":"${PASS}"@"${AXIS_IP}""$AXIS_SD" "$LOCAL_FOLDER";then
echo "[-] Error: could not mount..."
fi
}
function umountRemote(){
if ! fusermount -u "$LOCAL_FOLDER";then
echo '[-] Error: couldn'\''t umount...'
exit 6
fi
}
function arrange(){
for i in $(find "$LOCAL_FOLDER" -type f -name *."$EXTENSION"); do
local DAY=$(echo "$i" | grep -Eo '[0-9]{8}' | sort | uniq)
if [ ! -d "/$ARRANGED_FOLDER/$DAY" ]; then
mkdir -p /"$ARRANGED_FOLDER"/"$DAY"
fi
if ! rsync -vah --progress "$i" /"$ARRANGED_FOLDER"/"$DAY"/; then
echo "[-] Error: Could not rsync over folders"
fi
done
}
function deleteLocalFolder(){
sleep 1
if ! rm -rf "$LOCAL_FOLDER"; then
echo "[-] Error: could not delete mounted folder"
fi
}
function main(){
check_args "$@"
check_hdd
check_axis
mountRemote
arrange
umountRemote
deleteLocalFolder
exit 0
}
main "$@"
| true
|
85bb335428c1ad0dc7c4b8293f62e27f4041bcd2
|
Shell
|
jkliff/shell-misc-tools
|
/install-bin.sh
|
UTF-8
| 586
| 3.5
| 4
|
[] |
no_license
|
#!env bash
BIN=$HOME/bin
BACKUP=$BIN/.backup
[[ -e $BIN ]] || mkdir $BIN
[[ -e $BACKUP ]] || mkdir $BACKUP
INCLUDE="timetracker/tt.py \
misc/bulk_image_convert.py \
template_touch/tpltouch \
template_touch/prjtouch \
worklog/wl.py"
d=$(date +%s)
for x in $INCLUDE ; do
y=$(basename $x)
if [[ -e $BIN/$y ]] ; then
b=$BACKUP/$y-$d
echo "Saving backup of existing $x to $b"
cp -v $BIN/$y $b
fi
cp -v $x $BIN
done
echo $PATH | grep -q $BIN
if [[ $? != "0" ]] ; then
echo "WARNING: $BIN does not seem to be in your PATH."
fi
| true
|
0f2ac71f3728208adbdc614ce97d718e1b652a2f
|
Shell
|
cegodwin/BIOL5153HW
|
/Assn03.txt
|
UTF-8
| 836
| 2.84375
| 3
|
[] |
no_license
|
# assn03-1
for i in $(seq 808 8008) ; do echo "TR-$i" ; done
#assn03-2
alias c="ls -al"
alias rzr="ssh godwinc@razor.uark.edu"
#assn03-3
cd Desktop/gene_trees
for x in *.fasta ; do echo $x ; done | wc -l
#15085
#assn03-4
for x in *.tre ; do echo $x ; done | wc -l
#14640
#assn03-5
for x in *.sched ; do echo $x ; done | wc -l
#15262
#assn03-6
for i in *.fasta;do echo $i;done | wc -l
# 15085
for i in *.fasta;do echo ${i%.fasta};done
for i in *.fasta;do echo ${i%.fasta}_raxml.tre;done
for i in *.fasta;do test -e ${i%.fasta}_raxml.tre;done
#assn03-7
for i in *.fasta;do test -e ${i%.fasta}_raxml.tre && echo $i;done | wc -l
#14640 successful
for i in *.fasta;do test -e ${i%.fasta}_raxml.tre || echo $i;done | wc -l
#445 failed
#assn03-8
for i in *.fasta;do test -e ${i%.fasta}_raxml.tre || echo generate_pbs.py $i '>' ${i%.fasta}.pbs;done
| true
|
c8cfca5878db04a9055db42a52d6e337866c4806
|
Shell
|
scarfacedeb/dotfiles
|
/git/bin/pickaxe-diff
|
UTF-8
| 1,396
| 3.828125
| 4
|
[] |
no_license
|
#!/bin/bash
# pickaxe-diff : external diff driver for Git.
# To be used with the pickaxe options (git [log|show|diff[.*] [-S|-G])
# to only show hunks containing the searched string/regex.
echo_meta () {
echo "${color_meta}$1${color_none}"
}
path=$1
old_file=$2
old_hex=$3
old_mode=$4
new_file=$5
new_hex=$6
new_mode=$7
color_frag=$(git config --get-color color.diff.frag cyan)
color_func=$(git config --get-color color.diff.func '')
color_meta=$(git config --get-color color.diff.meta 'normal bold')
color_new=$(git config --get-color color.diff.new green)
color_old=$(git config --get-color color.diff.old red)
color_none=$(tput sgr 0)
diff_output=$(git diff --no-color --no-ext-diff -p $old_file $new_file || :)
filtered_diff=$( echo "$diff_output" | \
grepdiff "$GREPDIFF_REGEX" --output-matching=hunk | \
\grep -v -e '^--- a/' -e '^+++ b/' | \
\grep -v -e '^diff --git' -e '^index '
sed -e "s/\(@@ .* @@\)\(.*\)/${color_frag}\1${color_func}\2${color_none}/" | \
sed -e "s/^\(+.*\)/${color_new}\1${color_none}/" | \
sed -e "s/^\(-.*\)/${color_old}\1${color_none}/" )
a_path="a/$path"
b_path="b/$path"
echo_meta "diff --git $a_path $b_path"
echo_meta "index $old_hex..$new_hex $old_mode"
echo_meta "--- $a_path"
echo_meta "+++ $b_path"
echo "$filtered_diff"
| true
|
102c987f173ab1a9c6eb16ccf54b1cc29816aa23
|
Shell
|
tcler/kiss-vm-ns
|
/utils/fastesturl.sh
|
UTF-8
| 750
| 3.765625
| 4
|
[
"BSD-2-Clause"
] |
permissive
|
#!/bin/bash
fastesturl() {
local minavg=
local fast=
local ipv4Opt=
ping -h |& grep -q '^ *-4' && ipv4Opt=-4
for url; do
if curl -L -s --head --request GET ${url} | grep -q "404 Not Found"; then
echo "[ERROR] return 404 while access: ${url}" >&2
continue
fi
read p host path <<<"${url//\// }";
cavg=$(ping $ipv4Opt -w 4 -c 2 $host | awk -F / 'END {print $5}')
: ${minavg:=$cavg}
if [[ -z "$cavg" ]]; then
echo -e " -> $host\t 100% packet loss." >&2
continue
else
echo -e " -> $host\t $cavg \t$minavg" >&2
fi
fast=${fast:-$url}
if awk "BEGIN{exit !($cavg<$minavg)}"; then
minavg=$cavg
fast=$url
fi
done
echo $fast
}
[[ $# = 0 ]] && {
echo "Usage: $0 <url list>" >&2
exit 1
}
fastesturl "$@"
| true
|
8315df349e70081f91f70df345c03fa033fdd85d
|
Shell
|
willjasen/netscaler-bootstrap
|
/nsafter.sh
|
UTF-8
| 593
| 2.703125
| 3
|
[] |
no_license
|
#!/usr/bin/bash
# Download the script that generates the Netscaler's config
curl --insecure -o /nsconfig/nsconfig.sh https://raw.github.com/willjasen/netscaler-bootstrap/nsconfig.sh
# Make the downloaded script executable
chmod +x /nsconfig/nsconfig.sh
# Run the script to generate the Netscaler's configuration
/usr/bin/bash /nsconfig/nsconfig.sh \
/nsconfig/ns.conf \ # Path of Netscaler's configuration
DOMAIN \ # Domain name
DOMAINPASSWORD \ # Domain administrator password
https://certificates.url \ # Certificates file URL
PFXPASS # Certificates password
| true
|
c43b4b0b0c7dc15bbf5493e02370f7bccdeeeac4
|
Shell
|
bemre/cdap
|
/examples/Ticker/bin/generate-orders
|
UTF-8
| 581
| 3.609375
| 4
|
[
"Apache-2.0"
] |
permissive
|
#!/usr/bin/env bash
bin=`dirname "${BASH_SOURCE-$0}"`
bin=`cd "$bin"; pwd`
script=`basename $0`
function usage() {
echo "Usage: $script [--host <host>]"
echo ""
echo " Options"
echo " --host Specifies the host that Reactor is running on. (Default: localhost)"
echo " --help This help message"
echo ""
}
gateway="localhost"
while [ $# -gt 0 ]
do
case "$1" in
--host) shift; gateway="$1"; shift;;
*) usage; exit 1
esac
done
pushd $bin 2>/dev/null >/dev/null
./generateRandomOrderData.sh -h $gateway -p 10000
popd 2>/dev/null >/dev/null
| true
|
1fb998113618b127f0b63fef67ad8343a209f562
|
Shell
|
mesos-magellan/victoria
|
/linode/bootstrap/openvpn_client.sh
|
UTF-8
| 2,142
| 3.4375
| 3
|
[
"MIT"
] |
permissive
|
#!/usr/bin/env bash
echo "Hello from openvpn_client.sh!"
CN_OVPN=$1
apt-get install openvpn -y
set -x
cp /vagrant/secrets/${CN_OVPN}.ovpn /etc/openvpn/${CN_OVPN}.conf
systemctl enable openvpn@${CN_OVPN}.service
systemctl start openvpn@${CN_OVPN}.service
set +x
################
# Config notes #
################
#
# 1) Create individual .ovpn profiles from server for master and scheduler00{1..3}
# using github.com/Nyx/openvpn-install
# 2) Put those .ovpns in victoria/linode/secrets
# 2a) We take advantage of the fact that the local directory is rsync'd
# to the server as Vagrant
# 3) Set up the server to push static IPs based on CN as follows in the
# subsection below
# 4) When calling this script, use the same CN as $1
# ex: ./openvpn_client.sh magellan_master
#############################
# Setting up openvpn server #
#############################
# http://michlstechblog.info/blog/openvpn-set-a-static-ip-address-for-a-client/
#
# ## See the following for example staticclient configs
# root@debian:/etc/openvpn/staticclients# ls *
# magellan_master magellan_scheduler001 magellan_scheduler002 magellan_scheduler003
# root@debian:/etc/openvpn/staticclients# cat *
# ifconfig-push 10.8.0.210 255.255.255.0
# ifconfig-push 10.8.0.221 255.255.255.0
# ifconfig-push 10.8.0.222 255.255.255.0
# ifconfig-push 10.8.0.223 255.255.255.0
#
# ## The following are important settings we must manualyl add to the
# server config
# root@debian:/etc/openvpn/staticclients# cat /etc/openvpn/server.conf | tail -n 3
# client-to-client
# duplicate-cn
# client-config-dir /etc/openvpn/staticclients
# 5) If all goes well, tun0 should have the IP we want and we should
# be able to connect!
# root@master:~# ip addr show tun0
# 17: tun0: <POINTOPOINT,MULTICAST,NOARP,UP,LOWER_UP> mtu 1500 qdisc noqueue state UNKNOWN group default qlen 100
# link/none
# inet 10.8.0.210/24 brd 10.8.0.255 scope global tun0
# valid_lft forever preferred_lft forever
# inet6 fe80::cca:a260:e717:9659/64 scope link flags 800
# valid_lft forever preferred_lft forever
| true
|
5b02baa358d1a0ff115cfabc5f9e43f3f7090556
|
Shell
|
seb-v/vimfiles
|
/.custom.bash
|
UTF-8
| 904
| 2.578125
| 3
|
[] |
no_license
|
export GIT_PS1_SHOWDIRTYSTATE=
export GIT_PS1_SHOWSTASHSTATE=
export GIT_PS1_SHOWUNTRACKEDFILES=
export GIT_PS1_SHOWUPSTREAM=verbose GIT_PS1_DESCRIBE_STYLE=branch
export PROMPT_COMMAND='__git_ps1 "\[\033[01;32m\]\[\033[00m\]\[\033[01;34m\]\w\[\033[00m\]" " \\\$ "'
export PATH=$PATH:~/go/bin
__fzf_git__() {
local gitcmd="git branch --all | grep -v HEAD"
local cmd="${gitcmd:-"command find -L . -mindepth 1 \\( -path '*/\\.*' -o -fstype 'sysfs' -o -fstype 'devfs' -o -fstype 'devtmpfs' -o -fstype 'proc' \\) -prune \
-o -type f -print \
-o -type d -print \
-o -type l -print 2> /dev/null | cut -b3-"}"
eval "$gitcmd" | FZF_DEFAULT_OPTS="--height ${FZF_TMUX_HEIGHT:-40%} --reverse $FZF_DEFAULT_OPTS $FZF_CTRL_T_OPTS" fzf -m "$@" | while read -r item; do
printf '%q ' "$item"
done
echo
}
bind '"\eb": " \C-u \C-a\C-k`__fzf_git__`\e\C-e\C-y\C-a\C-y\ey\C-h\C-e\er \C-h"'
| true
|
f5d6ee7c701183e5ab9a0251ba4a2ada58452fc2
|
Shell
|
michaelgodley/devsetup
|
/scripts/awscli.sh
|
UTF-8
| 236
| 2.515625
| 3
|
[] |
no_license
|
#!/bin/bash
# source some env variables
. ../config.conf
. ./libs.sh
#
cd $HOME/temp
curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
unzip awscliv2.zip
sudo ./aws/install
rm awscliv2.zip
rm -rf ./aws
| true
|
367a6b97c313d5b6658ce3e4fb3dfcc26ef25873
|
Shell
|
packer-/regulars-xonotic-data.pk3dir
|
/cmake/qcc.sh
|
UTF-8
| 509
| 3
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
CPP=${CPP:-cpp}
QCC=${QCC:-$PWD/../../gmqcc/gmqcc${CMAKE_EXECUTABLE_SUFFIX}}
case $1 in
compile)
${CPP} ${@:3} | sed 's/^#\(line\)\? \([[:digit:]]\+\) "\(.*\)".*/\n#pragma file(\3)\n#pragma line(\2)/g' > $2
;;
link)
${QCC} \
-std=gmqcc \
-Ooverlap-locals \
-O3 \
-Werror -Wall \
-Wno-field-redeclared \
-flno -futf8 -fno-bail-on-werror \
-frelaxed-switch -freturn-assignments \
${@:2}
;;
esac
| true
|
8a9832e1cde55690c876bfacf1feb551cf49ef23
|
Shell
|
wkens/contents
|
/auto_gulp.sh
|
UTF-8
| 434
| 3.15625
| 3
|
[
"MIT"
] |
permissive
|
#/bin/bash
for i in {0..36000} ; do
ls -l --time-style=full-iso resources/assets/sass | egrep '^-' > .scsses.new
d=`diff .scsses.new .scsses 2>&1`;
if [ ! -z "$d" ] ; then
echo "" >&2
echo "Start gulp.js procession..." >&2
node_modules/gulp/bin/gulp.js > .gulp.log 2>&1
echo "End gulp.js procession." >&2
fi
cp -f .scsses.new .scsses
sleep 1;
done;
echo "Stop auto_grub.sh" >&2
| true
|
ff680a0854f956f25599c0278bbe41db16ea23e4
|
Shell
|
shunkakinoki/dotfiles
|
/src/shell/.zshrc
|
UTF-8
| 2,219
| 2.6875
| 3
|
[
"MIT"
] |
permissive
|
# shellcheck disable=SC2148
# Autoload Zsh Completion
autoload -Uz compinit
compinit
# Hyper Tab Title Settings
# From: https://github.com/zeit/hyper/issues/1188#issuecomment-332606903
# Override auto-title when static titles are desired ($ title My new title)
title() {
export TITLE_OVERRIDDEN=1
echo -en "\e]0;$*\a"
}
# Turn off static titles ($ autotitle)
autotitle() { export TITLE_OVERRIDDEN=0; }
autotitle
# Condition checking if title is overridden
overridden() { [[ $TITLE_OVERRIDDEN == 1 ]]; }
# Load Antibody Plugin Manager
source <(antibody init)
export NVM_AUTO_USE=true
# Install Antibody Plugins
antibody bundle Aloxaf/fzf-tab
antibody bundle b4b4r07/emoji-cli
antibody bundle b4b4r07/enhancd
antibody bundle buonomo/yarn-completion
antibody bundle caarlos0/zsh-git-sync kind:path
antibody bundle chrissicool/zsh-256color
antibody bundle darvid/zsh-poetry
antibody bundle lukechilds/zsh-better-npm-completion
antibody bundle lukechilds/zsh-nvm
antibody bundle MichaelAquilina/zsh-you-should-use
antibody bundle mollifier/cd-gitroot
antibody bundle paulirish/git-open
antibody bundle paulirish/git-recent
antibody bundle peterhurford/git-it-on.zsh
antibody bundle peterhurford/up.zsh
antibody bundle urbainvaes/fzf-marks
antibody bundle wfxr/forgit
antibody bundle zdharma/fast-syntax-highlighting
antibody bundle zdharma/zsh-diff-so-fancy
antibody bundle zsh-users/zsh-autosuggestions
antibody bundle zsh-users/zsh-completions
antibody bundle zsh-users/zsh-history-substring-search
antibody bundle zuxfoucault/colored-man-pages_mod
if [ -x notify-send ]; then
antibody bundle MichaelAquilina/zsh-auto-notify
fi
if [ -x pipenv ]; then
antibody bundle owenstranathan/pipenv.zsh
fi
if [ -x wakatime ]; then
antibody bundle sobolevn/wakatime-zsh-plugin
fi
fpath+=~/.zfunc
fpath+=~/dotfiles/src/shell/zsh_functions
autoload b c cdf cda cdp coden coder da drm ds ef emoji::cli fe fh fkill gbo gbor ghl gobt gobtp goc icoden icoder tm tmk tp ts
# Source Shell Files
for file in ~/.shell_*; do
source "$file"
done
source ~/.zshrc.local
# Eval Zsh Packages
eval "$(starship init zsh)"
if [[ -n $ZSH_INIT_COMMAND ]]; then
echo "Running: $ZSH_INIT_COMMAND"
eval "$ZSH_INIT_COMMAND"
fi
| true
|
b8137127a539c06debee0298a1b973a7107c612c
|
Shell
|
phoronix-test-suite/test-profiles
|
/pts/espeak-1.5.0/install.sh
|
UTF-8
| 462
| 2.796875
| 3
|
[
"MIT"
] |
permissive
|
#!/bin/sh
tar -zxvf gutenberg-science.tar.gz
tar -xf espeak-ng-1.50.tgz
cd espeak-ng
./autogen.sh
./configure --prefix=$HOME/espeak_
make # build seems to have problems with multiple cores
echo $? > ~/install-exit-status
make install
cd ~
rm -rf espeak-ng
echo "#!/bin/sh
cd espeak_/bin/
LD_LIBRARY_PATH=\$HOME/espeak_/lib/:\$LD_LIBRARY_PATH ./espeak-ng -f ~/gutenberg-science.txt -w espeak-output 2>&1
echo \$? > ~/test-exit-status" > espeak
chmod +x espeak
| true
|
01d92d87b4a60f9968e069fe3b3da7784c7a639a
|
Shell
|
harrifeng/system-config
|
/bin/emacs-quote-string
|
UTF-8
| 625
| 3.671875
| 4
|
[
"LicenseRef-scancode-warranty-disclaimer"
] |
no_license
|
#!/usr/bin/env bash
set -e
me=$(readlink -f $0)
if test ! -e "$me"; then
me=$(readlink -f "$(which $0)")
if test ! -e "$me"; then
die "Can't find out about me"
exit 1
fi
fi
abs0=$0
if ! [[ $abs0 =~ ^/ ]]; then
if [[ $abs0 =~ / ]] && test -e $PWD/$abs0; then
abs0=$PWD/$abs0
elif test -e "$(which $0)"; then
abs0=$(which $0)
else
die "Can't find abs path for $0"
fi
fi
b0=$(basename $0)
if test "${b0}" = emacs-quote-string; then
echo -n "$1" | perl -npe 's/\\/\\\\/g; s/"/\\"/g'
elif test "${b0}" = lua-quote-string; then
str.quote.lua "$1"
fi
| true
|
f0ea8984c14932a61214be118f23bd945d2c2ef6
|
Shell
|
KingsleyYau/LinuxShell
|
/build/other/webrtc.sh
|
UTF-8
| 528
| 3.125
| 3
|
[] |
no_license
|
#!/bin/sh
# Curl build script for android
# Author: Max.Chiu
# Description: asm
# WebRTC build script
# Getting Prerequisite software
WEBRTC_PATH=/Users/max/Documents/Project/webrtc/
mkdir -p $WEBRTC_PATH
export PATH=$PATH:$WEBRTC_PATH/depot_tools
# Getting code
#fetch --nohooks webrtc_ios
fetch --nohooks webrtc_android
cd webrtc
gclient sync
# Compiling
BUILD_ARCH=(arm arm64 x86 x64)
for var in ${BUILD_ARCH[@]};do
gn gen out/Debug/$var --args='target_os="android" target_cpu="$var"'
ninja -C out/Debug/$var
done
| true
|
97a95a7444935cc30093ed1eba233bdbb80d1782
|
Shell
|
mx-psi/dotfiles
|
/bashrc
|
UTF-8
| 3,384
| 3.34375
| 3
|
[] |
no_license
|
# If not running interactively, don't do anything
case $- in
*i*) ;;
*) return;;
esac
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific environment
if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
then
PATH="$HOME/.local/bin:$HOME/bin:$PATH"
fi
export PATH
# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth
# append to the history file, don't overwrite it
shopt -s histappend
# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000
HISTCONTROL=erasedups:ignorespace
xhost +local:root > /dev/null 2>&1
complete -cf sudo
# Bash won't get SIGWINCH if another process is in the foreground.
# Enable checkwinsize so that bash will check the terminal size when
# it regains control. #65623
# http://cnswww.cns.cwru.edu/~chet/bash/FAQ (E11)
shopt -s checkwinsize
shopt -s expand_aliases
# Enable history appending instead of overwriting. #139609
shopt -s histappend
source /usr/share/git/completion/git-prompt.sh
GIT_PS1_SHOWDIRTYSTATE='y'
GIT_PS1_SHOWSTASHSTATE='y'
GIT_PS1_SHOWUNTRACKEDFILES='y'
GIT_PS1_SHOWCOLORHINTS='true'
color_prompt=yes
if [ "$color_prompt" = yes ]; then PS1='\[\033[01;32m\]psi\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]$(__git_ps1 "(%s)")\$ '
else
PS1='\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt
# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
PS1="\[\e]0;\u@\h: \w\a\]$PS1"
;;
*)
;;
esac
# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
alias ls='ls --color=auto'
alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
fi
# colored GCC warnings and errors
export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
source ~/.profile
alias cp="cp -i" # confirm before overwriting something
alias df='df -h' # human-readable sizes
alias more=less
alias cat=bat
alias top=htop
alias sl='ls --color=auto'
alias dw='youtube-dl -i -x -o "%(title)s.%(ext)s" --audio-format mp3'
eval "$(pandoc --bash-completion)"
# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
if [ -f /usr/share/bash-completion/bash_completion ]; then
. /usr/share/bash-completion/bash_completion
elif [ -f /etc/bash_completion ]; then
. /etc/bash_completion
fi
fi
##############
# FUNCTIONS #
##############
# man colorized pages!
# boredzo.org/blog/archives/2016-08-15/colorized-man-pages-understood-and-customized
man() {
env \
LESS_TERMCAP_md=$'\e[1;36m' \
LESS_TERMCAP_me=$'\e[0m' \
LESS_TERMCAP_se=$'\e[0m' \
LESS_TERMCAP_so=$'\e[1;40;92m' \
LESS_TERMCAP_ue=$'\e[0m' \
LESS_TERMCAP_us=$'\e[1;32m' \
man "$@"
}
auto(){
while true; do
"$@"
inotifywait -r -e close_write,moved_to,create .
done
}
eval "$(starship init bash)"
# Add RVM to PATH for scripting. Make sure this is the last PATH variable change.
export PATH="$PATH:$HOME/.rvm/bin"
unset rc
. "$HOME/.cargo/env"
| true
|
b8d5b9464a003cf95ca6243e7a40017bf7eae29f
|
Shell
|
btison/docker-images
|
/s2i/jboss-eap-6/eap64-openshift/scripts/os-eap64-launch/added/launch/security-domains.sh
|
UTF-8
| 2,090
| 3.859375
| 4
|
[] |
no_license
|
function prepareEnv() {
unset SECDOMAIN_NAME
unset SECDOMAIN_USERS_PROPERTIES
unset SECDOMAIN_ROLES_PROPERTIES
unset SECDOMAIN_LOGIN_MODULE
unset SECDOMAIN_PASSWORD_STACKING
}
function configure() {
configure_security_domains
}
function configureEnv() {
configure
}
configure_security_domains() {
domains="<!-- no additional security domains configured -->"
if [ -n "$SECDOMAIN_NAME" ]; then
local configDir=${JBOSS_HOME}/standalone/configuration
if [ -f "${configDir}/${SECDOMAIN_USERS_PROPERTIES}" -a -f "${configDir}/${SECDOMAIN_ROLES_PROPERTIES}" ] ; then
local login_module=${SECDOMAIN_LOGIN_MODULE:-UsersRoles}
if [ $login_module == "RealmUsersRoles" ]; then
local realm="<module-option name=\"realm\" value=\"ApplicationRealm\"/>"
else
local realm=""
fi
if [ -n "$SECDOMAIN_PASSWORD_STACKING" ]; then
stack="<module-option name=\"password-stacking\" value=\"useFirstPass\"/>"
else
stack=""
fi
domains="\
<security-domain name=\"$SECDOMAIN_NAME\" cache-type=\"default\">\
<authentication>\
<login-module code=\"$login_module\" flag=\"required\">\
<module-option name=\"usersProperties\" value=\"\${jboss.server.config.dir}/$SECDOMAIN_USERS_PROPERTIES\"/>\
<module-option name=\"rolesProperties\" value=\"\${jboss.server.config.dir}/$SECDOMAIN_ROLES_PROPERTIES\"/>\
$realm\
$stack\
</login-module>\
</authentication>\
</security-domain>"
else
echo "WARNING! Both user and roles files must exist before an additional security domain can be configured, current values are ${SECDOMAIN_USERS_PROPERTIES} and ${SECDOMAIN_ROLES_PROPERTIES}."
fi
fi
if [ -n "$domains" ];then
sed -i "s|<!-- ##ADDITIONAL_SECURITY_DOMAINS## -->|${domains}<!-- ##ADDITIONAL_SECURITY_DOMAINS## -->|" "$CONFIG_FILE"
fi
}
| true
|
467fd322f6e47688ae9656be409e05ff5c6605cd
|
Shell
|
refenv/cijoe-pkg-lightnvm
|
/testcases/block_partial_read.sh
|
UTF-8
| 717
| 2.6875
| 3
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
#
# HANS FIX THE SHORT DESCRIPTION
#
# HANS FIX THE LONG DESCRIPTION
#
CIJ_TEST_NAME=$(basename "${BASH_SOURCE[0]}")
export CIJ_TEST_NAME
# shellcheck source=modules/cijoe.sh
source "$CIJ_ROOT/modules/cijoe.sh"
test::enter
test::require block
job_fname="block_partial_read.fio"
export FIO_FILENAME="$BLOCK_DEV_PATH"
export FIO_JOBFILE="$CIJ_TESTFILES/$job_fname"
export FIO_OUTPUT="/tmp/$job_fname.result.json"
export FIO_ARGS_EXTRA="--output-format=json"
res=0
if ! fio::run_jobfile "$FIO_JOBFILE"; then
cij::err "failed running fio"
res=$(( res + 1 ))
fi
if ! ssh::pull "$FIO_OUTPUT" "$CIJ_TEST_AUX_ROOT/"; then
cij::err "failed retrieving fio output"
res=$(( res + 1 ))
fi
test::exit $res
| true
|
a1accc34b792a0aebc35eac34baf1a7b6f176bb8
|
Shell
|
CSCfi/Kielipankki-utilities
|
/corp/byu/byu-convert-sbatch.sh
|
UTF-8
| 1,468
| 3.921875
| 4
|
[] |
no_license
|
#! /bin/bash
progname=$(basename $0)
progdir=$(dirname $0)
scriptdir=$progdir/../../scripts
usage_header="Usage: $progname [options] wlp_input.txt ...
Submit a SLURM batch job to convert BYU corpora from WLP to VRT."
action=sbatch
optspecs='
n|dry-run { action=cat }
l|log-dir=DIR "."
timelimit=MINS "10"
memory=MB "1000"
output-dir=DIR
metadata-file=FILE
v|verbose
'
. $scriptdir/korp-lib.sh
# Process options
eval "$optinfo_opt_handler"
if [ $action = sbatch ] && ! find_prog sbatch > /dev/null; then
error "Please run in a system with SLURM installed."
fi
for file in "$@"; do
jobname_base="$(basename $file .txt)"
jobname="byu_$jobname_base"
if [ -e "$file.vrt" ]; then
echo "Skipping $file: $file.vrt already exists"
continue
fi
if [ "x$output_dir" != x ]; then
outfile=$output_dir/$jobname_base.txt.vrt
else
outfile=$file.vrt
fi
if [ "x$verbose" != x ]; then
cat <<EOF
Submitting job "$jobname" to partition "serial"
Max run time: $timelimit mins
RAM per CPU: $memory MiB
EOF
fi
$action <<EOF
#! /bin/bash -l
#SBATCH -J $jobname
#SBATCH -o $log_dir/byu_log-$jobname_base-%j.out
#SBATCH -e $log_dir/byu_log-$jobname_base-%j.err
#SBATCH -t $timelimit
#SBATCH --mem-per-cpu $memory
#SBATCH -n 1
#SBATCH -p serial
. $scriptdir/korp-lib.sh
echo Job: \$SLURM_JOB_ID \$SLURM_JOB_NAME
echo Input: "$file"
$progdir/byu-convert.sh --metadata-file "$metadata_file" --verbose \
"$file" > "$outfile"
EOF
done
| true
|
cdc7410dde83ce28a4a0a77c819998a342842d78
|
Shell
|
lbarbisan/corba
|
/Applet/deploy-applet.sh
|
UTF-8
| 406
| 2.890625
| 3
|
[] |
no_license
|
if [ $# -lt 4 ]
then
echo "usage : <id applet> <class applet> <id package> <class package> [included classes ...]"
echo "exemple : 01 CalculatorRPNApplet 02 fr.umlv.ir3.corba.calculator.applet"
exit
fi
./compile-and-convert-applet.sh $*
echo press enter to continue > /dev/stderr
read key
./delete-applet.sh $1 $2 $3 $4
echo press enter to continue > /dev/stderr
read key
./install-applet.sh $1 $2 $3 $4
| true
|
dac0c0b48215471d0b3c46346dd2cfdeec35d9f6
|
Shell
|
ketanbhatt/retrospect
|
/get_active.sh
|
UTF-8
| 229
| 2.546875
| 3
|
[] |
no_license
|
#!/bin/bash
echo "" > output.txt
while true;
do
xprop -id $(xprop -root 32x '\t$0' _NET_ACTIVE_WINDOW | cut -f 2) _NET_WM_NAME WM_CLASS | cut -d" " -f3- >> output.txt
sleep 1
done
| true
|
9be6d6b74fcd8149b935ab7566c320f887aeb3e8
|
Shell
|
dhungvi/publiy
|
/publiy/misc/bash_bin/extract_all_timing_deliveries
|
UTF-8
| 218
| 3.5
| 4
|
[] |
no_license
|
#!/bin/bash
if [ ! -d "$1" ]; then
red "Working directory is not accessible ($0)";
exit -1; fi
workingdir="$1";
for resultsdir in `ls -d $workingdir/DT*/`; do
extract_timing_deliveries $resultsdir;
done
| true
|
7e95ddc697ef4b712ad735d7e21af0d74395e489
|
Shell
|
dc165015/docker
|
/settings.sh
|
UTF-8
| 1,877
| 2.9375
| 3
|
[] |
no_license
|
cd $HOME
# reconfigure timezone
#echo "Asia/Shanghai" | tee /etc/timezone
#localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
notify appending .bashrc
echo '
#export LIBGL_ALWAYS_INDIRECT=1
#export DISPLAY=:0
#export NO_AT_BRIDGE=1
#sudo service dbus start
#/etc/init.d/dbus start
#exec dbus-run-session -- bash
#export PULSE_SERVER=tcp:localhost
alias inst="apt-fast install -y"
alias srcbak="cp /etc/apt/sources.list.bak /etc/apt/sources.list"
alias src163="cp /etc/apt/163.xenial.sources.list /etc/apt/sources.list"
alias srcup="apt-fast update"
alias mn="meteor npm"
alias mni="meteor npm i"
alias mnr="meteor npm run"
PS1="\n\e[0;33m * * * * * * * * * * * * * * * * * * * \e[m\n$PS1"
[[ -f /usr/share/autojump/autojump.sh ]] && . /usr/share/autojump/autojump.sh
' | tee -a ~/.bashrc
notify amounting network shared folder: //dcx/coding...
if [ ! -d "/dcx/coding" ]; then
sudo mkdir /dcx /dcx/coding
fi
if [ $(ls /coding | wc -l) -eq 0 ]; then
echo "//dcx/sda4/coding /dcx/coding smbfs credentials=/home/dc/.smbcredentials,vers=1.0 0 0" | sudo tee -a /etc/fstab
fi
#cp /coding/tools/vagrant/lightdm.conf /etc/lightdm/lightdm.conf
#cp /coding/tools/vagrant/xorg.conf /etc/X11/xorg.conf
#如果想 Ubuntu 在每次启动到 command prompt ，可以输入以下指令:
#echo “false” | tee /etc/X11/default-display-manager
#当下次开机时，就会以命令行模式启动（text模式，字符界面登录），如果想变回图形界面启动（X windows启动），可以輸入:
if (which lightdm) then
echo “/usr/sbin/lightdm” | sudo tee /etc/X11/default-display-manager;
fi
if (which i3) then
echo 'exec i3' | sudo tee -a ~/.xinitrc;
fi
#如果在Ubuntn以命令行模式启动，在字符终端想回到图形界面的话只需以下命令:
#startx
cat ./vimrc >> ~/.vimrc
setsudoer
| true
|
4dceb7f6e532d0f7879d2ea5c781028dcb11d17c
|
Shell
|
montadigital/montadigital.com
|
/deploy.sh
|
UTF-8
| 503
| 3.453125
| 3
|
[] |
no_license
|
#!/bin/bash
BRANCH=$(git branch | sed -n -e 's/^\* \(.*\)/\1/p')
GIT_STATUS=$(git status)
WDC_MSG="working directory clean"
if [ "${GIT_STATUS/$WDC_MSG}" = "$GIT_STATUS" ] ; then
echo "FATAL: working directory not clean. Will not publish."
exit 1
fi
jekyll build
if [ "$BRANCH" == "master" ]
then
echo "Publishing to production (www.montadigital.com)"
s3_website push
else
echo "Publishing a preview build to preview.montadigital.com"
s3_website push --config-dir preview-build-config
fi
| true
|
cc8295c34e7a896e5821db2f68ae0b21b42fedf5
|
Shell
|
RossOgilvie/scripts
|
/volume_pulse
|
UTF-8
| 1,329
| 4.125
| 4
|
[] |
no_license
|
#!/bin/sh
completion='compctl -k "(up down set mute unmute toggle is_muted is_headphone is_speaker level show help)" volume'
function get_level {
pamixer --get-volume
}
function is_muted {
pamixer --get-mute
}
function is_headphone {
sinks=$(pactl list sinks)
if echo $sinks | grep -q "Active Port: analog-output-headphones"; then echo "true"; else echo "false"; fi
}
function is_speaker {
sinks=$(pactl list sinks)
if echo $sinks | grep -q "Active Port: analog-output-speaker"; then echo "true"; else echo "false"; fi
}
function show {
echo "showing"
/home/ross/.scripts/volume_show `get_level` `is_muted` `is_headphone` &
}
case $1 in
"up")
pamixer --increase 5
show
;;
"down")
pamixer --decrease 5
show
;;
"set")
pamixer --set-volume $2
show
;;
"mute")
pamixer --mute
show
;;
"unmute")
pamixer --unmute
show
;;
"toggle")
pamixer --toggle-mute
show
;;
"is_muted")
is_muted
;;
"is_headphone")
is_headphone
;;
"is_speaker")
is_speaker
;;
"level")
get_level
;;
"show")
show
;;
"bash-completion")
echo "$completion"
;;
"help"|*)
echo "Basically a wrapper on pulseaudio-ctl that also shows a volume notification"
echo "Usage: up|down|mute|unmute|toggle|is_muted|is_headphone|is_speaker|level"
echo "Volume: " `get_level`"%"
;;
esac
exit 1
| true
|
a22898bd43296246e9016e945e1237d195090bbd
|
Shell
|
Webhero9297/haroldcar_haskell
|
/examples/base.sh
|
UTF-8
| 277
| 3.0625
| 3
|
[] |
no_license
|
msgN () {
echo
printf '%s\n' "${1}"
}
lbl () {
printf '>: %s\n' "${1}"
}
msg () {
printf '%s\n' "${1}"
}
doone () {
echo
curl --silent --write-out "\n" localhost:300${1}/${2}
}
doall () {
for p in 1 2 3
do
doone ${p} ${1}
done
}
| true
|
c7306b06bb6a9adce18146f975c9edc326243558
|
Shell
|
tahti/dotfiles
|
/bin/pum
|
UTF-8
| 242
| 3.453125
| 3
|
[] |
no_license
|
#!/bin/bash
DEVICES=( $(pmount |grep -o "/dev/sd[a-z][0-9]\?") )
# get length of an array
tLen=${#DEVICES[@]}
# use for loop read all devices
for (( i=0; i<${tLen}; i++ ));
do
echo "Unmounting ${DEVICES[$i]}"
pumount ${DEVICES[$i]}
done
| true
|
d3c25dbeaf9d652d74eefdfdaaa2ea35a6bad6c0
|
Shell
|
weakish/hubsh
|
/bin/gogsh
|
UTF-8
| 3,393
| 4.15625
| 4
|
[
"LicenseRef-scancode-warranty-disclaimer",
"0BSD"
] |
permissive
|
#!/bin/sh
set -e # errexit
VERSION=0.0.0
gogsh_help() {
cat<<'END'
gogsh -- Gogs API client in sh
gogsh [ACTION]
Actions:
auth check if gogs acess token is available
clone supports clonning from `gogs_user/repo` and `repo` (your own repo)
create create this repository on GitHub and add GitHub as origin
whoami show gogsh username (specified in `$GOGS_USER`)
version show version
help this help page
gogs server is specified in `$GOGS_SERVER`.
If not specified, it defaults to `http://127.0.0.1:3000`.
Auth token is queried in the following order:
- Environment variable `$GOGS_OAUTH_TOKEN`
- content of file `$GOGS_OAUTH_FILE`
- content of file `~/.config/gogsh`
END
}
ex_usage() {
gogsh_help
exit 64 # command line usage error
}
readonly gogs_host=${GOGS_SERVER:-http://127.0.0.1:3000}
gogsh_whoami() {
if [ -n $GOGS_USER ]; then
echo $GOGS_USER
else
echo 'We do not know your username on gogs.'
echo 'Specify it in environment variable $GOGS_USER'
exit 67 # EX_NOUSER
fi
}
gogsh_auth() {
if [ -n "$GOGS_OAUTH_TOKEN" ]; then
echo "$GOGS_OAUTH_TOKEN"
elif [ -f "$GOGS_OAUTH_FILE" ]; then
cat "$GOGS_OAUTH_FILE";
elif [ -f "${XDG_CONFIG_HOME:-$HOME/.config}/gogsh" ]; then
cat "${XDG_CONFIG_HOME:-$HOME/.config}/gogsh"
else
cat<<'END'
Error: OAuth token not found.
http://127.0.0.1:3000/user/settings/applications
And paste the token value in
~/.config/gogsh
END
exit 77 # EX_NOPERM
fi
}
gogsh_clone() {
if [ -d "$1" ]; then
git clone "$1";
else
case "$1" in
*/*) git clone $gogs_host/"$1".git ;;
*) git clone $gogs_host/$(gogsh_whoami)/"$1".git ;;
esac
fi
}
ssh_prefix() {
local ssh_host=$(echo $gogs_host | grep -E -o '//[^:]+' | grep -E -o '[^/]+')
echo "gogs@$ssh_host:$(gogsh_whoami)"
}
gogsh_create() {
if [ -n "$1" ]; then
mkdir -p "$1"
cd "$1"
git init
fi
local name=$(basename $(pwd))
local apiUrl="/user/repos"
readonly gogsApiRoot="$gogs_host/api/v1"
readonly gogsApiPath="$gogsApiRoot$apiUrl"
# Note the difference with GitHub.
# GitHub uses `{field: name}`, while gogs uses `field=name`.
curl -H "Authorization: token $(gogsh_auth)" \
--data "name=$name" \
-X 'POST' \
$gogsApiPath
if [ $? -eq 0 ]; then
if (git remote get-url origin > /dev/null 2>&1); then
if (git remote get-url gogs > /dev/null 2>&1); then
echo 'Both `origin` and `gogs` already exist.'
read -p 'Please provide an remote name:' remote_name
if (git remote get-url remote_name > /dev/null 2>&1); then
echo "$remote_name already exist. Skip adding it."
fi
else
git remote add gogs "$(ssh_prefix)/$name.git"
fi
else
git remote add origin "$(ssh_prefix)/$name.git"
fi
else
exit $?
fi
}
if [ $# -eq 0 ]; then
ex_usage
else
case "$1" in
auth) gogsh_auth ;;
clone) gogsh_clone "$2" ;;
create) gogsh_create "$2";;
whoami) gogsh_whoami ;;
version) echo $VERSION;;
-h|--help|help) gogsh_help ;;
*) ex_usage ;;
esac
fi
| true
|
4d1f84a7aa9e275644d8ce73d7791fe03b6eb80a
|
Shell
|
codinn/SwiftSockets
|
/xcconfig/install.sh
|
UTF-8
| 1,938
| 3.5
| 4
|
[
"MIT"
] |
permissive
|
#!/bin/bash
# URLS
TT_SWIFTENV_URL="https://github.com/kylef/swiftenv.git"
TT_GCD_URL="https://github.com/apple/swift-corelibs-libdispatch.git"
#TT_GCD_SWIFT3_BRANCH=experimental/foundation
#TT_GCD_SWIFT22_1404_HASH=65330e06d9bbf75a4c6ddc349548536746845059
TT_GCD_SWIFT3_BRANCH=master
TT_GCD_SWIFT22_1404_HASH=master
# swiftenv
git clone --depth 1 ${TT_SWIFTENV_URL} ~/.swiftenv
export SWIFTENV_ROOT="$HOME/.swiftenv"
export PATH="${SWIFTENV_ROOT}/bin:${SWIFTENV_ROOT}/shims:$PATH"
# Install Swift
swiftenv install ${SWIFT_SNAPSHOT_NAME}
if [ `which swift` ]; then
echo "Installed Swift: `which swift`"
else
echo "Failed to install Swift?"
exit 42
fi
swift --version
# Environment
TT_SWIFT_BINARY=`swiftenv which swift`
TT_SNAP_DIR=`echo $TT_SWIFT_BINARY | sed "s|/usr/bin/swift||g"`
# Install GCD
if [[ "$TRAVIS_OS_NAME" == "Linux" ]]; then
IS_SWIFT_22="`swift --version|grep 2.2|wc -l|sed s/1/yes/|sed s/0/no/`"
echo "${IS_SWIFT_22}"
#GCD_DIRNAME="gcd-${SWIFT_SNAPSHOT_NAME}"
GCD_DIRNAME=gcd
git clone --recursive ${TT_GCD_URL} ${GCD_DIRNAME}
cd ${GCD_DIRNAME}
if [[ $IS_SWIFT_22 = "no" ]]; then
git checkout ${TT_GCD_SWIFT3_BRANCH}
else
git checkout ${TT_GCD_SWIFT22_1404_HASH}
fi
mkdir ~/swift-not-so-much
ln -s ${TT_SNAP_DIR} ~/swift-not-so-much/latest
export CC=clang
./autogen.sh
./configure --with-swift-toolchain=${TT_SNAP_DIR}/usr --prefix=${TT_SNAP_DIR}/usr
echo "---"
if [[ $IS_SWIFT_22 = "no" ]]; then
echo "Copying patched dispatch.h"
cp ${TRAVIS_BUILD_DIR}/xcconfig/dispatch.h-patched-swift3 dispatch/dispatch.h
ls dispatch
else
echo "NOT copying dispatch.h"
fi
echo "---"
#cd src && dtrace -h -s provider.d && cd ..
cp ${TRAVIS_BUILD_DIR}/xcconfig/trusty-provider.d src
make all
make install
find ~ -name "*dispatch*"
fi
if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
echo ${TT_SWIFT_BINARY}
fi
| true
|
b3c1b60bad2393f46f27f64b2c993fcb576498d3
|
Shell
|
CanadianMVP/linuxscripts
|
/bash/lab2/rollafood.sh
|
UTF-8
| 492
| 3.1875
| 3
|
[] |
no_license
|
#!/bin/bash
arrayvar=(apple grape pizza bananna chocolate ham pork steak watermelon pineapple pear)
#echo $((${arrayvar[$RANDOM % 6 ]}+${arrayvar[$RANDOM % 6]}))
#You want to get two variables, add them together, and then have that
#item selected from the array
array1=$(($RANDOM % 6 +1))
array2=$(($RANDOM % 6 +1))
total=$((array1 + array2))
index=$((total - 2))
#echo ${arrayvar[($RANDOM % 6 +1)+($RANDOM % 6 +1)]}
echo "I rolled $total and that correlates with ${arrayvar[$index]}!"
| true
|
726cb047971b8a75885e01e72322fd266efe12a3
|
Shell
|
axsh/wakame-ci-cluster
|
/kvm-guests/cluster-ctl.sh
|
UTF-8
| 487
| 3.859375
| 4
|
[] |
no_license
|
#!/bin/bash
#
# requires:
# bash
#
set -e
set -o pipefail
set -x
function nodes() {
:
}
case "${1}" in
replace | soft-replace | run | suspend | resume | stop | kill )
if [[ -f .cluster.sh ]]; then
. .cluster.sh
fi
for node in $(nodes); do
[[ -d "${node}" ]] || continue
(
cd ${node}
if [[ -x ./${1}.sh ]]; then
time sudo ./${1}.sh
fi
)
done
;;
*)
echo "no such subcommand: ${1}" >&2
;;
esac
| true
|
5eda4318bdf096bb2ee4482b11013bee8e7fae57
|
Shell
|
cawa0505/crosware
|
/recipes/tig/tig.sh
|
UTF-8
| 383
| 2.71875
| 3
|
[] |
no_license
|
rname="tig"
rver="2.5.0"
rdir="${rname}-${rver}"
rfile="${rdir}.tar.gz"
rurl="https://github.com/jonas/tig/releases/download/${rdir}/${rfile}"
rsha256="ff537c67af9201e7e7276ce8a0ff9961e9d9c6a8a78790f5817124bd7755aef4"
rreqs="make ncurses readline git"
. "${cwrecipe}/common.sh"
eval "
function cwgenprofd_${rname}() {
echo 'append_path \"${rtdir}/current/bin\"' > "${rprof}"
}
"
| true
|
238670639758d9b7f208a47e3941a9b5431b7f4e
|
Shell
|
jalenye/shell
|
/findHowManyNetUser.sh
|
UTF-8
| 255
| 2.9375
| 3
|
[] |
no_license
|
#/bin/bash
a=0
while :
do
a=$(($a+1))
if test $a -gt 255
then break
else
echo $(ping -c 1 192.168.1.$a |grep 'ttl'|awk '{print $4}'|sed 's/://g')
ip=$(ping -c 1 192.168.1.$a |grep 'ttl'|awk '{print $4}'|sed 's/://g')
echo $ip >> ip.txt
fi
done
| true
|
ff76a2f2b076e08b22306dd01e51c6f92106ddc4
|
Shell
|
s1van/gpudb-explore
|
/utility/qcompile.sh
|
UTF-8
| 824
| 3.90625
| 4
|
[] |
no_license
|
#!/bin/bash
CDIR=`dirname $0`
source $CDIR/gpudb_env.sh
TRANSLATE=$GPUDB_PATH/translate.py
usage() {
echo "Usage: `echo $0| awk -F/ '{print $NF}'` [-option]"
echo "[option]:"
echo " -i path : specify the path of the sqls"
echo " -s scheme: scheme file"
echo " -o path : specify the output path for the executables"
echo
}
if [ $# -lt 6 ]
then
usage
exit
fi
while getopts "i:s:o:" OPTION
do
case $OPTION in
i)
INPATH=$OPTARG;
;;
o)
OUTPATH=$OPTARG;
;;
s)
SCHEME=$OPTARG;
;;
?)
usage
exit
;;
esac
done
SQLS=$(ls $INPATH|grep '.sql');
for sql in $SQLS; do
echo "$sql"
cd $GPUDB_PATH && $TRANSLATE $INPATH/$sql $SCHEME
EXECUTABLE=$(echo $sql| sed 's/.sql//g')
cd $GPUDB_CUDA_PATH && make >/dev/null 2>&1 && cp $GPUDB_CUDA_PATH/GPUDATABASE $OUTPATH/$EXECUTABLE
done
| true
|
5fddf57222e2624b3f11118941def15b32916318
|
Shell
|
paulmagnus/CSPy
|
/submit/pbin/verify~
|
UTF-8
| 7,519
| 4.3125
| 4
|
[] |
no_license
|
#!/bin/bash
#------------------------------------------------------------------------------#
# verify #
# #
# This program is intended to be run by the professor to verify that their #
# directory is set up in a way that the submit program will be able to use #
# without errors. #
# #
# Usage: verify [OPTION]... PROFESSOR CLASS PROJECT #
# Verify all files for PROFESSOR, CLASS, and PROJECT exist #
# #
# OPTIONS: #
# -f, --fix fix any errors that are detected, if possible #
# -h, --help print this help documentation #
# -v, --verbose explain what is being done #
# #
# Written by Paul Magnus '18, Ines Ayara '20, Matthew R. Jenkins '20 #
# Summer 2017 #
#------------------------------------------------------------------------------#
verifyFile()
{
if [ $verbose ]; then
printf "Verifying '$1'..."
fi
if [ ! -f $1 ]; then
if [ $verbose ]; then
printf "missing\n"
else
printf "File '$1' is missing\n"
fi
exit 1
fi
if [ $verbose ]; then
printf "Done\n"
fi
}
verifyDirectory()
{
if [ $verbose ]; then
printf "Verifying '$1'..."
fi
if [ ! -d $1 ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Creating directory..."
fi
mkdir $1
else
if [ $verbose ]; then
printf "missing\n"
else
printf "Directory '$1' is missing\n"
fi
exit 1
fi
fi
if [ $verbose ]; then
printf "Done\n"
fi
}
print_help()
{
printf "Usage: verify [OPTION]... PROFESSOR CLASS PROJECT\n"
printf "Verify all files for PROFESSOR, CLASS, and PROJECT exist\n\n"
printf "OPTIONS:\n"
printf " -f, --fix\t\tfix any errors that are detected, if possible\n"
printf " -h, --help\t\tprint this help documentation\n"
printf " -v, --verbose\t\texplain what is being done\n\n"
printf "Written by Paul Magnus '18, Ines Ayara '18, Matthew R. Jenkins '20\n"
printf "Summer 2017\n"
}
while :; do
case $1 in
-f|--fix) fix=true
shift;;
-v|--verbose) verbose=true
shift;;
-h|--help) print_help
exit;;
*) break
esac
done
if [ $# != 3 ]; then
printf "verify: missing operands\n"
printf "Try 'verify --help' for more information\n"
exit 1
fi
professor=$1
course=$2
project=$3
# Get directory of script, resolving links
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
# make sure this program is in submit/bash
if [ "${DIR##*/}" != 'pbin' ]; then
printf "Verify script must be in directory 'submit/pbin'\n"
printf "Verify script is currently in '$DIR'\n"
exit 1
fi
dirname="${DIR%/*}"
if [ "${dirname##*/}" != 'submit' ]; then
printf "Verify script must be in directory 'submit/pbin'\n"
printf "Verify script is currently in '$DIR'\n"
exit 1
fi
if [ $fix ]; then
# verify that makeTemplate is in submit/bin and is executable
if [ ! -f "$dirname/pbin/makeTemplate" ]; then
printf "File '$dirname/pbin/makeTemplate' could not be found and is required for -f, --fix to work\n"
exit 1
fi
if [ $(stat -c "%a" "$dirname/pbin/makeTemplate") != "775" ]; then
chmod 775 "$dirname/pbin/makeTemplate"
fi
fi
# verify that submit is in submit/bin and is executable
verifyFile "$dirname/bin/submit"
if ! [ "$(stat -c "%a" "$dirname/bin/submit")" = "775" ]; then
if [ $fix ]; then
chmod 755 "$dirname/bin/submit"
else
printf "File '$dirname/bin/submit' does not have correct permissions\n"
exit 1
fi
fi
verifyDirectory "$dirname/$professor"
verifyDirectory "$dirname/$professor/$course"
# VERIFY current
if [ $verbose ]; then
printf "Verifying '$dirname/$professor/$course/current'..."
fi
if [ ! -f "$dirname/$professor/$course/current" ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Creating file..."
fi
touch "$dirname/$professor/$course/current"
else
if [ $verbose ]; then
printf "missing\n"
else
printf "File '$dirname/$professor/$course/current' is missing\n"
fi
exit 1
fi
fi
if [ $verbose ]; then
printf "Done\n"
fi
verifyDirectory "$dirname/$professor/$course/$project"
projectDir="$dirname/$professor/$course/$project"
verifyDirectory "$projectDir/students"
verifyDirectory "$projectDir/tests"
# VERIFY required_files
if [ $verbose ]; then
printf "Verifying '$projectDir/required_files'..."
fi
if [ ! -f "$projectDir/required_files" ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Creating file..."
fi
printf "*" > "$projectDir/required_files"
else
if [ $verbose ]; then
printf "missing\n"
else
printf "File '$projectDir/required_files' is missing\n"
fi
exit 1
fi
fi
if [ $verbose ]; then
printf "Done\n"
fi
# VERIFY optional_files
if [ $verbose ]; then
printf "Verifying '$projectDir/optional_files'..."
fi
if [ ! -f "$projectDir/optional_files" ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Creating file..."
fi
touch "$projectDir/optional_files"
else
if [ $verbose ]; then
printf "missing\n"
else
printf "File '$projectDir/optional_files' is missing\n"
fi
exit 1
fi
fi
if [ $verbose ]; then
printf "Done\n"
fi
# VERIFY run_all_tests
if [ $verbose ]; then
printf "Verifying '$projectDir/tests/run_all_tests'..."
fi
if [ ! -f "$projectDir/tests/run_all_tests" ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Creating file..."
fi
printf "#!/bin/bash\nprintf \"No tests to run\\n\"" > "$projectDir/tests/run_all_tests"
chmod 755 "$projectDir/tests/run_all_tests"
else
if [ $verbose ]; then
printf "missing\n"
else
printf "File '$projectDir/tests/run_all_tests' is missing\n"
fi
exit 1
fi
else
if [ $(stat -c "%a" "$projectDir/tests/run_all_tests") != "755" ]; then
if [ $fix ]; then
if [ $verbose ]; then
printf "Changing permission to 755..."
fi
chmod 755 "$projectDir/tests/run_all_tests"
else
printf "\nPermissions for 'run_all_tests' is incorrect\nShould be 755\n"
exit 1
fi
fi
fi
if [ $verbose ]; then
printf "Done\n"
fi
| true
|
937f05514784314e9136b704751309e6796a182f
|
Shell
|
JeanBaeez/dotfiles
|
/bin/getFonts
|
UTF-8
| 619
| 2.625
| 3
|
[
"MIT"
] |
permissive
|
#!/bin/sh
echo "Getting Fonts..."
mkdir ~/Fonts
# Papyrus
wget -O ~/Fonts/papyrus.ttf https://img.download-free-fonts.com/dl.php?id=89786&hash=4356adc4fd6ae9e1e32926682ef43287
# Cascadia Code
wget -O ~/Fonts/Cascadia.ttf https://github.com/microsoft/cascadia-code/releases/download/v1911.21/Cascadia.ttf
# Jetbrains Mono
wget -O ~/Fonts/JetbrainsMono.zip https://github.com/JetBrains/JetBrainsMono/releases/download/v1.0.3/JetBrainsMono-1.0.3.zip
unzip ~/Fonts/JetbrainsMono.zip -d ~/Fonts
mv ~/Fonts/JetBrainsMono-1.0.3-Source/ttf/* ~/Fonts
rm -rf ~/Fonts/JetBrainsMono-1.0.3-Source
rm ~/Fonts/JetbrainsMono.zip
| true
|
7b65bbd434000273b1e5d99b577d77e03ea3417b
|
Shell
|
deepkh/libex
|
/grpc/check_cmake.sh
|
UTF-8
| 1,224
| 3.765625
| 4
|
[] |
no_license
|
#!/bin/bash
vercomp () {
if [[ $1 == $2 ]]
then
return 0
fi
local IFS=.
local i ver1=($1) ver2=($2)
# fill empty fields in ver1 with zeros
for ((i=${#ver1[@]}; i<${#ver2[@]}; i++))
do
ver1[i]=0
done
for ((i=0; i<${#ver1[@]}; i++))
do
if [[ -z ${ver2[i]} ]]
then
# fill empty fields in ver2 with zeros
ver2[i]=0
fi
if ((10#${ver1[i]} > 10#${ver2[i]}))
then
return 1
fi
if ((10#${ver1[i]} < 10#${ver2[i]}))
then
return 2
fi
done
echo X0
return 0
}
testvercomp () {
vercomp $1 $2
case $? in
0) op='=';;
1) op='>';;
2) op='<';;
esac
if [[ $op != $3 ]]
then
echo "FAIL: Expected '$3', Actual '$op', Arg1 '$1', Arg2 '$2'"
return 1
else
echo "Pass: '$1 $op $2'"
fi
return 0
}
install_cmake() {
echo "=== install cmake ==="
sudo mv /usr/bin/cmake /usr/bin/cmake.old
wget -q -O cmake-linux.sh https://github.com/Kitware/CMake/releases/download/v3.16.1/cmake-3.16.1-Linux-x86_64.sh
sudo sh cmake-linux.sh -- --skip-license --prefix=/usr/
}
check_cmake_version() {
echo "=== check cmake version ==="
testvercomp "`cmake --version | grep version | awk '{print $3}'`" "3.16.0" '>'
if [ $? = 1 ];then
echo $?
install_cmake
fi
}
| true
|
fd04b6053d53cf22ae51b09954c57c0a0c3ee48e
|
Shell
|
osyoyu/report-md
|
/latex/report-md.sh
|
UTF-8
| 283
| 2.65625
| 3
|
[] |
no_license
|
#!/bin/sh
inputfile=`basename $1 .md`
templatename=RG_TEMP
cp $2 ${templatename}.tex
pandoc -f markdown -t latex -o mid-output.tex ${1}
platex ${templatename}.tex && dvipdfmx -o ${inputfile}.pdf ${templatename}.dvi && rm ${templatename}.dvi ${templatename}.log ${templatename}.tex
| true
|
b3e54fdeef4985787ab69901e6b590079fb90e84
|
Shell
|
oriane17/cartographie
|
/traceroute/traceroute.sh
|
UTF-8
| 2,543
| 3.25
| 3
|
[] |
no_license
|
#!/bin/bash
sites=(
"www.iutbeziers.fr"
"www.nimes-metropole.fr"
"www.alliancetelecom.fr"
)
color=(
"gold"
"purple"
"blue"
"fin"
)
ttl=1
nb=0
recurrence=""
for cible in "${sites[@]}"; ##Passage sur chaque site##
do
maxttl=$(traceroute -q 1 -n $cible | sed "1d" | wc -l)
>./traceroute.rte/$cible.rte ##J'enlève le contenu de mon fichier cible.rte
echo "$cible"
while (("$ttl" <= "$maxttl"));
do
for option in "-T" "-I" "-U" "-U -p 53" "-T -p 443" "-T -p 80" "-T -p 25" "-T -p 22"; ##Chaque option pour ma commande traceroute
do
tracert=$(traceroute -A -q 1 -n -f $ttl -m $ttl $option $cible | awk '{print $1,$2,$3}' | sed '1d') ##Je garde que le ttl, l'adresse IP du routeur, et l AS
adresse=$(echo "$tracert" | awk '{print $2}') ##Je garde que l'adresse IP du routeur
if [ "$adresse" == "*" ]; ##Je compare l'adresse IP du routeur avec une étoile
then
if [ "$option" == "-T -p 22" ]; ##Dans le cas où j'ai encore une étoile même après être passée par toutes les options
then
echo "->">>./traceroute.rte/$cible.rte ##Mise en forme du fichier cible.rte pour ensuite l'utiliser dans le .dot
echo "\"Routeur $ttl introuvable pour $cible\"">>./traceroute.rte/$cible.rte
echo "Routeur $ttl introuvable"
echo "$ttl" >> ./ttlintrouvable.txt ##Je rentre le ttl actif dans mon fichier ttlintrouvable pour l'utiliser après dans mon fichier .dot
fi
else
if [ "$adresse" != "$recurrence" ]; ##S il n y a pas d étoile, je vérifie que ca e soit pas la même adresse qeue celle du ttl d avant
then
echo "$tracert"
echo "->">>./traceroute.rte/$cible.rte
echo "\"$tracert\"">>./traceroute.rte/$cible.rte
break
else
break
fi
fi
done
recurrence=$adresse
ttl=$(($ttl+1)) ##J'incrémente mon ttl pour ma boucle while
done
ttl=1 ##Une fois le ttl max atteint, je remet mon ttl à 1 pour passer à mon 2eme site
echo "[color=${color[$nb]}]">>./traceroute.rte/$cible.rte ##Je définis la couleur pour ma flèche
nb=$(($nb+1))
if [ ${color[$nb]} == "fin" ]; ##Si la couleur est égale à fin, je recommence ma liste au début
then
nb=0
fi
for line in $(cat ttlintrouvable.txt); ##Mise en forme de mon .dot pour avoir des carrés lorsque mon routeur est introuvable
do
echo "\"Routeur $line introuvable pour $cible\" [shape=box]">>./traceroute.rte/$cible.rte
done
>./ttlintrouvable.txt
done
./xdot.sh ###Je lance le script qui permet de créer mon .dot
| true
|
ff76ee444e523d021048ecc098d278656e96000b
|
Shell
|
jschule/gsuite-automation
|
/move-students-to-ou.sh
|
UTF-8
| 423
| 3.0625
| 3
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
set -o pipefail -o errexit -o nounset
gam="$HOME/bin/gamadv-xtd3/gam"
if [ ! -x "$gam" ] ; then
echo "Need https://github.com/taers232c/GAMADV-XTD3 in $gam, please install"
exit 98
fi
source config.sh
test "$MASTERSHEET"
test "$MASTERUSER"
source _functions.sh
info Move all students to their OU
$gam loop gsheet "$MASTERUSER" "$MASTERSHEET" "gam Schüler" \
gam update user "~Email" \
ou "~OU"
| true
|
bcda0b87e1900305ffb196c7950aed335f20b6ef
|
Shell
|
FairwindsOps/rok8s-scripts
|
/bin/docker-build
|
UTF-8
| 3,999
| 3.734375
| 4
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
. k8s-read-config "$@"
. docker-resolve
if [ -z "$BASEDIR" ]; then echo BASEDIR must be set; exit 1; fi
if [ -z "$DOCKERTAG" ]; then echo DOCKERTAG must be set; exit 1; fi
if [ -z "$DOCKERFILE" ]; then echo DOCKERFILE must be set; exit 1; fi
PREVIOUS_COMMIT=$(git rev-parse HEAD~1)
CI_BRANCH=$(echo "${CI_BRANCH}" | tr / _)
# support overriding "latest"
DOCKER_LATEST_TAG=${DOCKER_LATEST_TAG:-latest}
if [ "$DOCKER_BUILD_CACHE_FROM" == "available" ]; then
echo "Using --cache-from to improve performance"
CACHE_FROM_TARGETS=""
# shellcheck disable=2086
while read -r CACHE_TARGET; do
if [ "${CACHE_TARGET}" == "" ]; then
break
fi
echo "Working on Dockerfile target[${CACHE_TARGET}]..."
TARGET_TAG=cache-${CI_BRANCH}-${CACHE_TARGET}
TARGET_IMAGE=${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}
echo "Checking for existing cache image for target[${CACHE_TARGET}]..."
docker pull "${TARGET_IMAGE}:${TARGET_TAG}" || true
docker pull "${TARGET_IMAGE}:cache-master-${CACHE_TARGET}" || true
docker pull "${TARGET_IMAGE}:cache-main-${CACHE_TARGET}" || true
echo "Building Dockerfile target[${CACHE_TARGET}]..."
# shellcheck disable=2086
docker build --rm=false -t "${TARGET_IMAGE}:${TARGET_TAG}" -f "${BASEDIR}/${DOCKERFILE}" \
--target "${CACHE_TARGET}" \
${CACHE_FROM_TARGETS} \
${ROK8S_DOCKER_BUILD_EXTRAARGS} \
--cache-from "${TARGET_IMAGE}:${TARGET_TAG}" \
--cache-from "${TARGET_IMAGE}:cache-master-${CACHE_TARGET}" \
--cache-from "${TARGET_IMAGE}:cache-main-${CACHE_TARGET}" \
"${BASEDIR}"
CACHE_FROM_TARGETS="${CACHE_FROM_TARGETS} --cache-from ${TARGET_IMAGE}:${TARGET_TAG}"
done <<< "$(grep -i '^FROM.* AS ' ${BASEDIR}/${DOCKERFILE} | awk '{print $4}')"
docker pull "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:$PREVIOUS_COMMIT" || true
docker pull "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:$CI_BRANCH" || true
docker pull "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:master" || true
docker pull "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:main" || true
if [ "${DOCKER_TARGET}" != "" ]; then
DOCKER_TARGET="--target=${DOCKER_TARGET}"
fi
# shellcheck disable=2086
docker build --rm=false -t "${DOCKERTAG}:${DOCKER_LATEST_TAG}" -f "${BASEDIR}/${DOCKERFILE}" \
${CACHE_FROM_TARGETS} \
${DOCKER_TARGET} \
${ROK8S_DOCKER_BUILD_EXTRAARGS} \
--cache-from "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:$PREVIOUS_COMMIT" \
--cache-from "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:$CI_BRANCH" \
--cache-from "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:master" \
--cache-from "${EXTERNAL_REGISTRY_BASE_DOMAIN}/${REPOSITORY_NAME}:main" \
"${BASEDIR}"
else
echo "--cache-from not available with this version of Docker"
# shellcheck disable=2086
docker build --rm=false -t "${DOCKERTAG}:${DOCKER_LATEST_TAG}" -f "${BASEDIR}/${DOCKERFILE}" ${ROK8S_DOCKER_BUILD_EXTRAARGS} "${BASEDIR}"
fi
# shellcheck disable=2181
if [ $? -ne 0 ]
then
echo "Docker build failed! Aborting"
exit 1
fi
if [ "$ROK8S_ENABLE_CHANGE_DETECTION" ]; then
#Check to see if the digest for this image has changed. If it has not, then indicate that
printf "\\nRunning change detection...\\n"
oldDigest=$(docker inspect "${EXTERNAL_REGISTRY_BASE_DOMAIN}"/"${REPOSITORY_NAME}":"$CI_BRANCH" | jq -r .[].Id)
newDigest=$(docker inspect "${EXTERNAL_REGISTRY_BASE_DOMAIN}"/"${REPOSITORY_NAME}":"${DOCKER_LATEST_TAG}" | jq -r .[].Id)
changeFile=".changesDetected"
if [ -f $changeFile ]; then
rm $changeFile
fi
if [ "$oldDigest" == "$newDigest" ]; then
echo "false" > $changeFile
else #Default to true so that tests will be run if something amiss
echo "true" > $changeFile
fi
printf "Result of change detection: %s\\n" "$(cat $changeFile)"
fi
# Fire the image scanner if enabled - see the `docker-microscanner` script for details
. docker-microscanner
| true
|
ed5b251f829a88f725edf8b23282294ad700a405
|
Shell
|
trifacta/floating-elephants
|
/cloudera/cdh5/hue/start.sh
|
UTF-8
| 366
| 2.90625
| 3
|
[
"LicenseRef-scancode-dco-1.1",
"Apache-2.0"
] |
permissive
|
#!/bin/bash
# Wait for DFS to come out of safe mode
until hdfs dfsadmin -safemode wait
do
echo "Waiting for HDFS safemode to turn off"
sleep 1
done
sudo -u hdfs hdfs dfs -mkdir /user/hue
sudo -u hdfs hdfs dfs -chmod -R 1777 /user/hue
sudo -u hdfs hdfs dfs -chown hue:hadoop /user/hue
service hue start
tail -f `find /var/log -name *.log -or -name *.out`
| true
|
c7a17100d012d82151cc3c226c3ec455bce8e4af
|
Shell
|
mingle/elasticsearch-opsworks
|
/init_rbenv
|
UTF-8
| 2,616
| 3.5
| 4
|
[] |
no_license
|
#!/bin/bash
BUNDLER_VERSION="1.11.2"
export RBENV_VERSION=$(cat .ruby-version)
export RBENV_ROOT=$HOME/.rbenv
unset GEM_PATH
unset GEM_HOME
if [ ! -d $RBENV_ROOT ]; then
echo "Installing rbenv."
git clone git://github.com/sstephenson/rbenv.git $RBENV_ROOT
fi
if [ ! -d $RBENV_ROOT/plugins/rbenv-update ]; then
echo "Installing rbenv-update plugin."
git clone https://github.com/rkh/rbenv-update.git $RBENV_ROOT/plugins/rbenv-update
fi
if [ ! -d $RBENV_ROOT/plugins/ruby-build ]; then
echo "Installing ruby-build plugin."
git clone https://github.com/sstephenson/ruby-build.git $RBENV_ROOT/plugins/ruby-build
fi
if [ ! -d $RBENV_ROOT/plugins/rbenv-gemset ]; then
echo "Installing rbenv-gemset plugin."
git clone https://github.com/jf/rbenv-gemset.git $RBENV_ROOT/plugins/rbenv-gemset
fi
if [ ! -d $RBENV_ROOT/plugins/rbenv-vars ]; then
echo "Installing rbenv-vars plugin."
git clone https://github.com/sstephenson/rbenv-vars.git $RBENV_ROOT/plugins/rbenv-vars
fi
if [ ! -d $RBENV_ROOT/versions/$RBENV_VERSION ]; then
echo "Installing ruby ${RBENV_VERSION}."
$RBENV_ROOT/bin/rbenv update
$RBENV_ROOT/bin/rbenv install $RBENV_VERSION
if [[ $RBENV_VERSION =~ "jruby" ]]; then
# should be the same as pristine since this is a new install, but `gem pristine` hits file permissions errors the first time
$RBENV_ROOT/bin/rbenv exec gem install jruby-launcher
fi
echo "done"
elif [[ ("true" = "${RBENV_UPDATE:-false}") || ($(uname -a) =~ Darwin) ]]; then
echo "Updating rbenv..."
$RBENV_ROOT/bin/rbenv update
else
echo "Environment up to date, ruby version: $RBENV_VERSION"
fi
if ! (echo $PATH | grep -F "$RBENV_ROOT" > /dev/null 2>&1 && grep -F 'export PATH="$HOME/.rbenv' $HOME/.bash_profile 2>&1 > /dev/null); then
echo "Adding rbenv to PATH"
echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> $HOME/.bash_profile
export PATH="$RBENV_ROOT/bin:$PATH"
fi
if ! (type rbenv > /dev/null 2>&1 && grep -F 'eval "$(rbenv init -)"' $HOME/.bash_profile 2>&1 > /dev/null); then
echo "Initializing rbenv in your .bash_profile"
echo 'eval "$(rbenv init -)"' >> $HOME/.bash_profile
eval "$(rbenv init -)"
fi
if ! ($RBENV_ROOT/shims/bundle --version 2> /dev/null | grep -F "$BUNDLER_VERSION" > /dev/null 2>&1); then
echo "installing bundler $BUNDLER_VERSION"
cmd="$RBENV_ROOT/bin/rbenv exec gem install --no-ri --no-rdoc bundler -v $BUNDLER_VERSION"
echo "executing: $cmd"
$cmd
echo "done, result: $?"
fi
unset BUNDLER_VERSION
$RBENV_ROOT/bin/rbenv exec ruby -S bundle install
$RBENV_ROOT/bin/rbenv rehash
| true
|
cdff291c017f9ddd28486c66a384569e8d8b7f39
|
Shell
|
NLGithubWP/LambdaML
|
/archived/ec2/kmeans/run_higgs_kmeans.sh
|
UTF-8
| 1,056
| 2.828125
| 3
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
world_size=$1
nr_cluster=$2
master_ip=$3
train_path="/home/ubuntu/dataset/higgs${world_size}"
for ((i=0; i<world_size; i++)); do
if [ $i == 0 ]
then
source /home/ubuntu/envs/pytorch/bin/activate
nohup python3.6 /home/ubuntu/LambdaML/ec2/kmeans/higgs_kmeans.py --init-method "tcp://${master_ip}" --rank 0 --communication all-reduce -k "${nr_cluster}" --world-size "${world_size}" --train-file "${train_path}/${i}_${world_size}" --no-cuda > "/home/ubuntu/log/distrb_higgs_kmeans_r${i}_w${world_size}_k${nr_cluster}.txt" 2>&1 &
else
ssh "higgs-node00${i}" "source /home/ubuntu/envs/pytorch/bin/activate; cd /home/ubuntu/LambdaML/ec2/kmeans; nohup python3.6 higgs_kmeans.py --init-method tcp://${master_ip} --communication all-reduce --rank ${i} -k ${nr_cluster} --world-size ${world_size} --train-file ""${train_path}"/${i}_"${world_size}"" --no-cuda > /home/ubuntu/log/distrib_higgs_kmeans_r${i}_w${world_size}_k${nr_cluster}.txt 2>&1 &"
fi
done
| true
|
7a65828ee555344bb5cfd427038b7150699fedf6
|
Shell
|
haamoon/lidar_transfer
|
/experiments/train.sh
|
UTF-8
| 722
| 2.625
| 3
|
[
"MIT"
] |
permissive
|
#!/bin/bash
# Parameter
EXP="2048@0.05x3"
VERSION="log_dropout_u0.1_l0.1"
PRETRAINED="/automount_home_students/flanger/workspace/msc/lidar-bonnetal/train/models/darknet53/"
MODEL="/media/flanger/SAMS1TB_0/msc/experiments/$EXP/logs/$VERSION"
DATA="/media/flanger/SAMS1TB_0/msc/experiments/$EXP"
source ~/workspace/msc/venv/bin/activate
# Training
cd ~/workspace/msc/lidar-bonnetal/train/tasks/semantic/
./train.py \
-d "$DATA/dataset/" \
-p "$PRETRAINED" \
-ac "$DATA/arch_cfg_dropout.yaml" \
-dc "$DATA/data_cfg.yaml" \
-l "$MODEL"
TITLE="$EXP/$VERSION done"
MSG=""
curl -u $PUSHBULLET_TOKEN: https://api.pushbullet.com/v2/pushes \
-d type=note -d title="$TITLE" -d body="$MSG" >/dev/null 2>&1
| true
|
a61726fc0f2e51f361b3034ac20ab15ea81dc83f
|
Shell
|
astropy/conda-builder
|
/continuous-integration/travis/install_osx.sh
|
UTF-8
| 293
| 2.59375
| 3
|
[
"CC0-1.0"
] |
permissive
|
MINICONDA_URL="http://repo.continuum.io/miniconda"
MINICONDA_FILE="Miniconda3-3.7.3-MacOSX-x86_64.sh"
wget "${MINICONDA_URL}/${MINICONDA_FILE}"
bash $MINICONDA_FILE -b
export PATH=/Users/travis/miniconda3/bin:$PATH
conda update --yes conda
conda install --yes pip conda-build jinja2 binstar
| true
|
40a3c159a6599d14e65508f6b75b4a28a5ded3e6
|
Shell
|
drankye/recordservice
|
/server/csd/RECORD_SERVICE/src/scripts/client.sh
|
UTF-8
| 5,757
| 3.515625
| 4
|
[
"Apache-2.0"
] |
permissive
|
#!/bin/bash
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
set -ex
CMD=$1
function log {
timestamp=$(date)
echo "${timestamp}: $1"
}
# Replaces all occurrences of $1 with $2 in file $3, escaping $1 and $2 as necessary.
function sed_replace {
sed -i "s/$(echo $1 | sed -e 's/\([[\/.*]\|\]\)/\\&/g')/$(echo $2 | sed -e 's/[\/&]/\\&/g')/g" $3
}
log "CMD: ${CMD}"
log "PLANNER_CONF_FILE: ${PLANNER_CONF_FILE}"
log "RECORDSERVICE_CONF_FILE: ${RECORDSERVICE_CONF_FILE}"
log "CONF_DIR: ${CONF_DIR}"
log "DIRECTORY_NAME: ${DIRECTORY_NAME}"
RECORDSERVICE_CONF_DIR="${CONF_DIR}/${DIRECTORY_NAME}"
log "RECORDSERVICE_CONF_DIR: ${RECORDSERVICE_CONF_DIR}"
PLANNER_FILE="${RECORDSERVICE_CONF_DIR}/${PLANNER_CONF_FILE}"
log "PLANNER_FILE: ${PLANNER_FILE}"
PW_FILE="${RECORDSERVICE_CONF_DIR}/${PW_CONF_FILE}"
log "PW_FILE: ${PW_FILE}"
SPARK_FILE="${RECORDSERVICE_CONF_DIR}/${SPARK_CONF_FILE}"
log "SPARK_FILE: ${SPARK_FILE}"
log "HDFS_CONFIG: ${HDFS_CONFIG}"
# As CM only copies $RECORDSERVICE_CONF_DIR to /etc/recordservice/conf.cloudera.record_service,
# we should also copy YARN / HADOOP conf into RECORDSERVICE_CONF_DIR.
YARN_CONF_DIR="${CONF_DIR}/yarn-conf"
HADOOP_CONF_DIR="${CONF_DIR}/hadoop-conf"
log "YARN_CONF_DIR: ${YARN_CONF_DIR}"
log "HADOOP_CONF_DIR: ${HADOOP_CONF_DIR}"
# Copy yarn-conf under recordservice-conf.
# Copy hadoop-conf under recordservice-conf, if yarn-conf is not there.
if [ -d "${YARN_CONF_DIR}" ]; then
log "Copy ${YARN_CONF_DIR} to ${RECORDSERVICE_CONF_DIR}"
cp ${YARN_CONF_DIR}/* ${RECORDSERVICE_CONF_DIR}
elif [ -d "${HADOOP_CONF_DIR}" ]; then
log "Copy ${HADOOP_CONF_DIR} to ${RECORDSERVICE_CONF_DIR}"
cp ${HADOOP_CONF_DIR}/* ${RECORDSERVICE_CONF_DIR}
fi
# Because of OPSAPS-25695, we need to fix HADOOP config ourselves.
log "CDH_MR2_HOME: ${CDH_MR2_HOME}"
log "HADOOP_CLASSPATH: ${HADOOP_CLASSPATH}"
for i in "${RECORDSERVICE_CONF_DIR}"/*; do
log "i: $i"
sed_replace "{{CDH_MR2_HOME}}" "${CDH_MR2_HOME}" "$i"
sed_replace "{{HADOOP_CLASSPATH}}" "${HADOOP_CLASSPATH}" "$i"
sed_replace "{{JAVA_LIBRARY_PATH}}" "" "$i"
done
# Adds a xml config to RECORDSERVICE_CONF_FILE
add_to_recordservice_conf() {
FILE=`find ${RECORDSERVICE_CONF_DIR} -name ${RECORDSERVICE_CONF_FILE}`
log "Add $1:$2 to ${FILE}"
CONF_END="</configuration>"
NEW_PROPERTY="<property><name>$1</name><value>$2</value></property>"
TMP_FILE="${RECORDSERVICE_CONF_DIR}/tmp-conf-file"
cat ${FILE} | sed "s#${CONF_END}#${NEW_PROPERTY}#g" > ${TMP_FILE}
cp ${TMP_FILE} ${FILE}
rm -f ${TMP_FILE}
echo ${CONF_END} >> ${FILE}
}
# Adds a properties conf to SPARK_FILE
add_to_spark_conf() {
log "ADD $1:$2 to ${SPARK_FILE}"
NEW_PROPERTY="$1=$2"
TMP_FILE="${RECORDSERVICE_CONF_DIR}/tmp-spark-conf-file"
cat ${SPARK_FILE} > ${TMP_FILE}
echo ${NEW_PROPERTY} >> ${TMP_FILE}
log "Add prefix spark. in each line"
sed -i -e 's/^/spark./' ${TMP_FILE}
cp ${TMP_FILE} ${SPARK_FILE}
rm -f ${TMP_FILE}
}
# Adds a xml config to hdfs-site.xml
add_to_hdfs_site() {
FILE=`find ${RECORDSERVICE_CONF_DIR} -name hdfs-site.xml`
CONF_END="</configuration>"
NEW_PROPERTY="<property><name>$1</name><value>$2</value></property>"
TMP_FILE="${CONF_DIR}/tmp-hdfs-site"
cat ${FILE} | sed "s#${CONF_END}#${NEW_PROPERTY}#g" > ${TMP_FILE}
cp ${TMP_FILE} ${FILE}
rm -f ${TMP_FILE}
echo ${CONF_END} >> ${FILE}
}
# Append to hdfs-site.xml if HDFS_CONFIG is not empty.
append_to_hdfs_site() {
if [[ -n ${HDFS_CONFIG} ]]; then
FILE=`find ${RECORDSERVICE_CONF_DIR} -name hdfs-site.xml`
CONF_END="</configuration>"
TMP_FILE="${CONF_DIR}/tmp-hdfs-site"
cat ${FILE} | sed "s#${CONF_END}#${HDFS_CONFIG}#g" > ${TMP_FILE}
cp ${TMP_FILE} ${FILE}
rm -f ${TMP_FILE}
echo ${CONF_END} >> ${FILE}
fi
}
CONF_KEY=recordservice.planner.hostports
CONF_VALUE=
copy_planner_hostports_from_file() {
log "copy from $1"
if [ -f ${PLANNER_FILE} ]; then
for line in $(cat $1)
do
log "line ${line}"
if [[ ${line} == *":"*"="* ]]; then
PLANNER_HOST=${line%:*}
PLANNER_PORT=${line##*=}
log "add ${PLANNER_HOST}:${PLANNER_PORT}"
CONF_VALUE="${CONF_VALUE},${PLANNER_HOST}:${PLANNER_PORT}"
fi
done
fi
}
case $CMD in
(deploy)
log "Deploy client configuration"
copy_planner_hostports_from_file ${PLANNER_FILE}
copy_planner_hostports_from_file ${PW_FILE}
log "CONF_KEY: ${CONF_KEY}"
log "CONF_VALUE: ${CONF_VALUE}"
if [ -n "${CONF_VALUE}" ]; then
# remove the first ','
CONF_VALUE=${CONF_VALUE:1}
add_to_recordservice_conf ${CONF_KEY} ${CONF_VALUE}
add_to_spark_conf ${CONF_KEY} ${CONF_VALUE}
fi
# Add zk quorum to hdfs-site.xml
add_to_hdfs_site recordservice.zookeeper.connectString ${ZK_QUORUM}
# Enable short circuit read in hdfs-site.xml.
add_to_hdfs_site dfs.client.read.shortcircuit true
# Append HDFS_CONFIG to hdfs-site.xml.
# This can overwrite the original value.
append_to_hdfs_site
;;
(*)
log "Don't understand [$CMD]"
;;
esac
| true
|
034b6b7d9f537c4ed2cb18cd57242378be783bc9
|
Shell
|
HughP/olac-1
|
/src/utils/ldc-server-check/syschk.sh
|
UTF-8
| 8,250
| 2.78125
| 3
|
[] |
no_license
|
#! /bin/sh
webroot=/web/org/language-archives
base=/home/olac/bin
dat=$base/syschk.dat
dat_xsv_html=$base/syschk.dat.xsv_html
dat_xercesj=$base/syschk.dat.xercesj
tmp=/tmp/olac.syschk.tmp.$$
PS="/bin/ps awx"
[ -f $dat ] && . $dat
grep -v '^_OLACSEARCH_' $dat > $dat.copy
mv -f $dat.copy $dat && chmod g+w $dat
SCRIPT_ACCESSLOG_CRON="$base/access_log-cron.sh"
HTTPD_ACCESS_LOG=`grep '^LOG=' $SCRIPT_ACCESSLOG_CRON | sed 's/^LOG=//'`
CHKSUM_PHP="/usr/local/libexec/apache/libphp5.so"
CHKSUM_PERL="/usr/bin/perl"
CHKSUM_JAVA="/usr/local/bin/java"
CHKSUM_JBOSS_JAVA=`$PS | grep jboss | grep java | grep -v grep | awk '{print $5}' | head -1`
CHKSUM_JBOSS=`$PS | grep jboss | grep java | grep -v grep | sed -E 's@.*[ :]([^:]*run\.jar)[ :].*@\1@' | head -1`
CHKSUM_XALAN="/mnt/unagi/speechd8/ldc/wwwhome/olac/xalan-J/bin/xalan.jar"
CHKSUM_XERCESJ="/mnt/unagi/speechd8/ldc/wwwhome/olac/xerces-J/xml-apis.jar"
CHKSUM_PYTHON="/usr/local/bin/python2.3"
CHKSUM_XSV1="/mnt/unagi/speechd8/ldc/wwwhome/olac/xsv/lib/python2.3/site-packages/XSV/commandLine.py"
CHKSUM_XSV2="/mnt/unagi/speechd8/ldc/wwwhome/olac/xsv/lib/python2.3/site-packages/XSV/driver.py"
#CHKSUM2_DCXMLS="http://dublincore.org/schemas/xmls/"
CHKSUM2_DC="http://dublincore.org/schemas/xmls/qdc/2006/01/06/dc.xsd"
CHKSUM2_DCTERMS="http://dublincore.org/schemas/xmls/qdc/2006/01/06/dcterms.xsd"
CHKSUM2_DCMITYPE="http://dublincore.org/schemas/xmls/qdc/2006/01/06/dcmitype.xsd"
CHKSUM2_SIMPLEDC="http://dublincore.org/schemas/xmls/qdc/2006/01/06/simpledc.xsd"
CHKSUM2_QUALIFIEDDC="http://dublincore.org/schemas/xmls/qdc/2006/01/06/qualifieddc.xsd"
CHKSUM2_OLACDC="http://www.language-archives.org/OLAC/1.0/dc.xsd"
CHKSUM2_OLACDCTERMS="http://www.language-archives.org/OLAC/1.0/dcterms.xsd"
CHKSUM2_OLAC="http://www.language-archives.org/OLAC/1.0/olac.xsd"
CHKSUM2_OLAC_EXTENSION="http://www.language-archives.org/OLAC/1.0/olac-extension.xsd"
RESULT=SUCCESS
##
## httpd
##
echo "Checking httpd ... "
echo
# get pid of the leader
printf " * Get pid: "
pid_httpd=`$PS -o comm,pid,ppid | grep httpd | egrep '\b1$' | awk '{print $2}'`
if [ -n "$pid_httpd" ] ; then
echo "OK ($pid_httpd)"
#echo
#$PS -p $pid_httpd -o pid,stat,%cpu,%mem,lstart
#ecjp
else
echo "Fail"
RESULT=FAIL
fi
printf " * Fetch l-a.org index page: "
# fetch header only
line=`curl -sI "http://www.language-archives.org/" | head -1`
if [ -n "$line" ] ; then
ret=`echo $line | awk '{print $2}'`
if [ "$ret" = "200" ] ; then
echo "OK"
else
echo "Fail"
RESULT=FAIL
fi
#echo
#echo $line
#echo
else
echo "Fail"
RESULT=FAIL
fi
echo
##
## mysql
##
echo "Checking mysql ..."
echo
# mysql is on brown
# its not so simple to have a remote process information
printf " * Get number of archives: "
mysql="mysql --defaults-file=/home/olac/.my.cnf.olac2"
q1="select count(*) from OLAC_ARCHIVE"
q2="select count(*) from ARCHIVED_ITEM"
narc=`echo $q1 | $mysql | sed 1d`
if [ "$narc" -gt 0 ] ; then
echo $narc
else
echo "Fail"
RESULT=FAIL
fi
printf " * Get number of archived items: "
nitm=`echo $q2 | $mysql | sed 1d`
if [ "$nitm" -gt 0 ] ; then
echo $nitm
else
echo "Fail"
RESULT=FAIL
fi
echo
##
## sendmail (actually postfix)
##
echo "Checking sendmail ..."
echo
## get pid of "master"
# note that i'm not familiar with postfix
# it seems that "master" is the deamon that takes send requests
printf " * Get pid of postfix/master: "
pid_master=`$PS -o comm,pid | grep '^master' | grep -v grep | awk '{print $2}'`
if [ -n "$pid_master" ] ; then
echo "OK ($pid_master)"
else
echo "Fail"
RESULT=FAIL
fi
# send HELO and QUIT commands to the smtp server
printf " * helo&quit test: "
$base/syschk.smtp.exp > /dev/null 2>&1
if [ $? -eq 0 ] ; then
echo "OK"
else
echo "Fail"
RESULT=FAIL
fi
echo
##
## logfile cycling
##
echo "Check http access log cycling ..."
echo
## get path
printf " * current access log is active: "
# last log line
a=`cat $HTTPD_ACCESS_LOG | grep www.language-archives.org | tail -1`
#a=`tail $HTTPD_ACCESS_LOG | grep www.language-archives.org | grep '/tools/search/' | grep -m 1 'query=' | tail -1`
#a=`tail -1 $HTTPD_ACCESS_LOG`
# date
b=`echo $a | awk '{print $5,$6}'`
echo "_OLACSEARCH_LAST_ACCESS='$b'" >>$dat
if [ -z "$b" -o "$b" = "$_OLACSEARCH_LAST_ACCESS" ] ; then
_OLACSEARCH_MATCH_COUNT=`expr $_OLACSEARCH_MATCH_COUNT + 1`
else
_OLACSEARCH_MATCH_COUNT=0
fi
if [ $_OLACSEARCH_MATCH_COUNT -lt 24 ] ; then
echo "OK"
else
echo "Fail"
RESULT=FAIL
fi
echo "_OLACSEARCH_MATCH_COUNT=$_OLACSEARCH_MATCH_COUNT" >>$dat
echo
##
## search/report alive?
##
echo "Checking OLAC Search/Report ... "
echo
URL_SEARCH="http://www.language-archives.org/tools/search/?query=hindi&archive=&page=1&webLangID=ENG"
URL_REPORT="http://www.language-archives.org/tools/reports/?archive=41"
printf " * Query OLAC Search: "
# fetch header only
line=`curl -sI "$URL_SEARCH" | head -1`
if [ -n "$line" ] ; then
ret=`echo $line | awk '{print $2}'`
if [ "$ret" = "200" ] ; then
echo "OK"
else
echo "Fail"
RESULT=FAIL
fi
else
echo "Fail"
RESULT=FAIL
fi
printf " * Query OLAC Report: "
# fetch header only
line=`curl -sI "$URL_REPORT" | head -1`
if [ -n "$line" ] ; then
ret=`echo $line | awk '{print $2}'`
if [ "$ret" = "200" ] ; then
echo "OK"
else
echo "Fail"
RESULT=FAIL
fi
else
echo "Fail"
RESULT=FAIL
fi
echo
##
## xsv run
##
echo "Checking XSV & XALAN ..."
echo
printf " * Running /pkg/ldc/wwwhome/olac/bin/xsv_html: "
/pkg/ldc/wwwhome/olac/bin/xsv_html /web/language-archives/OLAC/1.0/static-repository.xml > $tmp 2> /dev/null
if [ -z "`diff $tmp $dat_xsv_html`" ] ; then
echo "OK - got expected result"
else
echo "Fail - unexpected output"
RESULT=FAIL
fi
rm -f $tmp
echo " (for this to be successful, xsv and xalan should work correctly)"
echo
##
## xercesj run
##
echo "Checking Xerces-J ..."
echo
printf " * Running /pkg/ldc/wwwhome/olac/bin/xercesj.syschk: "
/pkg/ldc/wwwhome/olac/bin/xercesj.syschk /web/language-archives/OLAC/1.0/static-repository.xml 2>&1 | sed -E 's/[0-9]+ ms//' > $tmp
if [ -z "`diff $tmp $dat_xercesj`" ] ; then
echo "OK - got expected result"
else
echo "Fail - unexpected result"
RESULT=FAIL
fi
rm -f $tmp
echo
##
## disk space
##
echo "Checking disk space ..."
echo
printf " * Have enought space? "
n=`df -k /web/language-archives | tail -1 | awk '{print $4}'`
if [ "$n" -ge 200000 ] ; then
echo "OK - $n 1K-blocks available"
else
echo "Fail - only $n 1K-blocks remaining"
RESULT=FAIL
fi
echo
##
## symlinks
##
echo "Checking symbolic links ..."
echo
find $webroot -type l -exec ls -l \{} \; > $tmp 2> /dev/null
cat $tmp | $base/syschk.symlinks.py |
while read a ; do
echo " $a"
done | tee $tmp.2
echo
if [ -s $tmp.2 ] ; then
echo " Fail"
RESULT=FAIL
else
echo " OK"
fi
rm -f $tmp $tmp.2
echo
##
## file permissions
##
echo "Checking file/directory permissions ..."
echo
dir=/web/language-archives/tools/search/logs/
printf " * $dir "
if [ -r "$dir" -a -w "$dir" ] ; then
echo "is read-/writable - OK"
else
echo "is not read-/writable - Fail"
fi
echo
##
## md5 checksum
##
echo "Checking md5 checksum ..."
echo
for var in `set | grep '^CHKSUM_' | sed 's/=.*//' | sort` ; do
path=`eval 'echo $'$var`
printf " * %20s: %s" `echo $var | sed s'/[^_]*._//'` $path
md5old=`eval 'echo $MD5_'$var`
md5val=`md5 $path | awk '{print $NF}'`
if [ "$md5old" = "$md5val" ] ; then
echo " OK"
else
echo " <font color=red>Fail</font>"
RESULT=FAIL
fi
#echo "MD5_$var=\"$md5val\"" >>$dat
#echo "MD5_$var=\"$md5old\"" >>$dat
done
for var in `set | grep '^CHKSUM2_' | sed 's/=.*//' | sort` ; do
path=`eval 'echo $'$var`
printf " * %20s: %s" `echo $var | sed s'/[^_]*._//'` $path
md5old=`eval 'echo $MD5_'$var`
md5val=`curl -s "$path" | md5`
if [ "$md5old" = "$md5val" ] ; then
echo " OK"
else
echo " <font color=red>Fail</font>"
RESULT=FAIL
fi
#echo "MD5_$var=\"$md5val\"" >>$dat
#echo "MD5_$var=\"$md5old\"" >>$dat
done
echo
##
## return
##
if [ "$RESULT" = FAIL ] ; then
echo "Test failed"
exit 1
else
echo "Test succeeded"
exit 0
fi
| true
|
f2efa37ffd685eccf00e6811d7ecab1858ac67e4
|
Shell
|
petronny/aur3-mirror
|
/xkas/PKGBUILD
|
UTF-8
| 908
| 2.9375
| 3
|
[] |
no_license
|
# This is an example PKGBUILD file. Use this as a start to creating your own,
# and remove these comments. For more information, see 'man PKGBUILD'.
# NOTE: Please fill out the license field for your package! If it is unknown,
# then please put 'unknown'.
# Maintainer: Your Name <youremail@domain.com>
pkgname=xkas
pkgver=14
pkgrel=1
pkgdesc="A multi-target cross assembler"
arch=(i686 x86_64)
url="http://byuu.org/programming/"
license=(custom)
depends=(gcc-libs)
makedepends=()
optdepends=()
source=("http://byuu.org/files/${pkgname}_v$pkgver.tar.bz2")
md5sums=('4bcb467a4955240b2cdd96021781a74b')
build() {
cd "$srcdir/$pkgname"
sed -i -e '/^clear\|^strip/d' cc.sh
./cc.sh
}
package() {
cd "$srcdir/$pkgname"
install -d "$pkgdir/usr/share/licenses/xkas"
sed -n '2,5p' libxkas/libxkas.hpp > "$pkgdir/usr/share/licenses/xkas/LICENSE"
install -Dm755 xkas "$pkgdir/usr/bin/xkas"
}
# vim:set ts=2 sw=2 et:
| true
|
d7744239c230178ebc9bb451f6740fc53451c452
|
Shell
|
foobarjimmy/productionScripts
|
/bak/pinglive.sh
|
UTF-8
| 353
| 3.65625
| 4
|
[] |
no_license
|
#! /bin/bash
# written by jim.li@20160425
echo -e "This is a program used for ping hosts"
sec1=192.168.1
for sec2 in {1..10}
do
ipaddr="${sec1}.${sec2}"
ping -c 1 -w 1 "${ipaddr}" &> /dev/null && result=0 || result=1
if [ "${result}" == "0" ];then
echo "Server ${ipaddr} is alive!"
else
echo -e "\033[1;31mServer ${ipaddr} is down!\033[0m"
fi
done
| true
|
14e20ffdfbdfe4f868971bffc5afacdd809a7640
|
Shell
|
slspeek/fai-experiments
|
/das/install-golang.sh
|
UTF-8
| 351
| 2.953125
| 3
|
[] |
no_license
|
#!/bin/bash
VERSION=1.4.2
ARCH=386
if test $(uname -m) = x86_64 ; then
ARCH=amd64
fi
cd /var/tmp
wget -c https://storage.googleapis.com/golang/go${VERSION}.linux-${ARCH}.tar.gz
cd /usr/local/
tar xvzf /var/tmp/go${VERSION}.linux-${ARCH}.tar.gz
cd /usr/local/bin
ln -s /usr/local/go/bin/go
ln -s /usr/local/go/bin/gofmt
ln -s /usr/local/go/bin/godoc
| true
|
d765ccebf65d814fd6d4843c2ee54bbd60e26ec9
|
Shell
|
AtomToast/dotfiles
|
/.local/bin/scripts/killactive
|
UTF-8
| 118
| 2.625
| 3
|
[] |
no_license
|
#!/bin/sh
windowFocus=$(xdotool getwindowfocus)
pid=$(xprop -id $windowFocus | grep PID | cut -d' ' -f3)
kill -9 $pid
| true
|
b38c240496b17302b36143cbf12453c550868282
|
Shell
|
charkost/irc-bot
|
/scripts/mpd_random.sh
|
UTF-8
| 209
| 2.578125
| 3
|
[
"MIT"
] |
permissive
|
#!/usr/bin/env bash
RANDOM_ON=~/.mpd_random
mpc add "" && mpc -q random on && mpc -q play
QUEUESIZE=`mpc playlist | wc -l`
echo "$QUEUESIZE songs queued @ http://foss.tesyd.teimes.gr:8000/"
touch $RANDOM_ON
| true
|
dadf2d74844233f206781bbac47f487832f6034f
|
Shell
|
mrfireboy/cf
|
/ptran
|
UTF-8
| 330
| 3.375
| 3
|
[] |
no_license
|
#!/bin/bash
#
if [ -z "$1" -o -z "$2" ];then
exit
fi
# for in mysql environment
if [ "$1" = 'inmysql' ]; then
echo "$2" | sed -r -e "s/'/''/g" -e 's/\\/\\\\/g'
exit
fi
# for sed replacement environment
if [ "$1" = 'sed' ]; then
echo "$2" | sed -r -e 's/\\/\\\\/g' -e "s/\//\\\\\//g" -e 's/\&/\\\&/g'
exit
fi
| true
|
2e770e72ff56dcce3f427576221ef5cc647c672b
|
Shell
|
daiab/Train-To-Last
|
/utils/gen_lst/extract_file.sh
|
UTF-8
| 317
| 3.234375
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
root=`pwd`
echo "extract path: $root/data_extracted"
mkdir -p ./data_extracted
for file in `ls`; do
find -name "*.rar" | xargs -i rar e {} ./data_extracted
find -name "*.zip" | xargs -i unzip {} -d ./data_extracted
find -name "*.tar.gz" | xargs -i tar -xzf {} -C ./data_extracted
done
| true
|
97b0d0fb07dcb235e8b91f235c730ea3ab5047bb
|
Shell
|
IgnasiLucas/Brachionus
|
/results/2019-07-10/README.sh
|
UTF-8
| 4,476
| 3.578125
| 4
|
[] |
no_license
|
#!/bin/bash
#
# 2019-07-10
# ==========
#
# Once the genes and transcripts differentially expressed between selective
# regimes are identified (2019-04-03), I need to run the functional analysis.
# Genes in the B. plicatilis genome do not seem to have any functional annotation.
# I believe that Eva used Blast2GO, but I'd like to try something else. I note
# that the complete set of transcripts, including those discovered along this
# project, are in 2019-03-29/z1.gtf. This file does not have CDS information, but
# it includes all the genes and transcripts used in the differential gene expression
# analysis, properly identified with the names given by cuffmerge.
#
# The cleanest way to run the functional analysis is to start from a fasta file
# with all transcripts. While bedtools allows to extract sequences from gff files,
# it does not join exons from the same transcript together (unless using a BED 12
# file). I have looked for "gff2fasta.py" scripts, and I learned about cgat scripts,
# which can be installed with conda. They are not compatible with the current
# environment. Thus, to run this folder you need to activate the cgat environment,
# which is saved here as env-cgat.yaml, or spec-file.txt.
GFF="../2019-03-29/z1.gtf"
REF="../../data/reference.fa"
DATADIR="../../data/2019-07-10"
# gff2fasta outputs a header in the fasta file, which I want to re-direct to a log file.
# It can also include transcript attributes found in the gtf file in the name of the
# sequences in the fasta file. I want to process the output of gff2fasta in two different
# and simultaneous ways: redirect the header to a log, and remove unnecessary attributes
# from the names. I learned that I can do this with a named pipe and the tee command.
if [ ! -e transcripts.fa ]; then
mkfifo pipe
# Here, I make grep read the pipe in the background, before the pipe carries anything.
cat pipe | grep "^#" > transcripts.log &
# Now, I send the output of gff2fasta both to the pipe and to the other grep command.
cgat gff2fasta --genome-file $REF \
--merge-adjacent \
--is-gtf \
--header-attributes < $GFF | \
tee pipe | \
# I expect only the name lines of the fasta file to have spaces, and I expect the
# first and the forth fields to be transcript and gene ids, respectively.
grep -v "^#" | cut -d " " -f 1,4 > transcripts.fa
rm pipe
fi
# I use TransDecoder to identify the CDS within the transcripts.
if [ ! -e transdecoder/longest_orfs.pep ]; then
TransDecoder.LongOrfs -t transcripts.fa -S -O transdecoder
fi
# Following TransDecoder's recommendations, I use blastp and pfam searches to identify the
# most promising proteins.
if [ ! -d $DATADIR ]; then mkdir $DATADIR; fi
if [ ! -e transcripts.fa.transdecoder.pep ]; then
if [ ! -e blastp.outfmt6 ]; then
if [ ! -e $DATADIR/swissprot.00.phr ]; then
update_blastdb.pl --decompress swissprot
mv swissprot* $DATADIR/
mv taxdb* $DATADIR/
fi
blastp -query transdecoder/longest_orfs.pep -db $DATADIR/swissprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 10 > blastp.outfmt6
fi
if [ ! -e pfam.domtblout ]; then
if [ ! -e $DATADIR/Pfam-A.hmm.h3f ]; then
if [ ! -e Pfam-A.hmm ]; then
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
fi
hmmpress Pfam-A.hmm
mv Pfam* $DATADIR/
fi
# hmmscan searches protein sequences against an (indexed) HMM database.
hmmscan --cpu 50 --domtblout pfam.domtblout --noali $DATADIR/Pfam-A.hmm transdecoder/longest_orfs.pep > pfam.log
fi
TransDecoder.Predict -t transcripts.fa --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -O transdecoder --single_best_only
fi
#rm -r transdecoder
#rm -r transdecoder.__checkpoints
# There is a lot of rubbish generated. The main result here is the transcripts.fa.transdecoder.pep file,
# which is a fasta file with the selected proteins that have blastp and/or pfam hits. Their names now
# include information about those hits. The main identifier is the transcript_id. The gene_id is not
# included in the name, but can easily be tracked from the 2019-03-29/z1.gtf file.
#
# In all, there are 49663 proteins, from 49663 transcripts. At this point, I abandon the cgat environment
# and the present folder to run interproscan in the next one.
| true
|
2d68a938b2025c4a6c2f91cbc788b4747baaa19d
|
Shell
|
vektor330/malacky
|
/utils/utils.sh
|
UTF-8
| 1,249
| 4.21875
| 4
|
[] |
no_license
|
# Takes 2 arguments, environment name and "property key".
# Returns the value of the property of that environment, from environments.conf.
function getparam {
# TODO DIR needs to be set as argument too!
local _ENV="${1}"
local _KEY="${2}"
# TODO this grep has SERIOUS problems with prefix-ness!
# should probably be grep "^${_ENV}\.${_KEY}$"
cat "${DIR}/conf/environments.conf" | grep "${_ENV}.${_KEY}" | cut -d "=" -f 2 | tr -d "[[:space:]]"
}
# The same as echo, but writes on the standard error.
function echoerr {
echo "${@}" 1>&2
}
# Takes 1 argument, file name.
# Removes the BOM (byte order marker) from the specified file.
function remove_bom {
local _FILE="${1}"
if [[ "$(file "${_FILE}")" == *UTF-8\ Unicode\ \(with\ BOM\)* ]]
then
echoerr "Removing UTF-8 BOM for ${_FILE}"
tail -c +4 "${_FILE}" > "/tmp/killbom" || { echoerr "Failed to tail to /tmp/killbom"; exit 1; }
mv "/tmp/killbom" "${_FILE}"
fi
}
# Checks if the argument is a valid environment name, as described in the
# environment config file.
function is_environment {
local _ENV="${1}"
# TODO DIR needs to be a parameter, too
cat "${DIR}/conf/environments.conf" | grep -v "#" | cut -d "." -f 1 | sort | uniq | grep "." | grep -q "${_ENV}"
echo ${?}
}
| true
|
d9d20b0dd81302e364d0a4657384c1f0765c1776
|
Shell
|
danitfk/elkarbackup-docker
|
/elkarbackup/1.2/entrypoint.sh
|
UTF-8
| 4,821
| 3.765625
| 4
|
[] |
no_license
|
#! /bin/bash
dbadminusername=${EB_DB_USER:=root}
dbadminpassword=${EB_DB_PASSWORD:=$MYSQL_ROOT_PASSWORD}
dbhost=${EB_DB_HOST:=db}
dbname=${EB_DB_NAME:=elkarbackup}
dbusername=${EB_DB_USERNAME:=elkarbackup}
dbuserpassword=${EB_DB_USERPASSWORD:=elkarbackup}
# DB password empty?
if [ ! -n "${MYSQL_ROOT_PASSWORD}" ] && [ ! -n "${EB_DB_PASSWORD}" ] ;then
echo >&2 'error: unknown database root password'
echo >&2 ' You need to specify MYSQL_ROOT_PASSWORD or EB_DB_PASSWORD'
exit 1
fi
# Check database connection
until mysqladmin ping -h "${EB_DB_HOST:=db}" --silent; do
>&2 echo "MySQL is unavailable - sleeping"
sleep 1
done
# Check database configuration. Create DB if it does not exist.
if ! mysql -u"$dbusername" -p"$dbuserpassword" -h"$dbhost" "$dbname" </dev/null &>/dev/null
then
echo "Attempting to create DB $dbname and user $dbusername in $dbhost"
echo 'Create database'
echo "CREATE DATABASE IF NOT EXISTS \`$dbname\` DEFAULT CHARACTER SET utf8;" | mysql -u"$dbadminusername" -p"$dbadminpassword" -h"$dbhost"
echo 'Create user'
if [ "$dbhost" = localhost ]
then
user="'$dbusername'@localhost"
else
user="'$dbusername'"
fi
echo "GRANT ALL ON \`$dbname\`.* TO $user IDENTIFIED BY '$dbuserpassword';" | mysql -u"$dbadminusername" -p"$dbadminpassword" -h"$dbhost" || true
else
echo DB seems to be ready
fi
# Allow www-data and elkarbackup user to write to /dev/stderr
if [ ! -f /tmp/logpipe ]; then
mkfifo -m 600 /tmp/logpipe
fi
chown www-data:www-data /tmp/logpipe
setfacl -m u:www-data:rwx -m u:elkarbackup:rwx /tmp/logpipe
cat <> /tmp/logpipe 1>&2 &
# Log to stdout
sed -i 's/%kernel.logs_dir%\/BnvLog.log/\/tmp\/logpipe/g' /etc/elkarbackup/config.yml
sed -i 's/${APACHE_LOG_DIR}\/elkarbackup-ssl.access.log/\/proc\/self\/fd\/1/g' /etc/apache2/sites-available/elkarbackup-ssl.conf /etc/apache2/sites-available/elkarbackup.conf
sed -i 's/${APACHE_LOG_DIR}\/elkarbackup.error.log/\/proc\/self\/fd\/2/g' /etc/apache2/sites-available/elkarbackup-ssl.conf /etc/apache2/sites-available/elkarbackup.conf
# Configure parameters
echo 'Configure parameters'
sed -i "s#database_host:.*#database_host: $dbhost#" /etc/elkarbackup/parameters.yml
sed -i "s#database_name:.*#database_name: $dbname#" /etc/elkarbackup/parameters.yml
sed -i "s#database_user:.*#database_user: $dbusername#" /etc/elkarbackup/parameters.yml
sed -i "s#database_password:.*#database_password: $dbuserpassword#" /etc/elkarbackup/parameters.yml
# Migrate and delete cache content
echo Delete cache content
rm -fR /var/cache/elkarbackup/*
echo Update DB
php /usr/share/elkarbackup/app/console doctrine:migrations:migrate --no-interaction >/dev/null || true
echo Create root user
php /usr/share/elkarbackup/app/console elkarbackup:create_admin >/dev/null || true
echo Clean cache
php /usr/share/elkarbackup/app/console cache:clear >/dev/null || true
echo Dump assets
php /usr/share/elkarbackup/app/console assetic:dump >/dev/null || true
echo Invalidate sessions
rm -rf /var/lib/elkarbackup/sessions/*
# set rwx permissions for www-data and the backup user in the cache and log directories
# as described in http://symfony.com/doc/current/book/installation.html#configuration-and-setup
echo Changing file permissions
username="elkarbackup"
setfacl -R -m u:www-data:rwx -m u:$username:rwx /var/cache/elkarbackup 2>/dev/null || ( echo "ACLs not supported. Remount with ACL and reconfigure with 'dpkg --configure --pending'" && false )
setfacl -dR -m u:www-data:rwx -m u:$username:rwx /var/cache/elkarbackup
setfacl -R -m u:www-data:rwx -m u:$username:rwx /var/log/elkarbackup
setfacl -dR -m u:www-data:rwx -m u:$username:rwx /var/log/elkarbackup
chown -R $username.$username /var/cache/elkarbackup /var/log/elkarbackup /var/spool/elkarbackup
chown -R www-data.www-data /var/lib/elkarbackup/sessions /etc/elkarbackup/parameters.yml /var/spool/elkarbackup/uploads
uploadsdir="/var/spool/elkarbackup/uploads"
olduploadsdir=`cat /etc/elkarbackup/parameters.yml|grep upload_dir|sed 's/.*: *//'`
mkdir -p "$uploadsdir" || true
if [ ! "$olduploadsdir" == "$uploadsdir" ]; then
mv "$olduploadsdir"/* "$uploadsdir" || true
fi
chown -R www-data.www-data "$uploadsdir"
sed -i "s#upload_dir:.*#upload_dir: $uploadsdir#" /etc/elkarbackup/parameters.yml
sed -i -e "s#elkarbackupuser#$username#g" -e "s#\s*Cmnd_Alias\s*ELKARBACKUP_SCRIPTS.*#Cmnd_Alias ELKARBACKUP_SCRIPTS=$uploadsdir/*#" /etc/sudoers.d/elkarbackup
chmod 0440 /etc/sudoers.d/elkarbackup
# Delete apache pid file (https://github.com/docker-library/php/issues/53)
if [ -f /run/apache2/apache2.pid ]; then
rm -f /run/apache2/apache2.pid
fi
if [ "$DISABLE_CRON" == "true" ]; then
/usr/sbin/apache2ctl -D FOREGROUND
else
/usr/sbin/cron && /usr/sbin/apache2ctl -D FOREGROUND
fi
| true
|
ee169577dc86d93d5902d0b4bde99b1079f570f6
|
Shell
|
rff/cfgbin
|
/bin/betterterm.sh
|
UTF-8
| 631
| 3.4375
| 3
|
[
"Unlicense"
] |
permissive
|
#!/bin/sh
#
# source: http://rcr.io/words/dynamic-xterm-colors.html
# reddit: http://www.reddit.com/r/commandline/comments/2ds233/xterm_party/
A=0
F="0.1"
CODE=10
case ${1:-'fg'} in
'bg' ) CODE=11 ;;
'cu' ) CODE=12 ;;
'mo' ) CODE=13 ;;
'fg' ) CODE=10 ;;
* )
echo "Invalid option '$1'."
exit 1
;;
esac
while true; do
test $A -eq 628318 && A=0 || A=$((A + 1))
R=$(echo "s ($F*$A + 0)*127 + 128" | bc -l | cut -d'.' -f1)
B=$(echo "s ($F*$A + 2)*127 + 128" | bc -l | cut -d'.' -f1)
G=$(echo "s ($F*$A + 4)*127 + 128" | bc -l | cut -d'.' -f1)
printf "\033]%d;#%02x%02x%02x\007" ${CODE} $R $B $G
sleep 0.01
done
| true
|
ff828ca64926233685dee98b8da585930c86451a
|
Shell
|
JOravetz/Depth_Conversion
|
/wrapper.process.deviation.sh
|
UTF-8
| 261
| 3.15625
| 3
|
[] |
no_license
|
#! /bin/bash
### wrapper script to loop over each deviation survey - stored in deviations.lis ###
ls -alt *deviation_survey_from_Program.dat | awk '{print $9}' > deviations.lis
while read -r LINE ; do
process.deviation.sh -s ${LINE}
done < deviations.lis
| true
|
81db0a12c55cb96bba1387fa2624d5eeaa115366
|
Shell
|
dcosson/dotfiles
|
/misc/git-find-pr
|
UTF-8
| 926
| 3.96875
| 4
|
[] |
no_license
|
#!/bin/bash
# Find the PR that merged the given SHA into master, and open it in the browser.
# From http://genius.com/Andrew-warner-git-getpull-quickly-find-the-pull-request-that-merged-your-commit-to-master-annotated
if [ -z $1 ]; then
echo "Usage: git getpull <SHA>" 1>&2
elif [ -z "$(git rev-parse --git-dir 2>/dev/null)" ]; then
echo "Not in a git directory" 1>&2
else
repository_path=$(git config --get remote.origin.url 2>/dev/null | \
perl -lne 'print $1 if /(?:(?:https?:\/\/github.com\/)|:)(.*?).git/')
pull_base_url=https://github.com/$repository_path/pull
pull_id=$(git log $1..origin/master --ancestry-path --merges --oneline 2>/dev/null \
| perl -nle 'print $1 if /#(\d+)/' | tail -n 1)
if [ -n "$pull_id" ]; then
echo "$pull_base_url/$pull_id" | xargs open
else
echo "Sorry, couldn't find that pull" 1>&2
fi
fi
| true
|
ca7acafbf0fa1ae375b90004d9530aa1f724cc41
|
Shell
|
wdekkers/vagrant_php7_mysql_box
|
/etc/scripts/bootstrap.sh
|
UTF-8
| 1,147
| 3.109375
| 3
|
[] |
no_license
|
# Install SQL Client
yum install -y httpd mysql-server mysql-client
rpm -Uvh https://mirror.webtatic.com/yum/el6/latest.rpm
# Install PHP 7
yum install -y --enablerepo=webtatic-testing php70w php70w-opcache
# Change php conf to start php7 instead php5
sed -i 's/php5/php7/g' /etc/httpd/conf.d/php.conf
# Setup virtual hosts
echo "
<VirtualHost *:80>
DocumentRoot "/vagrant/websites/yoursite.local"
<Directory "/vagrant/websites/yoursite.local">
Allow From All
AllowOverride All
</Directory>
ErrorLog /vagrant/var/logs/yoursite
</VirtualHost>
" > /etc/httpd/conf.d/my-websites.conf
# Bind address to make MySQL available
grep -q -F 'bind-address = 127.0.0.1' /etc/my.cnf || printf '\n\nbind-address = 127.0.0.1\n' >> /etc/my.cnf
# Enable services
chkconfig mysqld on
chkconfig httpd on
# Start / Stop services
service mysqld start
service httpd start
service iptables stop
# Create database with user root and no password
mysql -u root -e "create database database_name;
create user 'root'@'%' identified by '';
grant all privileges on *.* to 'root'@'%' with grant option;
flush privileges;
"
| true
|
d1546d354b2fd1720f7821104d4ede981d951f90
|
Shell
|
ali4006/spot
|
/spot/pfs-example/command-line-script.sh
|
UTF-8
| 2,508
| 4.15625
| 4
|
[
"MIT"
] |
permissive
|
#!/bin/bash
function die {
# die $DIR Error message
local DIR=$1
shift
local D=`date`
echo "[ ERROR ] [ $D ] $*"
exit 1
}
INITDIR=$PWD
if [ $# -lt 2 ]; then
die ${INITDIR} "Needs 2 arguments and an optional flag. If you keep -r flag as an input, then the reprozip trace process is triggered . Usage: $0 [-r] <subject_folder> <name>"
fi
REPROZIP_FLAG=false
#If reprozip flag is set
if [ $# -eq 3 ]; then
if [ $1 = "-r" ]; then
REPROZIP_FLAG=true
SUBJECT_FOLDER=$2
NAME=$3
fi
else
SUBJECT_FOLDER=$1
NAME=$2
fi
EXECUTION_DIR=exec
#To maintain the same subject folder name while processing we are taking only the subject folder name
SUBJECT_FOLDER_ID="$(echo "$1" | awk -F"-" '{print $1}')"
BEFORE_FILE=${EXECUTION_DIR}/${SUBJECT_FOLDER_ID}/checksums-before.txt
AFTER_FILE=${EXECUTION_DIR}/${SUBJECT_FOLDER_ID}/checksums-after.txt
create-execution-dir.sh ${SUBJECT_FOLDER} ${SUBJECT_FOLDER_ID} ${EXECUTION_DIR} || die ${INITDIR} "Cannot create execution directory."
#checksums.sh ${EXECUTION_DIR}/${SUBJECT_FOLDER_ID} > ${BEFORE_FILE} || die ${INITDIR} "Checksum script failed."
monitor.sh &> ${EXECUTION_DIR}/${SUBJECT_FOLDER_ID}/monitor.txt || die ${INITDIR} "Monitoring script failed."
cd ${EXECUTION_DIR} || die ${INITDIR} "Cannot cd to ${EXECUTION_DIR}."
#Adding the reprozip command to trace the processing of subjects
if [ ${REPROZIP_FLAG} = true ]; then
reprozip trace PreFreeSurferPipelineBatch.sh --StudyFolder=$PWD --Subjlist=${SUBJECT_FOLDER_ID} --runlocal || die ${INITDIR} "Pipeline failed."
else
PreFreeSurferPipelineBatch.sh --StudyFolder=$PWD --Subjlist=${SUBJECT_FOLDER_ID} --runlocal || die ${INITDIR} "Pipeline failed."
fi
cd ${INITDIR} || die ${INITDIR} "cd .. failed."
#checksums.sh ${EXECUTION_DIR}/${SUBJECT_FOLDER_ID} > ${AFTER_FILE} || die ${INITDIR} "Checksum script failed."
#Copying the .reprozip-trace folder in execution directory to the subject folder.
if [ ${REPROZIP_FLAG} = true ]; then
cp -r ${EXECUTION_DIR}/.reprozip-trace ${EXECUTION_DIR}/${SUBJECT_FOLDER_ID}
fi
ln -s ${EXECUTION_DIR}/${SUBJECT_FOLDER_ID} ${SUBJECT_FOLDER}-${NAME} || die ${INITDIR} "Cannot link results."
| true
|
7b9644cc94d8b75c7ef8717da089b3f0352ab001
|
Shell
|
zv/metamage_1
|
/lamp/:/sbin/about
|
UTF-8
| 994
| 2.515625
| 3
|
[] |
no_license
|
#!/bin/sh
export APPLET=about
/usr/bin/touch /app/$APPLET/window/select 2> /dev/null && exit || /bin/true
rm /app/$APPLET 2> /dev/null
iconid=128
cd -P /gui/new/port
echo 0 > vis
echo 220,68 > size
echo About MacRelix > title
echo > procid 4
/usr/bin/touch window
echo 0 > window/text-font
/bin/ln /gui/new/stack view
/bin/ln /gui/new/frame view/icon
echo 32 > view/icon/width
echo 32 > view/icon/height
echo 13 > view/icon/.margin-top
echo 23 > view/icon/.margin-left
echo 23 > view/icon/.margin-right
/bin/ln /gui/new/icon view/icon/v
echo $iconid > view/icon/v/data
/bin/ln /gui/new/frame view/main
echo 13 > view/main/.margin-top
echo 13 > view/main/.margin-right
echo 78 > view/main/.margin-left
/bin/ln /gui/new/caption view/main/v
echo >> view/main/v/text "MacRelix"
echo >> view/main/v/text "by Joshua Juran"
echo 1 > view/icon/v/disabling
echo 1 > view/main/v/disabling
/usr/bin/daemonize --cwd --ctty=tty -- /usr/bin/idle
echo 1 > vis
/bin/ln -s $PWD /app/$APPLET
| true
|
e154385a48880ad8ebc54843dc8df98fe5af70eb
|
Shell
|
HugoWang3146/spring-demo-gradle-k8s
|
/scripts/start_spring_boot_demo_in_docker.sh
|
UTF-8
| 288
| 2.546875
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
set -eux
LOG_PATH='/var/log/spring-boot-demo'
docker rm -f spring-boot-demo || true
docker run \
-d \
-p 8080:8080 \
--name spring-boot-demo \
--mount type=bind,source=${LOG_PATH},target=${LOG_PATH} \
docker-registry.local:5000/spring-boot-demo
| true
|
d6576eacf942ad130153c76ae35075be8973e494
|
Shell
|
joeytwiddle/jsh
|
/code/shellscript/unixext/mkdirandmv.sh
|
UTF-8
| 79
| 2.671875
| 3
|
[] |
no_license
|
#!/bin/sh
TARGET_FOLDER=`lastarg "$@"`
mkdir -p "$TARGET_FOLDER" &&
mv "$@"
| true
|
48d68abae675994fa96246843b02ce48c420dd9d
|
Shell
|
grohiro/dotfiles
|
/bin/issvn
|
UTF-8
| 427
| 3.609375
| 4
|
[] |
no_license
|
#!/bin/bash
#
# This script returns string 'svn' when you are in a SVN working tree.
# カレントディレクトリがSVNのワーキングコピーの場合に文字列 "svn" を返す.
# shell のプロンプト(PS1)とかで使う.
# example: PS1="\w\$(issvn @)$ "
# ~/path/to/svn@svn$
#
SVN=/usr/bin/svn
if [ $($SVN info > /dev/null 2>&1; echo $?) == 0 ]
then
if [ $# -gt 0 ]
then
echo -n $1
fi
echo "svn"
fi
| true
|
11d6ec467714b74e0460683db00028e535d351f9
|
Shell
|
IanXTs/COMP206
|
/MakeProject.sh
|
UTF-8
| 461
| 2.9375
| 3
|
[] |
no_license
|
#bin/sh
#Ian Tsai MiniAssignment 2 260741766
cd ~
if [ ! -d project ]
then
mkdir project
fi
cd ./project/
if [ ! -d cs206 ]
then
mkdir cs206
fi
cd ./cs206/
if [ -d $1 ]
then echo "This project name has already been used"
exit 1
else
mkdir $1 archive backup docs assets database source
fi
cd ./source
"#!bin/sh
cp 'ls | grep -i "\.[ch]$"' ../backup
echo
"You project directories have been created." > backup.sh
chmod 755 backup.sh
| true
|
d2fd8ba2ffe00d28aeb6a2f7a2c061f53eebde8a
|
Shell
|
Richesee/RDB
|
/TERMUX-TOOLS-RDB.sh
|
UTF-8
| 2,024
| 2.890625
| 3
|
[] |
no_license
|
#!/bin/sh
#Code Warna
clear
r="\033[1;31m" # merah
g="\033[1;32m" # hijau
y="\033[1;33m" # kuning
b="\033[1;34m" # biru
p="\033[1;35m" # ungu
cy="\033[1;36m" # biru muda
w="\033[1;37m" # putih
#Banner1
clear
echo $g"######## ######## ########
## ## ## ## ## ##
## ## ## ## ## ##
######## ## ## ########
## ## ## ## ## ##
## ## ## ## ## ##
## ## ######## ######## "
echo $r
sleep 2
echo "====}Please Waiting{===="
sleep 3
echo "Tools Proses"
sleep 1
echo "DONE"
clear
#Banner2
echo $r"▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ஜ۩۞۩ஜ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬"
echo
echo $g "AUTHOR"$w":"$r"RDB"$w"[King]"
echo $g "GITHUB"$w":"$r"https://github.com/"$w"[Richesee]"
echo $g "TEAM" $w" :"$r"User Termux Beginners" $w"[U T B I]"
echo
echo $r"▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬"
#Title1
echo $y
sleep 3
echo $r
echo "[WARNING]"$b"DIWAJIBKAN INSTALL BAHAN BIAR GK EROR"$p
echo "╔════════════════════╗
[1] INSTALL BAHAN
╚════════════════════╝"
echo $y
echo "╔════════════════════╗
[2] MASUK TOOLS
╚════════════════════╝"
echo $cy
echo "╔════════════════════╗
[3] Keluar (EXIT)
╚════════════════════╝"
#Variabel1
echo $w
read -p "Pilih Mana : " pil
#If/elif/else
#Data1
if [ $pil = "1" ];
then
echo $HOME
cd cdm
sh bahan.sh
#Data2
elif [ $pil = "2" ];
then
echo $HOME
apt update && apt upgrade
pkg install bash -y
pkg install git -y
pkg install curl -y
pkg install figlet -y
cd cdm
sh tls.sh
#Data3
elif [ $pil = "3" ]
then
#warna
echo $b
clear
echo "Thaks You Telah Menggunakan Tools Ini"
sleep 1
exit
fi
| true
|
70288595808cd5fb5d14a4489dd1896c8301e9dc
|
Shell
|
chuanran/terraform_vsphere_provisioner
|
/files/customization.dd.sh.template
|
UTF-8
| 8,651
| 3.4375
| 3
|
[] |
no_license
|
#!/bin/bash
#This script is used to leverage TFD to customise configurations on fci Due Diligence
fci_install_kit_dir="/root/fci-install-kit"
fcdd_install_kit_dir="/root/fcdd-install-kit"
km_hosts_prop_template_file="${fci_install_kit_dir}/helm/install.hosts.properties.template"
custom_nfs_fcdd_file="${fcdd_install_kit_dir}/helm/CustomNFS-fcdd.yaml"
#step 1. For Due Diligence, do the corresponding customization on helm config and properties file
#step 1.1 For Due Diligence, copy generated install.hosts.properties to the corresponding dd folder
km_fcdd_hosts_prop_file="${fcdd_install_kit_dir}/helm/install.hosts.properties"
if [ -f "$km_fcdd_hosts_prop_file" ]; then
if [ ! -s "$km_hosts_prop_template_file" ]; then
echo "Attention!!! km template hosts prop file $km_hosts_prop_template_file failed to be copied to the vm. You may need to manually get it and put it on the vm"
else
cp $km_fcdd_hosts_prop_file "${km_fcdd_hosts_prop_file}.bak"
sed -i '/^[[:space:]]*$/d' $km_hosts_prop_template_file
cp $km_hosts_prop_template_file $km_fcdd_hosts_prop_file
fi
else
echo "This is not km server, or $km_fcdd_hosts_prop_file does NOT exist. skipping fcdd hosts prop file generation"
fi
#step 1.2 on km, for ${fcdd_install_kit_dir}/helm/install.properties, change external.docker.registry.url to the km hostname
km_fcdd_install_prop_file="${fcdd_install_kit_dir}/helm/install.properties"
if [ -s "$km_fcdd_install_prop_file" ]; then
orig_vm_type=$(echo "{vsphere_vm_hostname}" | awk -F "." '{print $1}' | awk -F "-" '{print $5}')
km_hostname=$(echo "{vsphere_vm_hostname}" | sed "s/-$orig_vm_type/-km/")
nfs2_hostname=$(echo "{vsphere_vm_hostname}" | sed "s/-$orig_vm_type/-nfs2/")
grep -Eq "^external.docker.registry.url =" $km_fcdd_install_prop_file
if [ $? -eq 0 ]; then
old_km_hostname=$(grep -E "^external.docker.registry.url =" $km_fcdd_install_prop_file | awk -F "=" '{print $2}' | awk -F ":" '{print $1}' | awk '{print $1}')
sed -i "s/$old_km_hostname/$km_hostname/g" $km_fcdd_install_prop_file
else
echo "external.docker.registry.url = ${km_hostname}:5000" >> $km_fcdd_install_prop_file
fi
grep -Eq "^external.nfsserver =" $km_fcdd_install_prop_file
if [ $? -eq 0 ]; then
old_nfs2_hostname=$(grep -E "^external.nfsserver =" $km_fcdd_install_prop_file | awk -F "=" '{print $2}' | awk '{print $1}')
sed -i "s/$old_nfs2_hostname/$nfs2_hostname/g" $km_fcdd_install_prop_file
else
echo "external.nfsserver = ${nfs2_hostname}" >> $km_fcdd_install_prop_file
fi
grep -qE "^mount_point.1 = --path" $km_fcdd_install_prop_file
if [ $? -eq 0 ]; then
sed -i "/^mount_point.1 = --path/c mount_point.1 = --path /fcidd/fcdd-node-instance" $km_fcdd_install_prop_file
else
echo "mount_point.1 = --path /fcidd/fcdd-node-instance" >> $km_fcdd_install_prop_file
fi
grep -qE "^mount_point.2 = --path" $km_fcdd_install_prop_file
if [ $? -eq 0 ]; then
sed -i "/^mount_point.2 = --path/c mount_point.2 = --path /fcidd/fcdd-ml" $km_fcdd_install_prop_file
else
echo "mount_point.2 = --path /fcidd/fcdd-ml" >> $km_fcdd_install_prop_file
fi
grep -qE "^chart.args =" ${km_fcdd_install_prop_file}
if [ $? -eq 0 ]; then
sed -i '/^chart.args =/c\chart.args = -f fcdd-values.yaml -f CustomNFS-fcdd.yaml --set global.coreReleaseName=fci/' ${km_fcdd_install_prop_file}
else
echo "chart.args = -f fcdd-values.yaml -f CustomNFS-fcdd.yaml --set global.coreReleaseName=fci" >> ${km_fcdd_install_prop_file}
fi
fi
#step 1.3 update datasource configuration in fcdd-values.yaml file
helm_fcdd_values_file="${fcdd_install_kit_dir}/helm/fcdd-values.yaml"
if [ -s "$helm_fcdd_values_file" ]; then
#change DNB_USERNAME, DNB_PASSWORD to the correct value defined in custom.properties file
grep "DNB_USERNAME:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_dnb_user_str=$(grep "DNB_USERNAME:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_dnb_user_str/DNB_USERNAME: '{new_dnb_user}'/g" $helm_fcdd_values_file
fi
grep "DNB_PASSWORD:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_dnb_pwd_str=$(grep "DNB_PASSWORD:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_dnb_pwd_str/DNB_PASSWORD: '{new_dnb_password}'/g" $helm_fcdd_values_file
fi
#change DOWJONES_USERNAME, DOWJONES_PASSWORD to the correct value defined in custom.properties file
grep "DOWJONES_USERNAME:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_dj_user_str=$(grep "DOWJONES_USERNAME:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_dj_user_str/DOWJONES_USERNAME: '{new_dj_user}'/g" $helm_fcdd_values_file
fi
grep "DOWJONES_PASSWORD:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_dj_pwd_str=$(grep "DOWJONES_PASSWORD:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_dj_pwd_str/DOWJONES_PASSWORD: '{new_dj_password}'/g" $helm_fcdd_values_file
fi
#change KYCKR_USERNAME, KYCKR_PASSWORD to the correct value defined in custom.properties file
grep "KYCKR_USERNAME:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_kyckr_user_str=$(grep "KYCKR_USERNAME:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_kyckr_user_str/KYCKR_USERNAME: '{new_kyckr_user}'/g" $helm_fcdd_values_file
fi
grep "KYCKR_PASSWORD:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_kyckr_pwd_str=$(grep "KYCKR_PASSWORD:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_kyckr_pwd_str/KYCKR_PASSWORD: '{new_kyckr_password}'/g" $helm_fcdd_values_file
fi
#change FACTIVA_EID, FACTIVA_NEWS_ENCRYTED_TOKEN_VALUE to the correct value defined in custom.properties file
grep "FACTIVA_EID:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_factiva_eid_str=$(grep "FACTIVA_EID:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_factiva_eid_str/FACTIVA_EID: '{new_factiva_eid}'/g" $helm_fcdd_values_file
fi
grep "FACTIVA_NEWS_ENCRYTED_TOKEN_VALUE:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_factiva_token_str=$(grep "FACTIVA_NEWS_ENCRYTED_TOKEN_VALUE:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_factiva_token_str/FACTIVA_NEWS_ENCRYTED_TOKEN_VALUE: '{new_factiva_token}'/g" $helm_fcdd_values_file
fi
#change BING_NEWS_SUBSCRIPTION_KEY_V7, BING_WEB_SUBSCRIPTION_KEY_V7 to the correct value defined in custom.properties file
grep "BING_NEWS_SUBSCRIPTION_KEY_V7:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_bing_news_key=$(grep "BING_NEWS_SUBSCRIPTION_KEY_V7:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_bing_news_key/BING_NEWS_SUBSCRIPTION_KEY_V7: '{new_bing_news_key}'/g" $helm_fcdd_values_file
fi
grep "BING_WEB_SUBSCRIPTION_KEY_V7:" $helm_fcdd_values_file | grep -qv "[[:space:]]#"
if [ $? -eq 0 ]; then
old_bing_web_key=$(grep "BING_WEB_SUBSCRIPTION_KEY_V7:" $helm_fcdd_values_file | grep -v "[[:space:]]#" | sed -e 's/^[ \t]*//')
sed -i "s/$old_bing_web_key/BING_WEB_SUBSCRIPTION_KEY_V7: '{new_bing_web_key}'/g" $helm_fcdd_values_file
fi
fi
# step 1.4: Ensure the CustomNFS-fcdd.yaml exists with correct configuration
echo "mlDataPvNfsPath: /fcidd/fcdd-ml" > ${custom_nfs_fcdd_file}
echo "wexPvNfsPath: /fcidd/fcdd-wex" >> ${custom_nfs_fcdd_file}
echo "nodejsPvNfsPath: /fcidd/fcdd-node-instance" >> ${custom_nfs_fcdd_file}
echo "mongodbPvNfsPath: /fcidd/fcdd-mongo-data" >> ${custom_nfs_fcdd_file}
echo "libertyPvNfsPath: /fcidd/fcdd-liberty-instance" >> ${custom_nfs_fcdd_file}
#step 1.5 make sure .acceptLicenseInformation.lock and .acceptLicenseAgreement.lock are created to ignore license accepting
if [ ! -f "${fcdd_install_kit_dir}/helm/.acceptLicenseInformation.lock" ]; then
touch ${fcdd_install_kit_dir}/helm/.acceptLicenseInformation.lock
fi
if [ ! -f "${fcdd_install_kit_dir}/helm/.acceptLicenseAgreement.lock" ]; then
touch ${fcdd_install_kit_dir}/helm/.acceptLicenseAgreement.lock
fi
| true
|
1939b479d2f9f6f402160f287a217e6bb15bbd1e
|
Shell
|
amerlyq/airy
|
/%wf/obsolete/ubuntu/gen/nosudo_reboot
|
UTF-8
| 762
| 3.15625
| 3
|
[
"MIT"
] |
permissive
|
#!/bin/bash -e
source ~/.shell/profile
# Reboot w/o sudo: remove all previous entries for user and append to end
# Or manually setting: launch editor of access file with errs checking '$ sudo visudo', and append your's user
# If all that will break sudo command: '$ pkexec bash', and then change file manually
CURR_USER=${CURR_USER:-${SUDO_USER:-${USER:-${USERNAME:-$(whoami)}}}}
SYS_ENTRY="$CURR_USER ALL=(ALL) \
NOPASSWD:/usr/sbin/pm-hibernate,/usr/sbin/pm-suspend,\
/sbin/reboot,/sbin/halt,/sbin/shutdown,/sbin/poweroff"
case "$CURR_PROF" in
laptop) SYS_ENTRY="$SYS_ENTRY,/usr/bin/intel_backlight" ;;
esac
dst=/etc/sudoers
sudo sed -i "/^$CURR_USER ALL=(ALL) NOPASSWD/d" $dst
echo "$SYS_ENTRY" | sudo tee --append $dst
echo "W: $dst <- reboot w/o sudo"
| true
|
043a522ce7166a97b5736ef2ac96ac7c303f5789
|
Shell
|
nvllsvm/dotfiles
|
/scripts/open-term
|
UTF-8
| 227
| 2.984375
| 3
|
[] |
no_license
|
#!/usr/bin/env sh
TARGET="$(basename "$0")"
if [ "$(hostname)" = "$TARGET" ]; then
exec alacritty --title "$TARGET" --command zsh -ic tmux-attach
else
exec alacritty --title "$TARGET" --command zsh -ic "ssh $TARGET"
fi
| true
|
46cdb7fe3977ea638ddace8d04cc55ceca9d94f8
|
Shell
|
Harrison21/progblack_lectures
|
/build.sh
|
UTF-8
| 296
| 2.734375
| 3
|
[
"CC0-1.0"
] |
permissive
|
#!/bin/bash
sed '/^---/ d' PITCHME.md | sed '/^@/ d' | sed '/^:::/ d' | sed 's/{.*}//' > README.md
PATHEND=$(pwd | rev | cut -d'/' -f-2 | rev)
pandoc -V theme=simple -t revealjs -s PITCHME.md -o PITCHME.html
git add .
git commit -m "Working on presentation $PATHEND"
git push -u origin main
| true
|
5892592597f849317fbea5bcbe44b0e34e017d02
|
Shell
|
salmanspice/k8s-ha-postgres
|
/chart/files/haproxy-scripts/manage-master.sh
|
UTF-8
| 697
| 3.3125
| 3
|
[] |
no_license
|
#!/bin/sh -e
pod_name=$(cat $1 | cut -s -d ',' -f 1)
addr=$(cat $1 | cut -s -d ',' -f 2)
echo "master backend state before:"
echo "show servers state master" | nc localhost 9998
echo "Disabling server master0 and shutting down the sessions..."
echo "set server master/master0 state maint" | nc localhost 9998
echo "shutdown sessions server master/master0" | nc localhost 9998
if [ -n "$pod_name" ]; then
echo "Enabling server master0 for pod $pod_name with ip $addr..."
echo "set server master/master0 addr $addr" | nc localhost 9998
echo "set server master/master0 state ready" | nc localhost 9998
fi
echo "master backend state after:"
echo "show servers state master" | nc localhost 9998
| true
|
e7d69bc5ec585927465e5542dde82de128875474
|
Shell
|
freebsd/freebsd-ports
|
/audio/logitechmediaserver/files/pkg-install.in
|
UTF-8
| 1,292
| 3.265625
| 3
|
[
"BSD-2-Clause"
] |
permissive
|
#!/bin/sh
name=%%PORTNAME%%
comment="Slim Devices SlimServer/SqueezeCenter pseudo-user"
slimdir="%%PREFIX%%/%%SLIMDIR%%"
statedir=%%SLIMDBDIR%%
cachedir=${statedir}/cache
prefsdir=${statedir}/prefs
playlistdir=${statedir}/playlists
oldprefsdir=/var/db/squeezecenter/prefs
logdir=/var/log/${name}
conffile=${prefsdir}/server.prefs
pidfile=/var/run/${name}/${name}.pid
newsyslogfile=/etc/newsyslog.conf
logcomment="# added by audio/${name} port"
serverlogfile=/var/log/${name}/server.log
serverlogline="${serverlogfile} ${u}:${g} 644 3 100 * J ${pidfile}"
case $2 in
POST-INSTALL)
if egrep -q "^${serverlogfile}\>" ${newsyslogfile}; then
echo "Using existing ${newsyslogfile} entry."
else
echo "Adding ${name} log entry to ${newsyslogfile}."
echo "$logcomment" >> ${newsyslogfile}
echo "$serverlogline" >> ${newsyslogfile}
fi
for file in %%CONFFILES%%; do
path="${slimdir}/${file}"
if [ ! -e ${path} ]; then
cp ${path}.sample ${path}
chmod 644 ${path}
fi
done
if [ ! -f ${serverlogfile} ]; then
touch ${serverlogfile}
chown -H ${u}:${g} ${serverlogfile}
fi
if [ ! -e ${conffile} ]; then
if [ -e ${oldprefsdir}/server.prefs ]; then
mkdir -p ${statedir}
cp -r ${oldprefsdir}* ${statedir}
chown -RH ${u}:${g} ${prefsdir}
fi
fi
;;
esac
| true
|
3cef9a246051f0570c28c6c13ad8761d40af8e25
|
Shell
|
nasrulain/assignment-guessinggame
|
/guessinggame.sh
|
UTF-8
| 963
| 4.03125
| 4
|
[] |
no_license
|
#!/usr/bin/env bash
# File: guessinggame.sh
# Peer graded assignment - The Unix Workbench by Coursera/John's Hopkins University
# Counting no. of files in the directory
filecount=$(ls -lA | wc -l)
num="^[0-9]+$"
# Function with IF condition to check guessed value
function output {
if [[ $guesscount -lt $filecount ]]
then
echo "Too low!"
elif [[ $guesscount -gt $filecount ]]
then
echo "Too high!"
else
echo ""
echo "Well done! Your guess is correct!"
exit 0
fi
}
# While loop
while [[ 0 ]]
do
echo "Guess how many files are in the current directory? "
read -p "Enter your Guess: " guesscount
if [[ $guesscount =~ $num ]]
then
output
elif ! [[ $guesscount =~ $num ]]
then
echo "You have entered non-integer value. Enter only integer value."
else
echo "You have entered non-integer value. Enter only integer value."
fi
echo ""
done
| true
|
5299d6d2ba069347b182c5bacb6c6b9b579abb9d
|
Shell
|
nicolasbock/ebuildtester
|
/ebuildtester.bash-completion
|
UTF-8
| 1,570
| 2.828125
| 3
|
[
"BSD-3-Clause"
] |
permissive
|
# vim: syntax=sh:tabstop=4:shiftwidth=4:expandtab
_ebuildtester() {
local cur prev opts prefix
COMPREPLY=()
cur="${COMP_WORDS[COMP_CWORD]}"
prev="${COMP_WORDS[COMP_CWORD-1]}"
opts=(
--help
--version
--atom
--binhost
--live-ebuild
--manual
--portage-dir
--overlay-dir
--update
--install-basic-packages
--threads
--use
--global-use
--unmask
--unstable
--gcc-version
--python-single-target
--python-targets
--rm
--storage-opt
--with-X
--with-vnc
--profile
--features
--docker-image
--docker-command
--pull
--show-options
--ccache
--batch
--debug
)
case "${prev}" in
--portage-dir|--overlay-dir|--ccache)
COMPREPLY=( $(compgen -o filenames -o dirnames -o plusdirs ${cur}) )
compopt -o nospace -o filenames -o dirnames -o plusdirs
;;
--features)
if [[ ${cur} =~ ^- ]]; then
prefix=("-P" "-")
else
prefix=()
fi
echo
COMPREPLY=( $(compgen ${prefix[@]} -W "ccache sandbox userfetch" -- ${cur#-}) )
;;
*)
if [[ ${cur} =~ ^-.* || ${COMP_CWORD} -eq 1 ]] ; then
COMPREPLY=( $(compgen -W "${opts[*]}" -- ${cur}) )
else
echo "I should not be here"
exit 1
fi
;;
esac
}
complete -F _ebuildtester ebuildtester
| true
|
185481346736b962dfbae7334abcfe25f414cc3f
|
Shell
|
lecorref/config_personnal
|
/aliases
|
UTF-8
| 806
| 3.15625
| 3
|
[] |
no_license
|
#!/bin/bash
# Definition des alias raccourcis
alias cdt='cd ~/test/'
# Definition des alias de compilation
alias gccf="gcc -Wall -Wextra -Werror"
alias g++f="g++ -Wall -Wextra -Werror"
# Definition des alias
alias clean="find . -name '*~' -execdir rm {} \;"
alias modsh="vim $C_PATH_TO_PERSONNAL_CONFIG/zshrc"
alias purgevim="rf -f ~/.vim/tmp/*.swp ~/.vim/tmp/.*.swp"
alias rl="source ~/.zshrc"
# School only aliases
if [[ `uname` = "Darwin" ]]; then
# misc
alias auteur="echo '$USER' > auteur"
alias libft="cp -r $LIB .; rm -rf libft/.git"
alias op=ocamlopt
# cd alias
alias cdc='cd ~/Rendu'
alias cdl='cd $LIB'
alias goinfre='cd /nfs/sgoinfre/goinfre/'
# compil alias
alias gccl="gcc -I $LIB/includes -L $LIB -lft"
alias gcclf="gcc -Wall -Wextra -Werror -I $LIB/includes -L $LIB -lft"
fi
| true
|
dd832d1622764c234a1d4caa40a824a0786497dc
|
Shell
|
fdinardo/arch_scripts
|
/custom/completions/eng.completion.bash
|
UTF-8
| 317
| 3.375
| 3
|
[] |
no_license
|
_eng()
{
local cur=${COMP_WORDS[COMP_CWORD]}
local list_path=$(echo $PATH | tr ":" "\n")
case "$cur" in
*)
for myPath in $list_path
do
list_files="$list_files $(ls $myPath -1 2> /dev/null)"
done
COMPREPLY=( $(compgen -W "$list_files" -- $cur) )
return 0
;;
esac
}
complete -F _eng eng
| true
|
fe5bed4148c0db42bf97bdd0e9f7027ede4fd607
|
Shell
|
Sakshi2106/Threading_Library
|
/many-one/test.sh
|
UTF-8
| 695
| 2.625
| 3
|
[] |
no_license
|
#!/bin/bash
echo ""
echo ""
echo -e "I)--------------------------------------------RUNNING MANY-ONE TESTING-------------------------------------------------"
echo ""
echo ""
echo -e "1)----------------------------------RUNNING APITEST TEST-----------------------------"
echo "./exe/apitest"
./exe/apitest
echo ""
echo ""
echo -e "2)----------------------------------RUNNING SPINLOCK TEST----------------------------"
echo "./exe/spinlocktest"
echo "Wait for a minute"
./exe/spinlock
echo ""
echo ""
echo -e "3)-----------------------------------RUNNING MATRIX MULTIPLICATION TEST-----------------------------"
echo "./exe/matrix"
echo "Reads matrix from matrix.txt"
./exe/matrix
echo ""
echo ""
| true
|
a55cc66188efa43678bc76068ba9252438ad588f
|
Shell
|
mswishe7/Scripts
|
/sshcommand
|
UTF-8
| 411
| 3.375
| 3
|
[] |
no_license
|
#!/bin/bash
#Usage: ./sshcommand <user> <host> <command>
BB=/bin/busybox
if [ "$#" -lt 3 ];then
echo "Usage: ./sshcommand <user> <host> <command>"
exit 1
fi
if [ -z "$SSHPASS" ];then
echo "SSHPASS Environment variable not set. Enter Password:"
read -s password
export SSHPASS=${password}
fi
sshpass -e scp ${BB} $1@$2:
sshpass -e ssh $1@$2 ./busybox $3
sshpass -e ssh $1@$2 ./busybox rm -f ./busybox
| true
|
b722836631ce3d638744114ecb0576667c1a0601
|
Shell
|
wolxXx/lxclister
|
/grab.sh
|
UTF-8
| 3,339
| 3.875
| 4
|
[] |
no_license
|
#!/bin/bash
function startUp () {
clear;
echo "wolxXxShellTools: grab containers and their meta.";
echo "v.0.2 | devops@wolxXx.de | git.wolxxx.de | https://github.com/wolxXx"
echo "licensed under MIT general public open source license. "
echo "love it, share it, extend it. improve the world!"
echo "________________________________________________";
echo "";
}
function checkRoot () {
ME=$(whoami);
if [ ! "root" == $ME ]; then
echo "you must be root!";
echo "you are $ME. you rock, sure, but root rocks more ;)";
echo "";
exit 1;
fi;
}
function displayHelp () {
echo "";
echo "HELP:";
echo "no params required!";
echo "you must be root to run this.";
echo "this script grabs all containers in /var/lib/lxc";
echo "and grabs their configuration";
echo "and writes it into containers.js file";
echo "for having it in list.html.";
echo "";
echo "it does NOT update existing section objects.";
echo "maybe later. if needed.";
}
startUp;
if [ "$1" == "--help" ]; then
displayHelp;
exit 0;
fi;
checkRoot;
here=$(dirname $(readlink -f $0));
cd $here;
rm containers.js;
echo "//containers in /var/lib/lxc" > containers.js;
echo "" >> containers.js;
echo "var containers = [];" >> containers.js;
chmod 777 containers.js;
CONTAINERS=$(for i in /var/lib/lxc/*; do test -e /var/lib/lxc/$i/config || basename $i; done)
for CONTAINER in $CONTAINERS
do
echo "";
echo "checking now container: $CONTAINER";
found=$(cat containers.js | grep "name: '$CONTAINER'");
if [ ! '' == "$found" ]; then
echo "found in containers.js";
continue;
fi;
echo "" >> containers.js;
echo "//container: $CONTAINER" >> containers.js;
echo "containers.push({" >> containers.js;
echo " name: '$CONTAINER'," >> containers.js;
ip=$(cat /var/lib/lxc/$CONTAINER/config | grep "ipv4");
if [ ! '' == "$ip" ]; then
ip=$(echo $ip | cut -d"=" -f2 | cut -d"/" -f1);
echo "found configured ip: $ip";
echo " ip: '$ip'," >> containers.js;
fi;
mac=$(cat /var/lib/lxc/$CONTAINER/config | grep "hwaddr");
if [ ! '' == "$mac" ]; then
mac=$(echo $mac | cut -d"=" -f2);
echo "found configured mac: $mac";
echo " mac: '$mac'," >> containers.js;
fi;
arch=$(cat /var/lib/lxc/$CONTAINER/config | grep "lxc.arch");
if [ ! '' == "$arch" ]; then
arch=$(echo $arch | cut -d"=" -f2);
echo "found configured arch: $arch";
echo " arch: '$arch'," >> containers.js;
fi;
echo "});" >> containers.js;
done
echo "" >> containers.js;
echo "var macs = [];" >> containers.js;
echo "containers.forEach(function (container) {" >> containers.js;
echo " if (-1 === macs.indexOf(container.mac)) {" >> containers.js;
echo "" >> containers.js;
echo " macs.push(container.mac);" >> containers.js;
echo "" >> containers.js;
echo " console.log('added mac ' + container.mac);" >> containers.js;
echo " return;" >> containers.js;
echo "" >> containers.js;
echo " }" >> containers.js;
echo "" >> containers.js;
echo " alert('duplicate mac: ' + container.mac + ' in ' + container.name);" >> containers.js;
echo "});" >> containers.js;
exit 0;
| true
|
2bf5fcc124c4e96e2aa84b9bf458f98245052dd4
|
Shell
|
ArielMn22/C
|
/programinc.sh
|
UTF-8
| 1,207
| 3.625
| 4
|
[] |
no_license
|
#!/bin/bash
PROGRAMS="vim git gcc make"
REPOSITORY="http://github.com/ArielMn22/C"
SN=0 # Sim ou Não
returno=0 # Checa o return do comando
clonar(){
echo "Clonando repositório..."
git clone $REPOSITORY &>/dev/null
var=$?
if [[ $var == 0 ]]; then
echo "Repositório clonado com sucesso..."
else
if [[ $var == 128 ]]; then
echo "Repositório já clonado..."
else
echo "Repositório não foi clonado..."
fi
fi
}
clear; echo "Atualizando..."
apt update &>/dev/null || echo "Algo deu errado com o update..."
for x in $PROGRAMS; do
echo "Instalando $x..."
apt install $x -y &>/dev/null || echo "Algo deu errado com $x..."
done
read -p "Deseja clonar o repositório \"$REPOSITORY\"? >" SN
SN=$(echo $SN | tr A-Z a-z)
case $SN in
"sim"|"s"|"ss"|"yes"|"si")
clonar
;;
"nao"|"não"|"no")
echo "Repositório não clonado..."
;;
*)
echo "Repositório não clonado"
;;
esac
echo '
set nocompatible
set nu
syntax on
set encoding=utf-8
set showcmd
filetype plugin indent on
set tabstop=2 shiftwidth=2
set expandtab
set backspace=indent,eol,start
set hlsearch
set incsearch
set ignorecase
set smartcase' > ~/.vimrc
| true
|
05b3b8db28bcb97f2d4d2777c6fe85e038baee9e
|
Shell
|
chnoeli/Arma-3-Mod-Download-Script
|
/linux.sh
|
UTF-8
| 2,700
| 3.78125
| 4
|
[
"MIT"
] |
permissive
|
#!/bin/bash
#*******************************************************************************
gameId="107410"
#The 'gameId' is the id of the game for which you want to download mods from the Steam workshop.
#
#For example:
#gameId="107410" # Arma 3
steamcmdLocation="./steamcmd"
#The 'steamcmdLocation' is the path to the folder where the stemacmd.sh file is located.
#The path can be either relative to the script or absolute.
#
#For example:
#steamcmdLocation="./steamcmd"
#steamcmdLocation="/home/steam/steamcmd"
modsDestFolder="/home/arma3server/serverfiles/mods"
#The 'modsDestFolder' is the path to the folder where the downloaded mods will be
#linked after downloading from the workshop. This is necessary because during download
#from the workshop the folders will be named with the id and stored in the workshop folder of Steam.
#By using a hard link to the 'modsDestFolder' the mods will be renamed (no additional disk space will be used).
#The path can be either relative to the script or absolute.
#
#For example:
#modsDestFolder="./arma3server/serverfiles/mods"
#modsDestFolder="/home/arma3server/serverfiles/mods"
#username=""
#password=""
#If you want to use the script in a non interactive way you can hardcode the Username and Password here and comment out the 'read' lines.
downloadPath="./mods"
#*******************************************************************************
workshopLoction=$steamcmdLocation/$downloadPath/steamapps/workshop/content/$gameId
arrPos=0
currI=0
#arma additional
#Read CSV file
IFS=","
while read f1 f2
do
arrModsId+=($f1)
arrModsName+=($f2)
let arrPos=$arrPos+1
done < modList.csv
read -p 'Steam username: ' username
read -sp 'password: ' password
#Steam download
for index in ${!arrModsId[*]}
do
echo
echo "*******************************************************************************"
echo "Start download of:" ${arrModsName[$index]}
echo "*******************************************************************************"
echo
$steamcmdLocation/"steamcmd.sh" +login $username $password +force_install_dir $downloadPath +workshop_download_item $gameId ${arrModsId[$index]} validate +quit
cp -al $workshopLoction/${arrModsId[$index]} $modsDestFolder/${arrModsName[$index]}
echo
echo "*******************************************************************************"
echo "Finished download of:" ${arrModsName[$index]}
echo
echo "$currI of" ${#arrModsId[*]} "done!"
echo "*******************************************************************************"
let currI=$index+1
done
| true
|
53b754406bc13404e2644f34673b351c8d64e131
|
Shell
|
closescreen/clhousesample
|
/to_history_ref_hours_wash.sh
|
UTF-8
| 1,909
| 3.140625
| 3
|
[] |
no_license
|
#!/usr/bin/env bash
#> Сохраняет из history_ref_from_history_v04.py в clickhouse history_ref_DAY
#> Один процесс на день. День либо залился, либо нет.
#> Если нет или частично - таблица удаляется и наливается заново.
#(
set -u
set +x
set -o pipefail
cd `dirname $0`
export PERL5LIB=${PERL5LIB:-""}:/usr/local/rle/var/share3/TIKETS/bike
# single process! --wait must be enabled for return status after washing
serv=`hostname`
if [[ ${1:-""} == "start" ]];then shift && nice fork -pf="$0.$serv.pids" --single "$0 $@" --wait --status # enable -wait
elif [[ ${1:-""} == "stop" ]];then shift && fork -pf="$0.$serv.pids" -kila
else
# --------- begin of script body ----
# Параметры:
day=${1?DAY!}
deb=${2:-""} # можно указать "0" (нет debug) / "1" (info) / "2" или "deb" (максимум отладки)
[[ -z "$deb" ]] && deb=0; # - debug off
[[ "$deb" != "0" ]] && [[ "$deb" != "1" ]] && deb=2 # full debug level
washdeb="" # указание debug для washing
[[ "$deb" == "2" ]] && washdeb="-d" && set -x
my_server=`hostname` # dm22
db="rnd600"
main_table="history_ref"
# каждый сервер хранит свои usergroups
ug_from="" && ug_to=""
[[ "$my_server" == "dm22" ]] && ug_from=1 && ug_to=128
[[ "$my_server" == "dm23" ]] && ug_from=129 && ug_to=256
[[ -z "$ug_from" ]] && echo "ug_from!">&2 && exit 2
d="$day"
#day_table="${main_table}_${d//-/_}" # like: history_ref_2015_05_16
hours -t=$day -n=24 | files "../../reg_history_ref/%F/%H_${my_server}.txt" |
washing $washdeb -r='[[ -s %f ]]' -comm="результ. файлы проверяются на непусто" \
-cmd=" ./to_history_ref_hour.sh \"%f\" \"$ug_from\" \"$ug_to\" " || exit 1 # ВЫХОД при ошибке
# --------- end of script bidy ------
fi
#)>>"$0.log" 2>&1
| true
|
8f64d83e44102805bd8e508a94478766d49d7bff
|
Shell
|
m301/ModularScripts
|
/custom/docker.sh
|
UTF-8
| 766
| 2.953125
| 3
|
[] |
no_license
|
#!/usr/bin/env sh
choices=( apache-start remove-none digi-start digi-stop clear-unused clean-unused)
case $1 in
"${choices[0]}")
# docker network create --subnet=172.18.0.0/16 net1
docker run --net net1 --ip 172.18.0.10 -v ~/Playground/docker-apache/apache2/sites-available/:/etc/apache2/sites-available/ -v /mnt/micro/:/mnt/yocto/ apache
;;
"${choices[1]}")
docker rmi $(docker images | grep "^<none>" | awk "{print $3}")
;;
"${choices[2]}")
docker run -d -p 5672:5672 -p 15672:15672 --name rabbitmq rabbitmq:management
;;
"${choices[4]}")
docker ps -aq | xargs docker rm
;;
"${choices[5]}")
docker ps -aq | xargs docker rm
;;
"shortlist")
echo "$(IFS=' ' ; echo "${choices[*]}")"
;;
*)
echo "[$(IFS=, ; echo "${choices[*]}")][$1]==-1 is true! Dude ? "
esac
| true
|
eab34117fabb99665478ce3c81f009f8eb0d0091
|
Shell
|
wangdabin/hdqsEJB
|
/bin/.svn/text-base/alterColumn.sh.svn-base
|
UTF-8
| 648
| 2.59375
| 3
|
[] |
no_license
|
#!/usr/bin/ksh
. ~/.bash_profile
export NLS_LANG=AMERICAN_AMERICA.UTF8
flog=$BASE_HOME/alertColumn.log
ouid="$SOP_USER/$SOP_PASSWD"
####################
CMD_SQLPLUS=$ORACLE_HOME/bin/sqlplus
####################
if [ ! -d $BASE_HOME ]; then
mkdir -p $BASE_HOME
fi
echo "*********************************************"
echo "*************init DB start *************"
echo "*********************************************"
$CMD_SQLPLUS -s $ouid 1>$flog 2>&1 <<!!!
set autocommit on
alter table PSQBM modify BEIYZF VARCHAR2(22);
commit;
!!!
echo "**************modify table PSQBM filed BEIYZF length compeleted****************************"
| true
|
1db47d526cc0e2c6f111cdb1139bbab19632d541
|
Shell
|
Mobasherah12/open-event-scraper
|
/build.sh
|
UTF-8
| 1,170
| 2.96875
| 3
|
[
"MIT"
] |
permissive
|
# thanks to https://gist.github.com/domenic/ec8b0fc8ab45f39403dd
#!/bin/sh
set -e
git config --global user.name "Travis CI"
git config --global user.email "noreply+travis@fossasia.org"
python scraper.py
python event.py
# don't continue if no changes
if git diff-index --quiet HEAD; then
exit 0
fi
git pull
git commit -m '[Auto] updated json files [ci skip]' out/*.json || echo "no changes"
git push "https://${GH_TOKEN}@github.com/OpenTechSummit/open-event-scraper" HEAD:master
git clone --depth=1 "https://${GH_TOKEN}@github.com/OpenTechSummit/2016.opentechsummit.net.git" ots-repo
node schedule/generator > ots-repo/programm/index.html
cd ots-repo
rm -rf programm
mkdir programm
cd programm
mkdir css
mkdir js
mkdir json
mkdir speakers
mkdir audio
node ../../schedule/generator.js>index.html
rsync -r ../../out/*.json json
rsync -r ../../css/schedule.css css
rsync -r ../../css/bootstrap.min.css css
rm -rf speakers
rsync -r ../../speakers/* speakers
rm -rf audio
rsync -r ../../audio/* audio
rsync -r ../../img/* img
git add index.html speakers/*.jpg json/*.json css/ audio/ img/
git commit -m '[Auto] updated schedule' || echo "no changes"
git push origin gh-pages
exit 0
| true
|
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