code stringlengths 1 1.96M | language stringclasses 1
value |
|---|---|
#!/bin/bash
defaultPrimer="ATTAGATACCC[ACTG]GGTAG" #default primer
nodes=8 #no. of cluster nodes to use
sfffile=$1; #first argument name of sff file (necessary)
primer=${2:-$defaultPrimer} #second argument primer as a Perl regular expression
stub=${sfffile%.sff};
echo $stub $sfffile $pr... | Shell |
#!/bin/bash
defaultPrimer="ATTAGATACCC[ACTG]GGTAG" #default primer
nodes=8 #no. of cluster nodes to use
sfffile=$1; #first argument name of sff file (necessary)
primer=${2:-$defaultPrimer} #second argument primer as a Perl regular expression
stub=${sfffile%.sff};
echo $stub $sfffile $pr... | Shell |
export nodes=4
export otu_dist=0.03
export primer=primer.fasta
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Tit... | Shell |
export bc=keys.csv
export nodes=4
export otu_dist=0.03
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_E123.dat
e... | Shell |
#!/bin/bash
export nodes=8
export otu_dist=0.03
export primer=primer.fasta
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FI... | Shell |
export nodes=2
export otu_dist=0.03
export primer=primer.fasta
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
if test $# -le 0; then
echo "Usage: RunFasta.sh filename... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MedianD.pl 3 $burn ${inputdir}/${stub}_LN_*.sample
MedianD.pl 3 $burn ${inputdir}/${stub}_IG_*.sample
MedianD.pl 4 $bu... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./Clean360.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
export nodes=8
export otu_dist=0.03
export primer=primer.fasta
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FI... | Shell |
#!/bin/bash
export nodes=8
export otu_dist=0.03
export primer=primer.fasta
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_F... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MedianD.pl 3 $burn ${inputdir}/${stub}_LN_*.sample
MedianD.pl 3 $burn ${inputdir}/${stub}_IG_*.sample
MedianD.pl 4 $bu... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MeanSeries.pl 4 $burn ${inputdir}/${stub}_LN_*.sample
MeanSeries.pl 4 $burn ${inputdir}/${stub}_IG_*.sample
MeanSeries... | Shell |
#!/bin/bash
stub=${1//.fasta}
stub=${stub//.fa}
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
nodes=4
export mpiextra="--mca btl tcp,self"
sed -i -e 's/\.00//' $1
FastaUnique -in $1 > $stub.U.fa
mpirun $mpiextra -np $nodes NDist -i -in $stub.U.fa > ${stub}.U.ndi... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./Clean360.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
inputdir=$1
burn=$2
effort=$3
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
cat ${inputdir}/${stub}_LN_*.sample > ${inputdir}/${stub}_LN.catsample
cat ${inputdir}/${stub}_IG_*.sample >... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./CleanMinMax.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
export nodes=8
export otu_dist=0.03
export primer=primer.fasta
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_F... | Shell |
export nodes=4
export otu_dist=0.03
export primer=primer.fasta
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_E12... | Shell |
#!/bin/bash
stub=${1//.fasta}
stub=${stub//.fa}
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
nodes=4
export mpiextra="--mca btl tcp,self"
sed -i -e 's/\.00//' $1
FastaUnique -in $1 > $stub.U.fa
mpirun $mpiextra -np $nodes NDist -i -in $stub.U.fa > ${stub}.U.ndi... | Shell |
export bc=keys.csv
export nodes=4
export otu_dist=0.03
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Titanium.d... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./CleanMinMax.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
inputdir=$1
burn=$2
effort=$3
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
cat ${inputdir}/${stub}_LN_*.sample > ${inputdir}/${stub}_LN.catsample
cat ${inputdir}/${stub}_IG_*.sample >... | Shell |
export bc=keys.csv
export nodes=4
export otu_dist=0.03
#Fixes warning message with uDAPL error message appearing:
export mpiextra="--mca btl tcp,self"
export CLASSPATH=$AMPLICON_NOISE_HOME/lib/ampliconflow.jar:$AMPLICON_NOISE_HOME/lib/core-1.8.1.jar
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_E123.dat
e... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MeanSeries.pl 4 $burn ${inputdir}/${stub}_LN_*.sample
MeanSeries.pl 4 $burn ${inputdir}/${stub}_IG_*.sample
MeanSeries... | Shell |
#!/bin/bash
defaultBarCode="ACACACGTCG" #default primer
fastafile=$1;
barcode=${2:-$defaultBarCode}
#second argument primer as a Perl regular expression
stub=${fastafile%.fa};
parseFile=${stub}_P.fa
echo $stub $fastafile $barcode
sed "s/^${barcode}//" $fastafile > $parseFile
Perseus -sin $parseFile > ${stub}_P.... | Shell |
#!/bin/bash
defaultBarCode="ACACACGTCG" #default primer
fastafile=$1;
barcode=${2:-$defaultBarCode}
#second argument primer as a Perl regular expression
stub=${fastafile%.fa};
parseFile=${stub}_P.fa
echo $stub $fastafile $barcode
sed "s/^${barcode}//" $fastafile > $parseFile
Perseus -sin $parseFile > ${stub}_P.... | Shell |
#!/bin/bash
nodes=4 #no. of cluster nodes to use
file=$1; #first argument name of dat file
defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
primer=${2:-$defaultPrimer}
mpirun $mpiextra -np $nodes PyroNoiseM -din ${stub}.dat -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01... | Shell |
#!/bin/bash
nodes=4 #no. of cluster nodes to use
file=$1; #first argument name of dat file
defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
primer=${2:-$defaultPrimer}
mpirun $mpiextra -np $nodes PyroNoiseM -din ${stub}.dat -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01... | Shell |
#!/bin/bash
export PYRO_LOOKUP_FILE=../Data/LookUp_Titanium.dat;
defaultPrimer="AGTGCGTAGTG[ACTG]CAGC[AC]GCCGCGGTAA" #default primer
nodes=2 #no. of cluster nodes to use
sfffile=$1; #first argument name of sff file (necessary)
primer=${2:-$defaultPrimer} #second argument primer as a Perl... | Shell |
#!/bin/bash
export PYRO_LOOKUP_FILE=../Data/LookUp_Titanium.dat;
defaultPrimer="AGTGCGTAGTG[ACTG]CAGC[AC]GCCGCGGTAA" #default primer
nodes=2 #no. of cluster nodes to use
sfffile=$1; #first argument name of sff file (necessary)
primer=${2:-$defaultPrimer} #second argument primer as a Perl... | Shell |
#!/bin/bash
#barcode file
bc=keys.csv
nodes=32
snodes=1
min_size=50
max_size=50000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_E123.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded parameter... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MedianD.pl 3 $burn ${inputdir}/${stub}_LN_*.sample
MedianD.pl 3 $burn ${inputdir}/${stub}_IG_*.sample
MedianD.pl 4 $bu... | Shell |
#!/bin/bash
#Variables needed for mpirun and PyroNoise
#(change these settings when installing webapp on new system)
export MPI_HOME=/usr/lib64/openmpi/1.4-gcc
#Max no. of unique sequences per sample after PyroNoise
#(Prevents very long running times caused by chimeras and other artefacts)
SEQ_LIMIT=5000
#number of... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./Clean360.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
# barcode file
bc=keys.csv
nodes=32
snodes=1
min_size=50
max_size=50000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Titanium.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded para... | Shell |
#!/bin/bash
inputdir=$1
burn=$2
printf "Sample, Log-normal, Invese Gaussian, Sichel\n";
for file in $inputdir/*_LN_0.sample
do
stub=${file%_LN_0.sample};
stub=${stub#$inputdir/}
printf "$stub,"
MedianD.pl 3 $burn ${inputdir}/${stub}_LN_*.sample
MedianD.pl 3 $burn ${inputdir}/${stub}_IG_*.sample
MedianD.pl 4 $bu... | Shell |
#!/bin/bash
#barcode file
bc=keys.csv
nodes=32
snodes=1
min_size=50
max_size=50000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_E123.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded parameter... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./Clean360.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
#barcode file
bc=keys.csv
nodes=2
snodes=1
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Titanium.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded paramet... | Shell |
#!/bin/bash
#Variables needed for mpirun and PyroNoise
#(change these settings when installing webapp on new system)
export MPI_HOME=/usr/lib64/openmpi/1.4-gcc
#Max no. of unique sequences per sample after PyroNoise
#(Prevents very long running times caused by chimeras and other artefacts)
SEQ_LIMIT=5000
#number of... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./CleanMinMax.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
# barcode file
bc=keys.csv
nodes=32
snodes=1
min_size=50
max_size=50000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Titanium.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded para... | Shell |
#!/bin/bash
for file in *.raw
do
stub=${file%.raw}
./CleanMinMax.pl "TGCTGCCTCCCGTAGGAGT" $stub < $file
echo "$stub $i";
done
| Shell |
#!/bin/bash
#barcode file
bc=keys.csv
nodes=2
snodes=1
min_size=50
max_size=2000
#Fixes warning message with uDAPL error message appearing:
mpiextra="--mca btl tcp,self"
export PYRO_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/LookUp_Titanium.dat
export SEQ_LOOKUP_FILE=$AMPLICON_NOISE_HOME/Data/Tran.dat
#hardcoded paramet... | Shell |
#!/bin/bash
defaultBarCode="ACACACGTCG" #default primer
fastafile=$1;
barcode=${2:-$defaultBarCode}
#second argument primer as a Perl regular expression
stub=${fastafile%.fa};
parseFile=${stub}_P.fa
echo $stub $fastafile $barcode
sed "s/^${barcode}//" $fastafile > $parseFile
Perseus -sin $parseFile > ${stub}_P.... | Shell |
#!/bin/bash
defaultBarCode="ACACACGTCG" #default primer
fastafile=$1;
barcode=${2:-$defaultBarCode}
#second argument primer as a Perl regular expression
stub=${fastafile%.fa};
parseFile=${stub}_P.fa
echo $stub $fastafile $barcode
sed "s/^${barcode}//" $fastafile > $parseFile
Perseus -sin $parseFile > ${stub}_P.... | Shell |
#!/bin/bash
nodes=4 #no. of cluster nodes to use
file=$1; #first argument name of dat file
defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
primer=${2:-$defaultPrimer}
echo $file
stub=${file%.dat}
echo "Calculating .fdist file"
mpirun $mpiextra -np $nodes PyroDist -in $file -out ${stub} > ${stub... | Shell |
#!/bin/bash
nodes=4 #no. of cluster nodes to use
file=$1; #first argument name of dat file
defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
primer=${2:-$defaultPrimer}
echo $file
stub=${file%.dat}
echo "Calculating .fdist file"
mpirun $mpiextra -np $nodes PyroDist -in $file -out ${stub} > ${stub... | Shell |
#!/bin/sh
REV=`hg log -l 1 | grep changeset | cut -d: -f 2 | tr -d ' '`
echo $(($REV+1))
| Shell |
#!/bin/bash
SCRIPT_PATH=$0
GP_HOME=`dirname "$SCRIPT_PATH"`
GP_LOG_DIR="$HOME/.ganttproject.d"
# Check if log dir is present (or create it)
if [ ! -d $GP_LOG_DIR ]; then
if [ -e $GP_LOG_DIR ]; then
echo "file $GP_LOG_DIR exists and is not a directory" >&2
exit 1
fi
if ! mkdir $GP_LOG_DIR ; then
ec... | Shell |
#!/bin/sh
set -e
if [ -e /usr/bin/ganttproject ]; then rm -f /usr/bin/ganttproject; fi
if [ -x "$(which update-mime >/dev/null 2>&1)" ]; then update-mime; fi
if [ -x "$(which update-menus 2>/dev/null)" ]; then update-menus; fi
| Shell |
#!/bin/sh
set -e
if [ "$1" = "configure" ]; then
if [ -e /usr/bin/ganttproject ]; then rm -f /usr/bin/ganttproject; fi
ln -s /usr/share/ganttproject/ganttproject /usr/bin/ganttproject
if [ -x "$(which update-menus 2>/dev/null)" ]; then update-menus; fi
if [ -x "$(which update-mime 2>/dev/null)" ]; then update... | Shell |
#!/bin/bash
cat $1 | sed s/^\\\([0-9_\\.a-zA-Z]\\+\\\)\\s\*=\\s\*/\\1\ =\ / | sed s/\\\\u\\\([0-9a-f]\\{4\\}\\\)/\\\\u\\U\\1\\E/g > $2
| Shell |
#! /bin/bash
# Location where to install GanttProject
INSTALL_PATH=/usr/local/share/ganttproject/
# Location of executable of GanttProject
GP_EXECUTABLE=/usr/local/bin/ganttproject
# Assuming that writing at INSTALL_PATH and GP_EXECUTABLE needs root rights:
if [ "$(id -u)" != "0" ]; then
echo "This script must be... | Shell |
#!/bin/bash
SCRIPT_PATH=$0
RESOLVED_PATH=`readlink -f "$SCRIPT_PATH"`
while [ ! "$RESOLVED_PATH" = "$SCRIPT_PATH" ]; do
SCRIPT_PATH=$RESOLVED_PATH
RESOLVED_PATH=`readlink -f "$SCRIPT_PATH"`
done
GP_HOME=`dirname "$SCRIPT_PATH"`
GP_LOG_DIR="$HOME/.ganttproject.d"
# Check if log dir is present (or create it)
if [ ... | Shell |
#! /bin/bash
# Binary of the Texturepacker:
TEXTUREPACKER_BINARY=/usr/local/bin/TexturePacker
# Shared Spritesheet-Output-Definitions:
SPRITESHEET_OUTPUT_DIRECTORY="../assets/gfx/spritesheets/"
SPRITESHEET_OUTPUT_JAVAIDS_PACKAGE="org.anddev.andengine.examples.spritesheets"
SPRITESHEET_OUTPUT_JAVAIDS_DIRECTORY="../src... | Shell |
#!/bin/bash
cd src/
javac -cp .:json_simple-1.1.jar ru/compscicenter/databases/zaikina/nodes/NodeMain.java
for i in {0..27}
do
java -cp .:json_simple-1.1.jar ru.compscicenter.databases.zaikina.nodes.NodeMain $i &
echo "Node $i started"
done
cd ../
| Shell |
#!/bin/bash
cd src/
javac -cp .:json_simple-1.1.jar ru/compscicenter/databases/zaikina/nodes/NodeMain.java
for i in {0..27}
do
java -cp .:json_simple-1.1.jar ru.compscicenter.databases.zaikina.nodes.NodeMain $i &
echo "Node $i started"
done
cd ../
| Shell |
#DEPS:
#Casava (to convert qseq to fastq)
#1)get fastq files,
usage="Usage: $0 --qseqDir=[qseqDir] --lanes=[lanes] --prefix=[prefix] --outdir=[outdir]\n
--qseqDir: directory where the compressed qseq files are\n
--lanes : comma seperated list of lanes\n
--prefix :this will be put infront of output file names\n
--... | Shell |
#DEPS:
#echo "The script you are running has basename `basename $0`, dirname `dirname $0`"
#echo "The present working directory is `pwd`"
SCRIPTS=`dirname $0`
#1)get fastq files,
usage="Usage: $0 --qseqDir=[qseqDir] --lanes=[lanes] --prefix=[prefix] --outdir=[outdir]\n
--qseqDir: directory where the compressed ... | Shell |
#!/bin/bash
# drawall.sh - script that draws all of tracks stored in LRN-files in base directory.
# It's intended to be called from root project directory: "amse-laser-mouse".
# The result will be PNG-plots located in "base/plots" directory.
#USAGE:
#./base/scripts/drawall.sh
ls -1 -B ./base | grep -E [[:alnum:]]+\.... | Shell |
#!/bin/bash
# draw.sh - script for BASH that draws only one track from one LRN-file (stored base directory).
# USAGE:
# ./base/scripts/draw.sh <track_id> <LRN-file> <resulting_PNG-file>
./base/scripts/extrack.pl $1 < $2 > track
FILESIZE=$(stat -c%s "track")
if (($FILESIZE < 5))
then
exit;
fi
echo "set terminal p... | Shell |
#!/bin/bash
# drawall.sh - script that draws all of tracks stored in LRN-files in base directory.
# It's intended to be called from root project directory: "amse-laser-mouse".
# The result will be PNG-plots located in "base/plots" directory.
#USAGE:
#./base/scripts/drawall.sh
ls -1 -B ./base | grep -E [[:alnum:]]+\.... | Shell |
#!/bin/bash
# draw.sh - script for BASH that draws only one track from one LRN-file (stored base directory).
# USAGE:
# ./base/scripts/draw.sh <track_id> <LRN-file> <resulting_PNG-file>
./base/scripts/extrack.pl $1 < $2 > track
FILESIZE=$(stat -c%s "track")
if (($FILESIZE < 5))
then
exit;
fi
echo "set terminal p... | Shell |
rm -rf build
rm -rf tmp
| Shell |
appcfg.py update build
| Shell |
python build.py
dev_appserver.py --port 9999 build
| Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
./kill_process.sh
$ADB shell rm -r /data/data/com.google.android.apps.iosched/* | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
$ADB shell am force-stop com.google.android.apps.iosched
| Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
$ADB shell "echo '$*' | sqlite3 -header -column /data/data/com.google.android.apps.iosched/databases/schedule.db" | Shell |
#!/bin/sh
# Sessions list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/sessions
# Vendors list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/vendors
# Session detail
#adb shell am start -a... | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
MAC_UNAME="Darwin"
if [[ "`uname`" == ${MAC_UNAME} ]]; then
DATE_FORMAT="%Y-%m-%dT%H:%M:%S"
else
DATE_FORMAT="%Y-%m-%d %H:%M:%S"
fi
if [ -z "$1" ]; then
NOW_DATE=$(date "+${DATE_FORMAT}")
echo Please provide a mock time in the format \"${NOW_DATE}\" or \"d\" to del... | Shell |
#!/bin/sh
adb shell cat /data/data/com.google.android.apps.iosched/shared_prefs/com.google.android.apps.iosched_preferences.xml | xmllint --format - | Shell |
#!/bin/sh
# Remember VERBOSE only works on debug builds of the app
adb shell setprop log.tag.iosched_SyncHelper VERBOSE
adb shell setprop log.tag.iosched_SessionsHandler VERBOSE
adb shell setprop log.tag.iosched_ImageCache VERBOSE
adb shell setprop log.tag.iosched_ImageWorker VERBOSE
adb shell setprop log.tag.iosched_I... | Shell |
#!/bin/sh
adb shell pm clear com.google.android.apps.iosched | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
$ADB shell am start \
-a android.intent.action.MAIN \
-c android.intent.category.LAUNCHER \
-n com.google.android.apps.iosched/.ui.HomeActivity
| Shell |
#! /bin/bash
cd boost_1_46_1
cp -v ../user-config.jam ./tools/build/v2/
bjam -j12 --without-python --disable-filesystem3 toolset=gcc-android4.6 link=static runtime-link=static target-os=linux --stagedir=android --user-config=./tools/build/v2/user-config.jam
cd ..
| Shell |
#! /bin/bash
if [ ! -f ./boost_1_46_1.tar.bz2 ]
then
wget http://downloads.sourceforge.net/project/boost/boost/1.46.1/boost_1_46_1.tar.bz2
fi
if [ ! -d ./boost_1_46_1 ]
then
tar -xvjf boost_1_46_1.tar.bz2
cd boost_1_46_1
patch -p1 < ../boost-libs-android.patch
cp -v ../user-config.jam ./tools/build... | Shell |
#! /bin/bash
adb uninstall csh.cryptonite
adb install bin/cryptonite-debug.apk
| Shell |
#! /bin/bash
./googlecode_upload.py --summary="Cryptonite Android Package" --project=cryptonite --user=christoph.schmidthieber --labels=Featured,Type-Package ${1}
| Shell |
#! /bin/bash
# Haven't managed to have Android.mk put my static libraries in front of
# libgcc.a and libgnustl_static.a so that I had to resort to this manual
# build script.
rm -rf obj
./cplibs-static.py
ARCH=armeabi
NDK=${HOME}/android-ndk-r7
HOSTOS=`uname -s`
case ${HOSTOS} in
'Darwin')
HOSTOS="darwin"
;;
*)
... | Shell |
g++ android_key.cpp -DSTANDALONE -lcrypto -o encrypt
| Shell |
#! /bin/bash
ant clean
ant debug
adb uninstall csh.cryptonite.test
adb install bin/cryptonitetest-debug.apk
adb shell am instrument -w csh.cryptonite.test/android.test.InstrumentationTestRunner
| Shell |
#! /bin/bash
ant clean debug
ant uninstall
ant installt
ant test
| Shell |
#! /bin/bash
if test -n $1; then
if [ "$1" = "1" ]; then
./jni-build.sh
fi
fi
# rm -rf bin/*
ant clean
ant debug
adb uninstall csh.cryptonite
adb install bin/cryptonite-debug.apk
# adb -d shell "am start -a android.intent.action.MAIN -n csh.cryptonite/.Cryptonite"
| Shell |
#! /bin/bash
~/android-ndk-r8d/ndk-build V=1 APP_STL=gnustl_static APP_ABI="armeabi armeabi-v7a" clean
rm -rf libs/armeabi/* obj/local/armeabi/*
rm -rf libs/armeabi-v7a/* obj/local/armeabi-v7a/*
./cplibs-static.py
~/android-ndk-r8d/ndk-build V=1 APP_STL=gnustl_static APP_ABI="armeabi armeabi-v7a" -j2
| Shell |
# Don't attempt a parallel build! (-jN)
OPENSSL_VERSION="1.0.0j"
cp -v Makefile.android openssl-${OPENSSL_VERSION}
cp -v Makefile.android.armv7 openssl-${OPENSSL_VERSION}
cd openssl-${OPENSSL_VERSION}
rm -rf libcrypto.a libssl.a armeabi
make -f Makefile.android clean
make -f Makefile.android
mkdir -p armeabi
mv lib... | Shell |
#! /bin/bash
wget http://www.openssl.org/source/openssl-1.0.0j.tar.gz
tar -xzf openssl-1.0.0j.tar.gz | Shell |
#! /bin/bash
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be... | Shell |
#! /bin/bash
cd protobuf-2.4.1
cp ../config-arm-protobuf.sh ./
./config-arm-protobuf.sh
make clean
make -j4
make install
./config-arm-protobuf.sh 1
make clean
make -j4
make install
cd ..
| Shell |
#! /bin/bash
wget --no-check-certificate https://protobuf.googlecode.com/files/protobuf-2.4.1.tar.bz2
tar -xjf protobuf-2.4.1.tar.bz2
| Shell |
#! /bin/bash
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be... | Shell |
#! /bin/bash
cd rlog-1.4
cp ../config-arm-rlog.sh ./
./config-arm-rlog.sh
make clean
make -j4
make install
./config-arm-rlog.sh 1
make clean
make -j4
make install
cd ..
| Shell |
#! /bin/bash
wget http://rlog.googlecode.com/files/rlog-1.4.tar.gz
tar -xzf rlog-1.4.tar.gz
| Shell |
#! /bin/bash
git clone https://github.com/seth-hg/fuse-android.git
find ./fuse-android \( -name "*.c" -o -name "*.h" \) -exec sed -i 's/off_t/loff_t/g' {} \;
patch -p1 < ./fuse-android.patch
| Shell |
#! /bin/bash
TOOLCHAIN="${HOME}/android-toolchain"
AR="${TOOLCHAIN}/bin/arm-linux-androideabi-ar crs"
RANLIB="${TOOLCHAIN}/bin/arm-linux-androideabi-ranlib"
STRIP="${TOOLCHAIN}/bin/arm-linux-androideabi-strip"
cd tinyxml
MARCH=armeabi
make -f ../Makefile.android ARCH=${MARCH}
rm -rf ${MARCH}
mkdir -p ${MARCH}
mv *.o ... | Shell |
#! /bin/bash
wget http://downloads.sourceforge.net/project/tinyxml/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz
tar -xzf tinyxml_2_6_2.tar.gz
| Shell |
#! /bin/bash
diff -x '*.in' -x '*.o' -x '*.lo' -x '*.1' -ur ${HOME}/encfs-1.7.4/encfs ./encfs-1.7.4/encfs > encfs-android.patch.new
| Shell |
#! /bin/bash
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be... | Shell |
#! /bin/bash
TOOLCHAIN=${HOME}/android-toolchain
MYSTRIP=${TOOLCHAIN}/bin/arm-linux-androideabi-strip
cd encfs-1.7.4
cp ../config-arm-encfs.sh ./
rm -rf armeabi
./config-arm-encfs.sh
make clean
make -j4
make install
${MYSTRIP} --strip-unneeded armeabi/bin/encfs
rm -rf armeabi-v7a
./config-arm-encfs.sh 1
make clean
... | Shell |
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