sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5d2cce0074ad28362547ba13e78db68d0cb043b265b871ae3f118fc2506bf110 | Shell | 495 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "BK_polyoma" -e "BK polyoma" -e "BK_virus" -e "BK virus" -e "BKPyV" -e "NC_001538" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 > 3000 && $2 < 7000) print $3"\t"$4; }' \
| head -n 1 \
| awk '{ print $... |
e7ddecc8612459b0ace03943180d104822239f7f6f4981b863f7ae2d26be5e50 | Shell | 497 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HERV" -e "endogenous retro" -e "endogenous_retro" \
| grep -a -e "human" -e "Human" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 7000 && $2 < 12000) print $3"\t"$4; }' \
| head -n 1 \
| awk '{ print... |
fadb94f57c31c49db9ed2baa5a79f5ecb6c20b56f0c0d89325c14119bcf00def | Shell | 499 | 8 | #!/usr/bin/bash
current_datetime=$(date +"%Y%m%d_%H%M%S")
mkdir "/home/$USER/.bciframework_docker_$current_datetime"
sudo chmod -R 777 "/home/$USER/.bciframework_docker_$current_datetime"
xhost +local:docker
docker pull dunderlab/bci_framework:latest
docker run --name=bciframework --network=host --privileged -it --rm ... |
cb350fe4725f4954cdebdf4f88e3ad560009d32bc1be3bd44120274fcee13024 | Shell | 500 | 7 | rm requirements.txt
pipreqs --ignore bci_framework/default_projects,bci_framework/documentation,bci_framework/extensions/stimuli_delivery/path,bci_framework/kafka_scripts/latency_synchronization_stimuli_marker --savepath requirements.txt --force bci_framework
sed -i '/kafka==/d' requirements.txt
sed -i '/browser==/d' r... |
77aeebb044bb5bd1b1a2be78c0b3790fe83d693aa5398820488832f5ea6d0078 | Shell | 505 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "hepatitis" -e "Hepatitis" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 1500 && $2 < 6000) print $3"\t"$4; }' \
| head -n 1 \
| awk ... |
40efe82964b8d6c34b959590143ffa362dbf9ae04b884bf3ccb51cbc183e48d4 | Shell | 506 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "HHV-6" -e "erpesvirus 6" -e "erpesvirus_6" \
| grep -a -e "Human" -e "human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t"$4; }' \
| head -n 1 \
| awk... |
c01db76e9c3bacf54e9f9e17c75bcb69546a9b5207eab591a07ee2958309528a | Shell | 508 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "imian virus 40" -e "imian_virus_40" -e "imian_Virus_40" -e "imian Virus 40" -e "simian virus 40" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 2000 && $2 < 6000) print $3"\t"$4; }' \
| head -n 1 \
| a... |
f771c78aad302d4d13d4366d3840afed7cc2c8419add134cad0f10f380f228d0 | Shell | 513 | 20 | #!/bin/bash
ORGAN=$1; shift
Virus=$1; shift
MetaFile=$1; shift
TopFile=$1; shift
#
awk -v Virus="$Virus" -F '\\t' '
BEGIN{OFS="\t";bestSim="-";bestAcc="-";bestLen="-"}
(ARGIND == 1){if($2==Virus){InSet[$1]=1};next}
{
sub("NC_","NC-",$4);
split($4,a,"_");
acc = a[1];
sub("NC-"... |
3c4eddda05172fa6bbc5d5b5fcd6a7b6be011b8cbb9d1ca9d313dcfd5279ff7e | Shell | 516 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-7" -e " HHV7" -e "erpesvirus_7" -e "erpesvirus 7" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t"$4; }' \
| head -n... |
76457c1f4f30e2563b0250987e26ec029d431882cd080984be99ef0043be6bf8 | Shell | 516 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "erpesvirus_3" -e "erpesvirus 3" -e " HHV-3" -e " HHV3" \
| grep -a -e "Human" -e "human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 220000) print $3"\t"$4; }' \
| head -n... |
12c731258971d96dc8c8c158d6b209993a0fef2af06743ec29a45c44e6df129b | Shell | 519 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Epstein" -e "epstein" -e "erpesvirus_4" -e "erpesvirus 4" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 220000) print $3"\t"$4; }' \
| head... |
081faded5575a687128cda1825e3e60a0b295360a022fdfa144dec0a77bc9756 | Shell | 520 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-6B" -e " HHV6B" -e "erpesvirus_6B" -e "erpesvirus 6B" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t"$4; }' \
| hea... |
10e9d3b89535bd1067c1bf01a9735a98216b97585bfb5199a25d855a4b23c18a | Shell | 520 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-6A" -e " HHV6A" -e "erpesvirus_6A" -e "erpesvirus 6A" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t"$4; }' \
| hea... |
d57834bbb1d623d893fcb515f444316577a64d03b64c8595b7536d45ce723a3b | Shell | 520 | 19 | #!/bin/bash
release=release1-7
rootDir=/fslhome/mpeter55/fsl_groups/fslg_csf_autism/compute/HBN_Project
scriptDir=${rootDir}/code/auto_code
subjidsDir=${rootDir}/code/subjids
var=`date +"%Y%m%d-%H%M%S"`
for i in `cat ${subjidsDir}/${release}_ids.txt`;do
rm -r ${rootDir}/output/${release}/${i}
mkdir -p /fslhome/mpe... |
13c783ed13b63ba8c08f2d655d3f185171bc6e27a46225a664d01dd6c06dc72e | Shell | 521 | 29 | #!/bin/sh
#set -x
echo "Inserisci il nome dell'archivio FSDA da analizzare : "
read what
if [ ! -d "$what" ]
then
echo "ERRORE :" $what " non esiste !!!!"
exit 1
fi
find $what -name "*.m" >lista_func
>REP/func_without_example.txt
cat lista_func | while read nome
do
grep "%{" $nome >/dev/null
if [ $... |
af1710c5c0b9d3cce2887637e104836613a979f4bda65c995018d5916379f119 | Shell | 525 | 10 | #!/bin/bash
#
cat $1 | grep -v "erpes" | grep -v "papilloma" | grep -v "erythroparvovirus" \
| grep -v "parvovirus" | grep -v "erythrovirus" \
| grep -v "endogenous_retrovirus" | grep -v "_B19_" | grep -v "_B19V_" \
| grep -v "JC_virus" | grep -v "polyomavirus" | grep -v "Hepatitis_B" \
| gr... |
7d3236be7bf1ea9bbe40908f85b763f09e17ea2216c8bf1f6442a37ef48131cd | Shell | 527 | 12 | #!/bin/sh
### Job name
#PBS -N indexFungiProtistVirus
### Number of nodes
##PBS -l nodes=1:ppn=8
#PBS -l nodes=1:ppn=64
#PBS -q bigmem
#PBS -j oe
cd /home/rrk24/scratch_grace/ANNOTATIONS/Genomes_BacteriaFungiMammalPlantProtistVirus && mkdir STAR_GENOME_FUNGI_PROTIST_VIRUS
/gpfs/scratch/fas/gerstein/rrk24/bin/STAR_... |
beba5ff5bab12644678c218288d164184de896a6583ad01f5d391e76cb8e3ffb | Shell | 528 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "HHV-6" -e "erpesvirus 6" -e "erpesvirus_6" \
| grep -a -e "Human" -e "human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t"$4; }'... |
fc6e1eee535825630df4b61b5d86a7533c266a74b3906d98433d7f651209fad7 | Shell | 535 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "_HCMV" -e " HCMV" -e "erpesvirus_5" -e "erpesvirus 5" -e "ytomegalovirus" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3"\t... |
7c1d3c7ddc72315a555d2b650474b22f061df041d23f3d1324b3df3c57864b6f | Shell | 538 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-7" -e " HHV7" -e "erpesvirus_7" -e "erpesvirus 7" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $3... |
9cfbc5d3c890b02f17b1bd996c4e7982142ec3581abd676053ece7b823c595f8 | Shell | 538 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "erpesvirus_3" -e "erpesvirus 3" -e " HHV-3" -e " HHV3" \
| grep -a -e "Human" -e "human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 220000) print $3... |
cd826301126b8699b3801242e2cd286751d4e1499fc4b34ad613d2755130959c | Shell | 538 | 14 | layer=$1
kernels=$2
threads=$3
motif_nb=$4
bash idx.sh $kernels | xargs -n 1 -P $threads bash sampling.sh $layer
python decouple.py $threads $layer $kernels $motif_nb
bash idx.sh $kernels | xargs -n 1 -P $threads bash visualize.sh $layer $kernels
bash idx.sh $kernels | xargs -n 1 -P $threads bash tree... |
df1ad12fbc6c2c417a7a6eb8e8ef7c1ff5169e3868344c983027eaf03db0d4c3 | Shell | 538 | 14 | layer=$1
kernels=$2
threads=$3
motif_nb=$4
bash idx.sh $kernels | xargs -n 1 -P $threads bash sampling.sh $layer
python decouple.py $threads $layer $kernels $motif_nb
bash idx.sh $kernels | xargs -n 1 -P $threads bash visualize.sh $layer $kernels
bash idx.sh $kernels | xargs -n 1 -P $threads bash tree... |
22cc26767ebd1b92143ebf4eddad9c2cad1c4e0eed21717f8344cb6cac42851a | Shell | 539 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-1" -e " HHV1" -e " HSV1" -e " HSV-1" -e "erpesvirus_1" -e "erpesvirus 1" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print $... |
6c270d165acfed79cae78527a8663154c509c58d98ad63973739a3bdbd64cff4 | Shell | 539 | 14 | #!/bin/bash
# Enters into docker container and then starts running do_data run for DeepDraw models
# Kai Sandbrink, 2020.11.09
# idea: https://stackoverflow.com/questions/35547966/how-to-write-a-bash-script-which-automate-entering-docker-container-and-doing
docker start kai_dlcdocker_data_tf15
docker exec --user kai... |
329e1accdd0ae8652cfa8ce1654380d8f6085efd77f70081ee8e30d33f840ceb | Shell | 540 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-8" -e " HHV8" -e "erpesvirus_8" -e "erpesvirus 8" -e " Kaposi" -e " KSHV" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) print ... |
6011c6a385572d4e6da5970ef32eda999af98d3c188f84f11009d5e3726ddf41 | Shell | 541 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Epstein" -e "epstein" -e "erpesvirus_4" -e "erpesvirus 4" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 220000) print... |
46230c0c36d7803e8726ae6747b9da5af9bec392e612cf328804cbfb9a4fead2 | Shell | 542 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-6B" -e " HHV6B" -e "erpesvirus_6B" -e "erpesvirus 6B" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) prin... |
8c5ea46f94f19ba948d1e70f57457b05cec2fef8649b80c698bcae810a54b185 | Shell | 542 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-6A" -e " HHV6A" -e "erpesvirus_6A" -e "erpesvirus 6A" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) prin... |
e1e95aeb2078b964fffe23c331deeefd712d71961d8223937ee545014a01707e | Shell | 542 | 21 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
function fail {
echo FAIL: $@
exit -1
}
export DGLBACKEND=$1
export DGLTESTDEV=gpu
export DGL_LIBRARY_PATH=${PWD}/build
export PYTHONPATH=tests:${PWD}/python:$PYTHONPATH
export DGL_DOWNLOAD_DIR=${PWD}/_download
export TF_FORCE_GPU_ALLOW_GROWTH=true
export CUDA... |
ad90b633219346f2119393a62a8b6804fb9c791606889ac7a8c0ddbc27b3e9b1 | Shell | 543 | 12 | #!/bin/bash
#
# ==============================================================================
#
rm -f mitochondrion.1.1.genomic.fna.gz mitochondrion.2.1.genomic.fna.gz MTs.fa
#
wget https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/mitochondrion.1.1.genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/refseq/relea... |
309d97be96a99be29f48414d1d4195a958c6718b6584a70564c4a62b0a1cf164 | Shell | 546 | 14 | #!/bin/bash
resDir="./results/" # Directory name to save the results
train_x="train_X.csv" # Training dataset filename
train_y="train_Y.csv" # Subtype label filename for training dataset
test_x="test_X.csv" # Testing dataset filename
test_y="test_Y.csv" # Subtype label filename for testing dataset
num_gene="100"... |
e985597bb95ace65d27e00514c906f1990799c2d86c813889b01942d75b6e9f0 | Shell | 546 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HCMV" -e "erpesvirus_5" -e "erpesvirus 5" -e "ytomegalovirus" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 && $2 < 300000) ... |
675e782be45de7b287964301c59187d4d675c074f498a2ca0805dc8f580b0271 | Shell | 554 | 26 | #!/bin/bash
# Add slice timing information to epi files
osf_loc=$(which osf)
if [[ $osf_loc =~ "not found" ]]
then
echo "Cannot find osf client on path."
echo "Is it properly installed?"
exit 1
fi
orig_dir=$(pwd)
osf -p qaesm clone $QC_DATA_ROOT
cd $QC_DATA_ROOT/osfstorage
tar -xf fmri-open-qc-rest01.ta... |
e238264ca4f52d776460951de7a80ae6509d9eee9be78e4289113e4b781ec696 | Shell | 554 | 11 | #!/bin/bash
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT FILES EXIST:
# NP-o_fw_pr.fq NP-o_fw_unpr.fq NP-o_rv_pr.fq NP-o_rv_unpr.fq
#
## EXTRACT MTDNA FROM THE SAMPLES
MAGNET -v -F -n 12 -m 6:1:1:0/0 -m 13:20:1:3/10 -t 0.3 -o MT-o_fw_pr.fq mtDNA.fa NP-o_fw_pr.fq
MAGNET -v -F -n 12 -m 6:1:1:0/0 -m 13:20:1:3/10 -t 0.3 -o MT-... |
9e5b3dfe4110bdefcdd2663958748d95623e6fa5f8ea05eb731a0f94c78916e8 | Shell | 557 | 19 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "bocavirus 2" -e "bocavirus 3" -e "bocavirus 4" -e "Bocavirus 2" -e "Bocavirus 3" -e "Bocavirus 4" -e " HBoV2" -e " HBoV3" -e " HBoV4" \
| grep -a -e "human" -e "Human" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 4000 && ... |
79f72f907a1ad273317f523153e93c4365d369c0e9734a42033680af11a2d82a | Shell | 558 | 23 | #!/bin/bash
#
if [ -z "$1" ]
then
echo "ERROR: No coverage BED file provided."
echo "Example: ./TRACES_normalized_depth.sh ../output_data/TRACES_viral_bed/B19-coverage-blood.bed 500"
exit;
fi
#
if [ -z "$2" ]
then
echo "ERROR: NO maximum depth provided."
echo "Example: ./TRACES_normalized_depth.sh ../outp... |
3c561247fde331b322ac6e12aed1310986bc788072377f748b10467d1a158130 | Shell | 560 | 10 | #!/bin/sh
# Installs Python $1 (the repo's `.python-version`, passed as the `PYTHON_VERSION` build arg) with uv, in a venv at
# `$VIRTUAL_ENV`. The Dockerfile sets `VIRTUAL_ENV`, `UV_PYTHON_INSTALL_DIR` and puts the venv first on `PATH`, so
# `python`, `python3` and `pip` all resolve to it.
set -e
: "${1:?usage: instal... |
dc0acbc5dd28e77f71fcb8adc247bbee33140c60979658eef1657512e50d5407 | Shell | 561 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-1" -e " HHV1" -e " HSV1" -e " HSV-1" -e "erpesvirus_1" -e "erpesvirus 1" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 &... |
24bbadee4a44bd1314baecfa409f6351a20a50f60c10d4927b2a2e9fe826cc15 | Shell | 562 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-8" -e " HHV8" -e "erpesvirus_8" -e "erpesvirus 8" -e " Kaposi" -e " KSHV" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 100000 ... |
fcacad7aa6eb0b05e7e55981c3d96751901bdbe0a79288c61c2c3f31bcae88a6 | Shell | 562 | 14 | #!/usr/bin/bash
sudo pacman -S --needed python python-pip gcc cython hdf5
sudo pip install -U openbci-stream systemd_service
stream_install_kafka.sh
sudo stream_configure_kafka.sh
sudo stream_configure_ntpd.sh
sudo stream_access_point.sh
sudo stream_eeg systemd
sudo stream_rpyc systemd
sudo stream_bin2eeg systemd
sudo... |
d03314aecb399eb2fa3bef8ffb3afc12556a0a257245400b4b6babe7ef0ab48a | Shell | 564 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "STL_polyomavirus" -e "STL_virus" -e "STLPyV" -e "olyomavirus_11" -e "STL polyomavirus" -e "STL Polyomavirus" -e "STL virus" -e "olyomavirus 11" -e "NC_020106" -e "NC020106" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 > 2... |
4a69a149a714a8153490a831836e44b2d667bff6a035e0ff0d45f9228167d191 | Shell | 567 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_7" -e "polyomavirus_7" -e "Polyoma_7" -e "polyoma_7" -e "Polyomavirus 7" -e "polyomavirus 7" -e "Polyoma 7" -e "polyoma 7" -e "HPyV7" -e "NC_014407" -e "NC014407" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 ... |
5b49001228b89089589a903923135a7a734116fbe9352c3a21657111548aca55 | Shell | 567 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_9" -e "polyomavirus_9" -e "Polyoma_9" -e "polyoma_9" -e "Polyomavirus 9" -e "polyomavirus 9" -e "Polyoma 9" -e "polyoma 9" -e "HPyV9" -e "NC_015150" -e "NC015150" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 ... |
9a03be1fb4a3c84889fa1f6628d95a77707e4893d9345ad08d70e8ff354aa715 | Shell | 567 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_6" -e "Polyomavirus 6" -e "polyomavirus_6" -e "polyomavirus 6" -e "Polyoma_6" -e "Polyoma 6" -e "polyoma_6" -e "polyoma 6" -e "HPyV6" -e "NC_014406" -e "NC014406" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 ... |
b2da58fb55b33082786765920c76c20d6cbea52ad7fe3e4a7eb1f48d6f917695 | Shell | 567 | 20 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e " HHV-2" -e " HHV2" -e " HSV2" -e " HSV-2" -e "erpesvirus_2" -e "erpesvirus 2" \
| grep -v "African horse" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($3 > 0 && $2 > 10... |
ca6996b9412011b2bae09ff002954cf8bae56ed76bfbfba7bb8a60d7c1fabf41 | Shell | 567 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_8" -e "polyomavirus_8" -e "Polyoma_8" -e "polyoma_8" -e "Polyomavirus 8" -e "polyomavirus 8" -e "Polyoma 8" -e "polyoma 8" -e "TSPyV" -e "NC_014361" -e "NC014361" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $2 ... |
564284db9ca36fc5d4f566a419454dc61681e8211668bd4e1b5abc530ad10f8e | Shell | 568 | 21 | #!/bin/bash
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT FILES EXIST:
# MT-o_fw_pr.fq MT-o_rv_pr.fq MT-o_fw_unpr.fq MT-o_rv_unpr.fq
#
# ASSEMBLE
Label=$1; shift
NThread=$1; shift
BResume=$1; shift
workDir="out_spades_$Label"
MemLimit=350;
#If not attempting to resume, or the attempt to resume fails run the asembly from... |
bc573de163c221836dc0e795ab06eee829a7ee10efcca4f9155a3facef7c34fe | Shell | 569 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "MW_polyomavirus" -e "MW_virus" -e "MWPyV" -e "olyomavirus_10" -e "MW polyomavirus" -e "MW virus" -e "MWPyV" -e "olyomavirus 10" -e "MW polyomavirus" -e "NC_018102" -e "NC018102" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 && $... |
63ce8ee1e8905d4dac6115dccc4a451d53cb1bc1b00934b402e031377786e396 | Shell | 571 | 11 | mkdir layer${1}
lk=layer${1}/vislock${3}
if [[ ! -e $lk ]]; then
mkdir layer${1}/vislock${3}
python chen2html.py layer${1}/kernel-${3}.ppm.h5 ${3} layer${1}/${3} ${2}
python tochen.py $1 $3
chen2meme layer${1}/kernel-${3}.sel.ppm.chen > layer${1}/kernel-${3}.sel.ppm.meme
tomtom layer${1}/kernel-${3... |
57b39a0b6acf905103b7d13b84b45d349bfe47da891e4c65ddf98d67698b1a64 | Shell | 572 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "STL_polyomavirus" -e "STL_virus" -e "STLPyV" -e "olyomavirus_11" -e "STL polyomavirus" -e "STL Polyomavirus" -e "STL virus" -e "olyomavirus 11" -e "NC_020106" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > 0 &... |
c48af66e6c04a4fb2ec5e883c621fac2235c49253d23287cd1c573a62fe06775 | Shell | 572 | 13 | #!/bin/bash
#
# $1 -> NUMBER OF THREADS
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT FILES EXIST:
# o_fw_pr.fq o_fw_unpr.fq o_rv_pr.fq o_rv_unpr.fq
#
## REMOVE PHIX FROM THE SAMPLES
MAGNET -v -F -n $1 -m 6:1:1:0/0 -m 13:20:1:3/10 -t 0.9 -i -o NP-o_fw_pr.fq F_PHIX.fa o_fw_pr.fq
MAGNET -v -F -n $1 -m 6:1:1:0/0 -m 13:20:1:3/1... |
2f26521374ea60467b84e720c6a5c74596bf06e1dc4b9c3d22a4b3ecf726153e | Shell | 575 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_13" -e "polyomavirus_13" -e "Polyomavirus 13" -e "polyomavirus 13" -e "Polyoma_13" -e "polyoma_13" -e "Polyoma 13" -e "polyoma 13" -e "NJPyV" -e "NC_024118" -e "NC024118" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > ... |
72db3e9e40e3a56bc00aad8c952e74d4e894ee99c11ee717b73233a13029811f | Shell | 575 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_7" -e "polyomavirus_7" -e "Polyoma_7" -e "polyoma_7" -e "Polyomavirus 7" -e "polyomavirus 7" -e "Polyoma 7" -e "polyoma 7" -e "HPyV7" -e "NC_014407" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > ... |
7fcea77fd79af128a92b0456a8b4ebaa50dd6a68bef29b3049276ed4aaaaccc9 | Shell | 575 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_8" -e "polyomavirus_8" -e "Polyoma_8" -e "polyoma_8" -e "Polyomavirus 8" -e "polyomavirus 8" -e "Polyoma 8" -e "polyoma 8" -e "TSPyV" -e "NC_014361" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > ... |
bc9cef3605c6d41425ae297b14fd8e044b89f111172c26cfcbbe0ee5087e1725 | Shell | 575 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_9" -e "polyomavirus_9" -e "Polyoma_9" -e "polyoma_9" -e "Polyomavirus 9" -e "polyomavirus 9" -e "Polyoma 9" -e "polyoma 9" -e "HPyV9" -e "NC_015150" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > ... |
c4b623844953b6a22773bf8007a0b5c074894ce29a1106c9d1a57a9f2ac8cc99 | Shell | 575 | 13 | #!/bin/bash
#
declare -a INDIVIDUALS=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I27' 'I28' 'I29' 'I30' 'I31' 'I32' 'I33' 'I34' 'I35' 'I36' 'I37' 'I38' 'I40' 'I41' 'I42' 'I43' 'I44' 'I45' 'I46' 'I47' 'I48' 'I49' 'I5... |
d17d43f4135d0c6dd23c22edab8917e1dd133de37d34b918842e0bb6d431a953 | Shell | 575 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_6" -e "Polyomavirus 6" -e "polyomavirus_6" -e "polyomavirus 6" -e "Polyoma_6" -e "Polyoma 6" -e "polyoma_6" -e "polyoma 6" -e "HPyV6" -e "NC_014406" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 > ... |
8854ab3460d2a4db17c1b538d06691510cd11cb5acfceff6436e6efad71ec7aa | Shell | 576 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "olyomavirus_3 " -e "olyomavirus_3|" -e "olyomavirus 3" -e "olyomavirus 3|" -e "KI_polyomavirus" -e "KI polyomavirus" -e "KI_virus" -e "KI virus" -e "KIPyV" -e "NC_009238" -e "NC009238" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 >... |
d7f541bb119a947045711a0d078183d6815ead8ded9fe062557b24b48d8291c6 | Shell | 576 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_12" -e "polyomavirus_12" -e "Polyoma_12" -e "polyoma_12" -e "Polyomavirus 12" -e "polyomavirus 12" -e "Polyoma 12" -e "polyoma 12" -e "HPyV12" -e "NC_020890" -e "NC020890" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 >... |
596220f78b3f2944dd03c73113cc65e5c6dcb67dff7958044cd3673b3767bb8f | Shell | 577 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "MW_polyomavirus" -e "MW_virus" -e "MWPyV" -e "olyomavirus_10" -e "MW polyomavirus" -e "MW virus" -e "MWPyV" -e "olyomavirus 10" -e "MW polyomavirus" -e "NC_018102" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3 ... |
95f84b01f71c09a56679c71e6c16ccc4ab634a17366ae3dddd8cc8b72c2dc068 | Shell | 578 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "olyomavirus_4 " -e "olyomavirus_4|" -e "olyomavirus 4 " -e "olyomavirus 4|" -e "WU_polyomavirus" -e "WU polyomavirus" -e "WU_virus" -e "WU virus" -e "WUPyV" -e "NC_009539" -e "NC009539" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($3... |
a2df76e7403250baa2b2b8494a943fb076eaae62afe67d5b2cc3055db18751dc | Shell | 579 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "Polyomavirus_14" -e "polyomavirus_14" -e "Polyoma_14" -e "polyoma_14" -e "Polyomavirus 14" -e "polyomavirus 14" -e "Polyoma 14" -e "polyoma 14" -e "LIPyV" -e "NC_034253.1" -e "NC034253.1" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ if($... |
b49cfa9b93174b46e41848478c941ace508650c5b707bb948ebfe8765c4b001a | Shell | 579 | 21 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "bocavirus 2" -e "bocavirus 3" -e "bocavirus 4" -e "Bocavirus 2" -e "Bocavirus 3" -e "Bocavirus 4" -e " HBoV2" -e " HBoV3" -e " HBoV4" \
| grep -a -e "human" -e "Human" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '{ if($... |
25d3aa2efc3a39594aa49190200370a35560ac6189617ee1345b6eb715cb7260 | Shell | 580 | 13 | #!/bin/bash
#
declare -a INDIVIDUALS=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I27' 'I28' 'I29' 'I30' 'I31' 'I32' 'I33' 'I34' 'I35' 'I36' 'I37' 'I38' 'I40' 'I41' 'I42' 'I43' 'I44' 'I45' 'I46' 'I47' 'I48' 'I49' 'I5... |
dade733e1fd0e3b9e06ed1e4b021c7f2b745a794f98df54d922ac4030e5655e4 | Shell | 583 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_13" -e "polyomavirus_13" -e "Polyomavirus 13" -e "polyomavirus 13" -e "Polyoma_13" -e "polyoma_13" -e "Polyoma 13" -e "polyoma 13" -e "NJPyV" -e "NC_024118" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{ ... |
dbdd25a34ec9b5eab941af536d8cded11bacbb05a842a02317dd1d9595c5dcbb | Shell | 584 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_12" -e "polyomavirus_12" -e "Polyoma_12" -e "polyoma_12" -e "Polyomavirus 12" -e "polyomavirus 12" -e "Polyoma 12" -e "polyoma 12" -e "HPyV12" -e "NC_020890" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{... |
f27e83a7b17000a81b2bbf274530ea528ea6161677686c2ed625b9e7e576ee6e | Shell | 584 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "olyomavirus_3 " -e "olyomavirus_3|" -e "olyomavirus 3" -e "olyomavirus 3|" -e "KI_polyomavirus" -e "KI polyomavirus" -e "KI_virus" -e "KI virus" -e "KIPyV" -e "NC_009238" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '{... |
a3d68d9a08db9ccd6e9f4f43e33292815fe97e725ed675e38a01edf0a5746ee0 | Shell | 585 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "Polyomavirus_14" -e "polyomavirus_14" -e "Polyoma_14" -e "polyoma_14" -e "Polyomavirus 14" -e "polyomavirus 14" -e "Polyoma 14" -e "polyoma 14" -e "LIPyV" -e "NC_034253.1" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk '... |
9b0672ed941786fd525cacd08fa95cf93a4d417d98367b3983e2ea1d94b3626a | Shell | 586 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "olyomavirus_4 " -e "olyomavirus_4|" -e "olyomavirus 4 " -e "olyomavirus 4|" -e "WU_polyomavirus" -e "WU polyomavirus" -e "WU_virus" -e "WU virus" -e "WUPyV" -e "NC_009539" \
| grep -a -e "complete genome" -e "complete_genome" \
| awk ... |
c339d93eecf4b35a02c24afe418ef00509d51da28d311b5907e22838a4cb794e | Shell | 589 | 22 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e " HHV-2" -e " HHV2" -e " HSV2" -e " HSV-2" -e "erpesvirus_2" -e "erpesvirus 2" \
| grep -v "African horse" \
| grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
| grep -a -e "omplete genome" -e "omplete_genome" \
| awk '... |
0f01f56f30461cd2f11443987dadd98ab6598c8f032545ad4d22298857816af1 | Shell | 590 | 26 | #!/bin/bash
set -e
DEVICE=$1
ROOT=/asv/dgl
. /opt/conda/etc/profile.d/conda.sh
conda activate base
pip install --upgrade pip
# Newer asv version like 0.5.1 has different result format,
# so we fix the version here. Or `generate_excel.py` has to be changed.
pip install asv==0.4.2
pip uninstall -y dgl
export DGL_BEN... |
3b6096663524e406e9e4fceb02445fac3a62f3c6623f778ee2e7df4996283c9d | Shell | 591 | 20 | #!/bin/bash
release=release9
rootDir=/fslhome/mpeter55/fsl_groups/fslg_autism_asym/compute/HBN_Project
codeDir=${rootDir}/code/preproc
textDir=${rootDir}/code/preproc
dataDir=${rootDir}/data/reformat/${release}/t1
outDir=${dataDir}
var=`date +"%Y%m%d-%H%M%S"`
for subj in `cat ${textDir}/${release}_ids.txt`; do
mkdi... |
8053dbefc7ccff9349a8b9d8b9df93562654cd4fc493736558cd03c320d60f8c | Shell | 592 | 18 | #!/bin/bash
#
ORGAN="$1";
THREADS="$2";
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT FILES EXIST:
# o_fw_pr.fq o_fw_unpr.fq o_rv_pr.fq o_rv_unpr.fq
#
mkdir -p ../output_data/TRACES_results;
#
cat o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq > READS_TO_CY.fq
#
MAGNET -v -F -n $THREADS -m 6:1:1:0/0 -m 13:20:1:5/1 -t 0.3 -... |
c710e911e089c8da4778ed81b9c612be068d08751e96803c3d38d7d50d41915e | Shell | 595 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "olyomavirus_5" -e "olyomavirus 5" -e "MC_polyomavirus" -e "MC polyomavirus" -e "MC_virus" -e "MC virus" -e "Merkel_cell_polyomavirus" -e "Merkel cell polyomavirus" -e "MCPyV" -e "NC_010277" -e "NC010277" \
| grep -a -e "complete genome" -e "complete_genome"... |
d6c7d29c32afc291e61b106229d3bd0444a04025166361d63b5c0f75836c8cef | Shell | 597 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "_TT_virus" -e " TT virus" -e "anello" -e "Anello" -e " torque " -e " Torque " -e "_torque_" -e "_Torque_" -e "MN765195.1" -e "MN765195.1" -e "AB00A394" -e "AJ620212" -e "AB049607" -e "AB038622" -e "AB064604" \
| grep -a -e "omplete genome" -e "omplete_genom... |
7ead47100db75fa543a6dd0f6ff4b7e2cf9d15adf163f6367d2d2ba272098244 | Shell | 599 | 20 | #!/bin/bash
#
index_f="../encrypted_data/index.txt";
for file in ../encrypted_data/*
do
if [[ "$file" == "$index_f" ]];
then
echo -e "\e[34m[TRACESPipe]\e[32m Jumping index file ($file) \e[0m";
else
echo -e "\e[34m[TRACESPipe]\e[32m Decrypting $file \e[0m";
out_file=$(basename $file);
echo -e "\e[34m[T... |
0c185476389a5e8ee19718fc4e8719f96d484f3a16cf1327f4ff8472f991a421 | Shell | 603 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "olyomavirus_5" -e "olyomavirus 5" -e "MC_polyomavirus" -e "MC polyomavirus" -e "MC_virus" -e "MC virus" -e "Merkel_cell_polyomavirus" -e "Merkel cell polyomavirus" -e "MCPyV" -e "NC_010277" \
| grep -a -e "complete genome" -e "complete... |
6c6f812e41b6cf32a374e09553d0d0635021cb0cd041fc22e42a766dcf9db7b8 | Shell | 610 | 28 | #!/bin/bash
# Job name:
#SBATCH --job-name=connect_train_evalute
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=15:00:00
#
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
so... |
7b1f656752d2ef12acfef8e08bab636de71181291fcb3ea300c1f7693a8ae119 | Shell | 610 | 15 | #!/bin/bash
# Enters into docker container and then starts running do_data run for DeepDraw models
# Kai Sandbrink, 2020.11.09
# idea: https://stackoverflow.com/questions/35547966/how-to-write-a-bash-script-which-automate-entering-docker-container-and-doing
docker start kai_dlcdocker_data_tf15
docker exec --user kai... |
5fd48974f0791dd5e75d1274c512d0c1ebb0b7dc058ede46ec16ab8724edfa3c | Shell | 621 | 27 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
function fail {
echo FAIL: $@
exit -1
}
export DGLBACKEND=pytorch
export DGL_LIBRARY_PATH=${PWD}/build
export PYTHONPATH=tests:${PWD}/python:$PYTHONPATH
export DGL_DOWNLOAD_DIR=${PWD}/_download
conda activate pytorch-ci
pushd dglgo
rm -rf build *.egg-info dis... |
a4514cbcdb5146164e15fbf024d205b2496d4d39d7caddca780aee5857a7c239 | Shell | 632 | 29 | #!/usr/bin/env bash
module load afni
module load fsl
module load matlab/R2021B
# args: 1=TB_PATH, 2=SRC_DIR, 3=OUTPUT_DIR, 4=SUB, 5=SES,
# 6=NORDIC_END, 7=DONORDIC, 8=FORCE 9=script_dir
unset $SUB
unset $SES
TB_PATH="$1"
SRC_DIR="$2"
OUTPUT_DIR="$3"
SUB="$4"
SES="$5"
NORDIC_END="$6"
DONORDIC="$7"
FORCE="$8"
unset... |
0cc85b1648e7efde4ed9240f56169b5b01553b51eee50f128003298e21daede7 | Shell | 633 | 20 | mkdir -p ./data/ISRUC_S3/ExtractedChannels
mkdir -p ./data/ISRUC_S3/RawData
echo 'Make data dir: ./data/ISRUC_S3'
cd ./data/ISRUC_S3/RawData
for i in `seq 1 10` #seq是一个命令，顺序生成一串数字或者字符
do
# wget http://dataset.isr.uc.pt/ISRUC_Sleep/subgroupIII/$i.rar
unrar x $i.rar
done
echo 'Download Data to "./data/ISRUC_S3/... |
7bc984ab16480c8ae0f0ad4ebfb6d95ee630b993ce22ed389fdcaa7504345d4b | Shell | 635 | 22 | #!/bin/bash
echo -e "\n========== Installing gptoolbox ==========\n"
if [[ -d "gptoolbox" ]]
then
echo "The directory 'gptoolbox' already exists. Remove it to reinstall."
else
git clone https://github.com/alecjacobson/gptoolbox.git
fi
echo -e "\n========== Installing vtkToolbox ==========\n"
if [[ -d "vtkToolbox" ]... |
d9c66a9f29b59e1d7e9a54f28d780135309b8ea84eaf2489ac599ac771a738fc | Shell | 639 | 18 | #!/bin/bash
#
RESULT=`cat top-metagenomics.csv \
| grep -a -e "JC polyomavirus" -e "JC_polyomavirus" -e "JC_virus" -e "JC virus" -e "olyomavirus_2 " -e "olyomavirus 2 " -e "olyomavirus_2|" -e "olyomavirus 2|" -e "JCPyV" -e "NC_001699" -e "NC001699" -e "MF662195.1" -e "MF662183.1" -e "MF662192.1" -e "MF662193.1" \
| gre... |
c15e679e615528f091cb3519b4c1af201bc061c817d9bb3b8d71991da9406310 | Shell | 640 | 21 | #!/bin/bash
release=release9
rootDir=/fslhome/mpeter55/fsl_groups/fslg_autism_asym/compute/HBN_Project
codeDir=${rootDir}/code/preproc
textDir=${rootDir}/code/preproc
dataDir=${rootDir}/data/reformat/${release}/t1
outDir=${rootDir}/preproc/${release}
var=`date +"%Y%m%d-%H%M%S"`
for subj in `cat ${textDir}/${release}_... |
6b63459da3b6a9f6519de66943aae570c036bc6c20d3b4abe3ea5701e4eff7bf | Shell | 641 | 32 | #!/bin/sh
set -x
#echo "Inserisci il nome dell'archivio FSDA da analizzare : "
#read what
what=$1
if [ ! -d "$what" ]
then
echo "ERRORE :" $what " non esiste !!!!"
exit 1
fi
/usr/bin/find $what -name "*.m" -not -name "examples_*" >lista_func
>func_without_examples.txt
echo -e "The following MATLAB... |
be1f94644a363008ffac1efbbc0ad3bc77f56f9e48c3d101f3969fa94a1740db | Shell | 646 | 20 | #!/bin/bash
#
# UPDATE =======================================================================
#
mkdir -p ../system_files/blast_dbs
mkdir -p ../system_files/blast_dbs/nt
cd ../system_files/blast_dbs/nt/
if [ ! -f nt.ndb ];
then
echo -e "\e[31mERROR: Unable to find nt blast database!\e[0m"
echo "TIP: before this,... |
30ce2ae65032a86049225cfaeb264abdefc82c9d1c9890c51cc5b50b297700d1 | Shell | 647 | 20 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "JC polyomavirus" -e "JC_polyomavirus" -e "JC_virus" -e "JC virus" -e "olyomavirus_2 " -e "olyomavirus 2 " -e "olyomavirus_2|" -e "olyomavirus 2|" -e "JCPyV" -e "NC_001699" -e "MF662195.1" -e "MF662183.1" -e "MF662192.1" -e "MF662193.1"... |
076d0e50ac61ceefac9493a1cb3f29d7358bf23d821fe5c2e4e9033d0d5f8444 | Shell | 652 | 20 | #!/bin/bash
#
index_f="../to_encrypt_data/index.txt";
echo -e "\e[34m[TRACESPipe]\e[32m Please, enter the password to encrypt the files contained in ../to_encrypt_data directory: \e[0m";
read -s password
echo "$password" > key.txt
for file in ../to_encrypt_data/*
do
if [[ "$file" == "$index_f" ]];
then
echo -e ... |
770d10b24c5a32d8a0a693784c4b39c947ec1e4a04593a7f29335e94ed32c1fb | Shell | 663 | 36 | #!/bin/zsh
# zsh script to check that necessary environment variables are set
# check for data root
if [[ ! -d $QC_DATA_ROOT ]]
then
echo "QC_DATA_ROOT not set or not a valid directory"
exit 1
fi
# check for code root
if [[ ! -d $QC_CODE_ROOT ]]
then
echo "QC_CODE_ROOT not set or not a valid directory"
... |
a239623d38f76c8c62fe3d5e4bae6b963d9c9e3167137f9de2e21ed5fc8f5244 | Shell | 665 | 31 | #!/bin/bash
# Job name:
#SBATCH --job-name=make_atlas
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=02:00:00
#
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
source $(pipe... |
d2647793d0c5e145484ef3cd3ad0ece5ae56e05cca4982c8ff8973d6545d6d84 | Shell | 667 | 10 | #!/bin/sh
java -cp `ls target/*-fatjar.jar` -Xms512M -Xmx192G -Dslf4j.internal.verbosity=WARN --add-modules jdk.incubator.vector --enable-native-access=ALL-UNNAMED "$@"
# 2>&1 | grep -v "WARNING: Using incubator modules"
# Notes:
# - "WARNING: Using incubator modules: jdk.incubator.vector" cannot be suppressed, so ju... |
21ac1236a46a44f4e85e878bec7e6185cc298b9ad0ffe62c0b6eee900cca5743 | Shell | 668 | 19 | #!/usr/bin/env bash
# Input python command to be submitted as a job
#SBATCH --array=0-40
#SBATCH --output=logs/searchlight-%j.out
#SBATCH --job-name searchlight
#SBATCH -p psych_week
#SBATCH --mem-per-cpu 16G -t 100:00:00 --mail-type ALL -n 12 -c 1 -N 1
# Set up the environment
module load miniconda
module load OpenM... |
8ca7393a2648462ed657f5c77fdf9a6f4a52daa9225ad960faf5833d7a992142 | Shell | 668 | 23 | #!/bin/bash
#
gto_fasta_extract_read_by_pattern -p "$2" < $1 > tmp_exists_or_not.fa
FIRST_LINE=`head -n 1 tmp_exists_or_not.fa`;
NUMBER_OF_LINES=`wc -l tmp_exists_or_not.fa |awk '{print $1;}'`;
if [ $NUMBER_OF_LINES -ge "2" ]
then
echo -e "\e[31mERROR: This sequence seems to already exist in the VDB.fa.\e[0m"
echo ... |
cc0aeeda265590085b5e46cef5321658a5a45ea8bade6be5c037476a3b351f4a | Shell | 668 | 25 | #!/bin/sh
# ENCODE
wget -r ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform
# rearrange
mv hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform encode
rm -r hgdownload.cse.ucsc.edu
# make sample-BED table
./make_encode_beds.py
# Roadmap
wget -r -A "*DNase.hotspot.... |
d894e68aebd33c9885e2a06f50af2fe787ecd94e23f7bc3590e7b1dd555ca086 | Shell | 674 | 21 | #!/bin/bash
# | grep -a -e "human" -e "Human" -e "omo sapiens" -e "omo_sapiens" \
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "_TT_virus" -e " TT virus" -e "anello" -e "Anello" -e " torque " -e " Torque " -e "_torque_" -e "_Torque_" -e "MN765195.1" -e "AB00A394" -e "AJ620212" -e "AB049607" -... |
ad4bb78b539ecb1710e6620fdd7d929015ac403b25ba281187739611c75253b8 | Shell | 681 | 16 | #!/bin/bash
# Template for setting up QC project environment
export QC_DATA_ROOT=/Volumes/NIMH_SFIM/handwekerd/Frontiers_QC_2022
export QC_CODE_ROOT=/Users/handwerkerd/code/nimh-sfim/SFIM_Frontiers_Neuroimaging_QC_Project/code/
export QC_FS_ROOT="${QC_DATA_ROOT}/freesurfer"
export SUBJECTS_DIR=$QC_FS_ROOT
export QC_C... |
4e22b672a96d60b0eb69be13874cbda18190e413dcf7556090a17a99bb237cf3 | Shell | 687 | 19 | #!/bin/sh
export LANG=C.UTF-8 LC_ALL=C.UTF-8
export PATH=/opt/conda/bin:$PATH
apt-get update --fix-missing && \
apt-get install -y wget bzip2 ca-certificates curl git && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~... |
2b76c14faa471a9192d58fe04459a3e59d3804a28384cbe4ea401330d01f48df | Shell | 694 | 11 | env CUDA_VISIBLE_DEVICES=0 python -u train.py --save_model tmp_model.ptbest --test --title --lp 1.0 --beam_size 1
if [ ! detokenizer.perl ]; then
wget https://raw.githubusercontent.com/moses-smt/mosesdecoder/8c5eaa1a122236bbf927bde4ec610906fea599e6/scripts/tokenizer/detokenizer.perl
fi
if [ ! multi-bleu.perl ]; t... |
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