sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
eca5dd6055cc3fd3b6234a19a7adbbd98c55da765e3f8f6117cebaa54cfa3c86 | Shell | 417 | 15 | #!/bin/bash
genDir=/fslgroup/fslg_spec_networks/compute
codeDir=${genDir}/code/HCPD_analysis/freesurfer
dataDir=${genDir}/data/HCPD_BIDS
for subj in `cat ${codeDir}/subjids.txt`; do
mkdir -p ${codeDir}/logfiles
sbatch \
-o ${codeDir}/logfiles/output_sub-${subj}.txt \
-e ${codeDir}/logfiles/err... |
fd3776101eaf4eb1cb21aea96f2c029aa42804ee7552cbe8e8be0eeed7be73a6 | Shell | 417 | 13 | #!/bin/bash
#SBATCH --time=00:40:00
#SBATCH --mem=10G
#SBATCH --array=1-96
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H5-fakecorr-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" nodes.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/... |
e421bfc39df610b4b61d2e777e610ffcd6bccab25e42f692e6ea8b5b0201155b | Shell | 418 | 17 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=5:00:00
Dmem=10G
threads=1
if [ $# -ne 1 ]
then
echo "Please, give these following inputs:"
echo "1) bam file"
exit
fi
inf=${1%.bam}
echo "python /hpc/hub_oudenaarden/aalemany/bin/mapandgo2/tablator_bwa.py $1" | qsub -V -cwd -N bwatab-${inf} -o bwatab-${inf}.ou... |
c7126fdd438c6d99ec3e5dffda78cd2b2c9d15cbb1a9e48130b544e273f8526e | Shell | 419 | 12 | #!/usr/bin/env bash
## install-spellcheck.sh: run during a CI build to install Pandoc spellcheck dependencies.
# Set options for extra caution & debugging
set -o errexit \
-o pipefail
sudo apt-get update --yes
sudo apt-get install --yes aspell aspell-en
wget --directory-prefix=build/pandoc/filters \
https://gi... |
3cbbb5b577b52f4eaddc32543bd11d600416ca80e17f5e45c3a0f9e908878cd6 | Shell | 421 | 15 | #!/bin/sh
juliapath=`which julia`
compiled_code="./SimplicialTS/Simplicial.so"
nthreads=$1
input_file=$2
output_file_scaffold=$3
output_file_triangles=$4
scaffold_flag=1 # Flag 1-> frequency, Flag 2 -> persistence
##Launching the code
time julia -J ${compiled_code} --threads ${nthreads} simplicial_multivariate.jl ... |
bab1350e509b8f251d00c2c8872e6922a041af57077e185e2e1f6bce245db821 | Shell | 422 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
./strc -in::pdb=test_inputs/4rm4.pdb -select::chains=A -out::pdb=4rm4A.pdb
./strc -in::pdb=test_inputs/5ofq.pdb -select::chains=A -out::pdb=5ofqA.pdb
echo -e "# Running ap_superimpose_pdb_by_ligand 4rm4A.pdb HEM 5ofqA.pdb"
./ap_superimpose_pdb_by_ligand 4rm... |
38cdca37cfbc4cc0fdc1101a203c39fee531674632df1bef6e43bfb06b5a0664 | Shell | 425 | 25 | function show_help {
echo "example usage: ./VCF_to_MS.sh CEU22"
echo "Options:"
echo " -h, --help Show this help message and exit"
echo ""
echo "Arguments:"
echo " chromosome number Example: CEU22"
echo ""
echo "Pipeline steps:"
echo " 1. Run VCF_MS.py to... |
b8dc1be91090dc5a06c619dd8b21e189eceb6498984ba5ab798edaab8b34272b | Shell | 425 | 12 | #!/bin/bash
#==================================================
# list NACCIDs in ADGC imputed using TOPMed panel
# (run in gazelle)
#==================================================
for i in {1..12}
do
file=$(ls /data_global/ADGC_GWAS/ADGC_NHW/ADC$i/RawGenotypes/ | egrep '.*.fam')
cat /data_global/ADGC_GWAS... |
d1f6fdd4934f065813c8b888be4a0e0971919f486455a2d717947b31595fa13d | Shell | 426 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 convert_msa.py test_inputs/1crn.hssp 1crn.aln"
python3 convert_msa.py test_inputs/1crn.hssp 1crn.fasta
echo -e "#Running python3 convert_msa.py CYP109B1.aln CYP109B1.fasta"
python3 convert_msa.p... |
78dbfa7532a61059940fb4f43dca5344485df7e87e66fd9e81445e56236677f2 | Shell | 428 | 13 | #!/bin/bash -xe
apt-get install -y ${HIVE_PACKAGE} ${HIVE_PACKAGE}-server2
STANDALONE_JAR=$(find $HIVE_HOME/lib | grep 'jdbc-standalone' | tr '\n' ':' )
if [ "" = "$STANDALONE_JAR" ]
then
find $HIVE_HOME/lib | grep '.jar' | \
grep -E 'hive-jdbc|hive-common|hive-exec|hive-service|hive-metastore|libfb303|li... |
03e298e75d390a1fc2feee28c8257243efe24201bf6fa88cdb1c0724fbd06793 | Shell | 429 | 16 | #!/bin/sh
set -eu
ROOT=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
cd "$ROOT"
if [ -x "$HOME/.pixi/bin/pixi" ]; then
PIXI="$HOME/.pixi/bin/pixi"
elif command -v pixi >/dev/null 2>&1; then
PIXI="$(command -v pixi)"
else
curl -fsSL https://pixi.sh/install.sh | sh
PIXI="$HOME/.pixi/bin/pixi"
fi
"$PIXI" in... |
1cc28b25b2af51b93cfab84e995c04f8edb19d70889b3db7bb12274b3c1145ae | Shell | 429 | 18 | #!/bin/bash
INPUT="2gb1A"
./surpass -verbose=FINER \
-in:pdb=test_inputs/$INPUT.pdb \
-in:ss2=test_inputs/$INPUT.ss2 \
-sample:replicas:observation_mode=1 \
-sample:t_start=1.2 \
-sample:mc_outer_cycles=1000 \
-sample:mc_inner_cycles=100 \
-sample:mc_cycle_factor=1 \
-sample:perturb:range=0.7 \
-out:pdb:min_... |
91c146d7b72529156a6191f76805bf5563c1a29c16bfb5e6b55649623cd9c451 | Shell | 429 | 18 | #!/bin/bash
#SBATCH --job-name="GER_D1"
#SBATCH -D .
#SBATCH --output="output_amr/german_dip1_1.out"
#SBATCH --error="output_amr/german_dip1_1.err"
#SBATCH --ntasks=1
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module loa... |
10247d019a76b382e9311ba0ae2f8c6ea9fd9cd49a9b22301ea696e3a8a2e21d | Shell | 430 | 20 | #!/bin/bash
#SBATCH --job-name="SW_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/swiss_%a.out"
#SBATCH --error="output_amr/swiss_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matlab... |
6fce852442048b2f25316940d1e2fa5ce6e703616e492b1b1c66776dc5c36e88 | Shell | 432 | 24 |
source config.sh
source samples.sh
for i in ${SAMPLES[$(($LSB_JOBINDEX - 1))]};
do
$bbduk -Xmx7g t=4 \
in1=fastq/${i}_L003_R1_001.fastq.gz \
in2=fastq/${i}_L003_R2_001.fastq.gz \
out1=fastq/trim/${i}_R1trim.fastq.gz \
out2=fastq/trim/${i}_R2trim.fastq.gz \
ref=$bbadapters \
ktrim=r \
... |
7463f33823cfa7076f64977161bb6ce9571d9340a22bff133d4ec4f698e9151b | Shell | 432 | 3 | #! /usr/bin/env bash
ELEPHANT_PROFILE= kernprof -l -v -o ~/train.py.lprof /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_profile_seg.json seg /opt/elephant/script/train_configs/profile_seg.json
# ELEPHANT_PROFILE= python -m memory_profiler /opt/elephant/script/train.py --baseconfig /... |
102251bd13c1560fc3c58b6e47d69b1cc8aab70437029c5d0e4f2e165ca710d6 | Shell | 433 | 13 | for dataset in test train dev
do
wget https://raw.githubusercontent.com/jiangfeng1124/ChemRxnExtractor/main/tests/data/role/$dataset.txt
done
cat train.txt dev.txt test.txt > role.txt
rm train.txt dev.txt test.txt
for dataset in test train dev
do
wget https://raw.githubusercontent.com/jiangfeng1124/ChemRxnExtracto... |
3779393744990a79210775b73899a9fcbc2f6e867617cfef28399627c3e3ef8b | Shell | 433 | 21 | #!/bin/bash
maindir='ATACseq'
datadir=$maindir/DiffBind
outdir=$maindir/motifanalysis_HOMER
mkdir $outdir
samplenames='' # add sample names for comparisons of interest
# run motif analysis for sites with increased accessibility
for s in $samplenames
do
outdir=$maindir/${s}_inc_FDR005_sizegiven
mkdir $outdir... |
2e4680564b1d1f693dc5e72cc983f15313e1301c4573d55acfa92ebaafb402d2 | Shell | 434 | 20 | #!/bin/bash
#SBATCH --job-name="SET_DIPO"
#SBATCH -D .
#SBATCH --output="output_dipoles/set_dipoles_%a.out"
#SBATCH --error="output_dipoles/set_dipoles_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module pu... |
4ee38a70ebf218d5dc69074de42b470b25580f573a7092e3d043d3b3d020997a | Shell | 434 | 26 |
source config.sh
source samples.sh
for i in ${SAMPLES[$(($LSB_JOBINDEX - 1))]};
do
$bbduk -Xmx7g t=4 \
in1=fastq/${i}_L003_R1_001.fastq.gz \
in2=fastq/${i}_L003_R2_001.fastq.gz \
out1=fastq/trim/${i}_R1trim.fastq.gz \
out2=fastq/trim/${i}_R2trim.fastq.gz \
ref=$bbadapters \
ktrim=r \
... |
d644e9eadb05b85965af287b385263c5ad3cc3ea9f848df06f0ca431cc8d857c | Shell | 434 | 20 | #!/bin/bash
#SBATCH --job-name="GH_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/german_%a.out"
#SBATCH --error="output_amr/german_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matl... |
ee43581fd706526ae5c0b37b07762a9f3b2e3660ee04bf51c62719b09cba4095 | Shell | 435 | 20 | #!/bin/bash
#SBATCH --job-name="SW_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/swiss_%a.out"
#SBATCH --error="output_bem/swiss_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matlab... |
15de05e784e6082515b29ec7a4d152f1baad78fe8ad1d03b7dd15f7eb213b509 | Shell | 438 | 17 | #!/bin/bash -l
sudo pip3 install silence_tensorflow
sudo pip3 install tensorflow-addons
sudo pip3 install matplotlib==3.4.3
sudo pip3 install pandas
sudo pip3 install dm-sonnet==2.0.0
sudo pip3 install tensorflow-probability
sudo pip3 install seaborn
sudo pip3 install einops
sudo pip3 install tqdm
sudo pip3 install sc... |
68370553057c2414d80db06010e19424a7e06a515132199d4e3023f9bca58693 | Shell | 438 | 20 | #!/bin/bash
#SBATCH --job-name="SN_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/SimNIBS_%a.out"
#SBATCH --error="output_amr/SimNIBS_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load ma... |
5633828b62c13d32aa5f38df1ce65b3f202146dd9579a3a77f0dec56f93f8bc8 | Shell | 439 | 20 | #!/bin/bash
#SBATCH --job-name="GE_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/german_%a.out"
#SBATCH --error="output_bem/german_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matl... |
11c74a748e1ab5ea941efe60e8812cbccffff7d2fbf23bf068ad6bc7b0229fd8 | Shell | 440 | 14 | #!/bin/sh
DATADIR=/Users/ctsu0221/data/asl/fsl_course/
#DEBUG=--debug
oxasl -i ${DATADIR}/mpld_asltc --casl --iaf=tc --ibf=tis --slicedt=0.0452 \
--tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 \
--fslanat=${DATADIR}/T1.anat --senscorr \
-c ${DATADIR}/aslcalib --tr=4.8 --cmethod=voxel \
--cblip=$... |
e3cc3e73282465dd7c6a4e9088025cf3211a465ba09f7ccb8089071deed85291 | Shell | 440 | 17 | #!/bin/bash
pot='data/pot.tab'
tname='ucrispr'
cp $pot /usr/local/tool/uCRISPR/data/
cd /usr/local/tool/uCRISPR
awk 'BEGIN{FS="\t";OFS=" "}NR>1{print $2,$3}' data/pot.tab > data/$tname.dat
./uCRISPR -off ./data/$tname.dat > data/$tname.out
#awk 'NR==FNR{a[i]=$0;i++}NR>FNR{print a[j]"\t"$3;j++}' data/pot.tab data/$... |
444e84ef11e5c27ca8fe7f82be4e4e2510761f4197ace307298e7a9176dcb6e4 | Shell | 441 | 20 | #!/usr/bin/env bash
set -euo pipefail
DT=$(date +"%Y-%m-%d_%T")
DEST_DIR=archived_logs
echo "Adding current datatime as a tag: $DT"
mkdir -p $DEST_DIR
for dir in logs cluster_logs benchmarks .snakemake; do
archive=${DEST_DIR}/${DT}_${dir}.tar.gz
if [ -d "$dir" ]; then
echo "Compressing $dir into $archive"
... |
64bbd6c110b9b5f43ebef9c6d6de1a54fc1d09975ae84af50c4460f75beadd03 | Shell | 441 | 9 | a=0;
for n in task-movie_SGdetrend_24HMP-8Phys-4GSR-Spike_HPF_smooth-6mm.nii task-movie_SGdetrend_24HMP-8Phys-Spike_HPF.nii task-movie_SGdetrend_24HMP-8Phys-4GSR-Spike_HPF.nii task-movie_SGdetrend_24HMP-8Phys-Spike_HPF_smooth-6mm.nii; do
echo $n
echo "subjs={" > "subjects"$a".m"
find /m/cs/scratch/networks-pm/pm... |
69287a8b7e7da9dee859db26dfca30f61e26ea45983b66cffe4a78b027d35784 | Shell | 441 | 54 | #!/bin/bash
# Author-Chaitanya Goswami
# Contact - cgoswami@andrew.cmu.edu
pip install -r requirements.txt #Installing Required Packages
nrnivmodl mechanisms #Compiling required Mechanisms for NEURON
... |
0a85498d0179e21115b5d939d503714fad49f0187759f96756a5c0cc3d3ea639 | Shell | 442 | 10 | # Kill user space driver program first if it happens to be running, because otherwise shutting down the kernel
# module would crash the system if the userland program was still accessing it.
echo Killing existing instances of user space driver program fbcp-ili9341
sudo pkill fbcp-ili9341
sudo pkill fbcp-ili9341-stable
... |
860e29d84fadef4ecfddf7dc670db780f9fc2e026b5563f701ddc57ee2ba76cc | Shell | 442 | 20 | #!/bin/bash
#SBATCH --job-name="SWISS_AMR"
#SBATCH -D .
#SBATCH --output="output_3shell/swiss_%a.out"
#SBATCH --error="output_3shell/swiss_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module lo... |
b42080484b85c85b96c27259570145a97628d175ec3b56bfc5d0c936311ace22 | Shell | 442 | 13 | #!/bin/bash
#inspired from https://www.biostars.org/p/61081/
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt
head -5000 assembly_summary.txt | awk -F '\t' '{if($12=="Complete Genome") print $20}' > assembly_summary_complete_genomes.txt
mkdir tmpbac
for next in $(cat assembly_summary_com... |
a9c60b3651df6f233e753cec9847b0e7006f3558899048280634b855c99e6554 | Shell | 443 | 20 | #!/bin/bash
#SBATCH --job-name="GER_3S"
#SBATCH -D .
#SBATCH --output="output_3shell/german_%a.out"
#SBATCH --error="output_3shell/german_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module loa... |
adcf6872cd53cc0267ec93d7a66afa30034e5dbc35f7741325b985b8e207936f | Shell | 443 | 20 | #!/bin/bash
#SBATCH --job-name="SN_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/SimNIBS_%a.out"
#SBATCH --error="output_bem/SimNIBS_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load ma... |
46e96b7fea2be0bafa1b968aa5118d44c15f7b38f6d3dd30cafa92e715bc24a2 | Shell | 444 | 13 | #!/bin/bash
julia -e 'Pkg.clone(pwd())'
julia -e 'Pkg.build("Agglomeration")'
if [ -f test/runtests.jl ]; then
julia --check-bounds=yes -e 'Pkg.test("Agglomeration", coverage=false)'
fi
#That warning occurs when inlining is turned off.
#Pkg.test turns off inlining when called with `coverage=true`.
#This is so the c... |
527ccacb927cbfb9f36598306adafc9c3ecd4d022ef7f2745d501486e15af17f | Shell | 444 | 20 | #!/bin/bash
#SBATCH --job-name="SW_HR"
#SBATCH -D .
#SBATCH --output="output_amr/swiss_hr_%a.out"
#SBATCH --error="output_amr/swiss_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load m... |
60c425617d51acef0458ebcbac048a81c45fd1111b46847f1d14aa333e03830d | Shell | 445 | 18 | #!/bin/bash
# File: run_combine_results.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to combine AP simulation results.
#
# combine fixed-input simulation results
Rscript combine_results.R
# combine uncertainty-input simulation results
Rscript comb... |
0250f827e2410e5738fb5dd4822cb512787db4d7e06a90d58aa8a65f3d6f63dc | Shell | 446 | 11 | #!/bin/bash
#
# This script will extract CHR, POS and rsID
# columns from .clumped files.
##############################
# PATHS
inDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/plink/"
##############################
awk -v OFS='\t' '{print $1, $4, $3}' ${inDir}GenomicSEM_multivarGWAS_CPM_dys_rhyimp_... |
0ad588598d359f2bb3d8d4e92337793490101149043edbd6641e2436db4e551b | Shell | 447 | 21 | #!/bin/bash
# test Open Babel with CML, if the CML test suite exists
builddir=`pwd`
export builddir
if `env | grep ^srcdir > /dev/null 2>&1`; then
cmltestdir=$srcdir/cmltest
else
srcdir=`pwd`
export srcdir
cmltestdir=./cmltest
export cmltestdir
fi
echo
echo "# Testing CML support..."
if [ -f $cmltestdi... |
147118a0062fa9f3da5f2751bd5ec70257d44ab817fb5c82b6dd881e6a77de7d | Shell | 447 | 20 | #!/bin/bash
#SBATCH --job-name="SN_AMR"
#SBATCH -D .
#SBATCH --output="output_3shell/SimNIBS_%a.out"
#SBATCH --error="output_3shell/SimNIBS_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module l... |
88532ba0386d5c744dc4705ae7d9d7d01c5f89b6ca34a8520fa37600f5aaea8e | Shell | 447 | 18 | #!/bin/bash
#SBATCH --time=2-23:00:00
#SBATCH --mail-type=ALL
#SBATCH --cpus-per-task=1
#SBATCH --partition=ga100
#SBATCH --mem=200G
#SBATCH --gres=gpu:1
#SBATCH --output=slurm-nucleus2-%j.out
# submit as sbatch run_nucleus.sh
ml foss
ml Anaconda3
source nucleus-2/bin/activate
unset XDG_RUNTIME_DIR; python -m jupyt... |
ca952cde6e2ea401b85ce12f8e05b9a41f0c4208f40d1f1b7da085111accc432 | Shell | 447 | 20 | #!/bin/bash
#SBATCH --job-name="SN_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/SimNIBS_%a.out"
#SBATCH --error="output_bem/SimNIBS_%a.err"
#SBATCH --array=4,5,8,10
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module loa... |
da4bf754e63cfed84dc01979b2d931f3bb9f4778b69af46819dde341383aef29 | Shell | 447 | 16 | #!/usr/bin/env bash
set -euo pipefail
PREFIX=${MINIFORGE_PREFIX:-$HOME/miniforge3}
wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O /tmp/miniforge.sh
if [[ -d "$PREFIX" ]]; then
bash /tmp/miniforge.sh -b -u -p "$PREFIX"
else
bash /tmp/miniforge.sh -b -p "$PRE... |
859f40afa67b3fcfdc34a07630d341bb1b7db174eca4f689c28ea41afbf920b5 | Shell | 450 | 16 | #!/bin/bash
#SBATCH --export=run=$run,tag=$tag
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=8G
#SBATCH --time=48:00:00
#SBATCH --mincpus=8
#SBATCH --output=logs/%j.tracking.%x.out
echo $run
echo $tag
#echo "track_v100.sh"
cd /scratch/n.tan/extended-event-modeling/
source activate pt-37
python src/tracking/tracki... |
e72f0607b2b75aae091fa7539626fb80197880b7e408757dd63f3edb76bf1dbf | Shell | 450 | 20 | #!/bin/bash
#SBATCH --job-name="GER_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/german_hr_%a.out"
#SBATCH --error="output_amr/german_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module lo... |
bec1eef516926780335ad1465e88bea48e1758a9b3b892990788ef528a628cf9 | Shell | 451 | 20 | #!/bin/bash
#SBATCH --job-name="SWH_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/swiss_hr_%a.out"
#SBATCH --error="output_bem/swiss_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load... |
08ba13bdbf41b8b497bad320a7c56588787ad346a3129a656d3aac6429aedf97 | Shell | 452 | 9 | #!/bin/sh
RES_DIR_ML="/home/webermau/rey-figure/lukas-final/final-aug_01/rey-multilabel-classifier/"
RES_DIR_REG="/home/webermau/rey-figure/lukas-final/final-reg_01/rey-regressor-v2"
for contrast in $(seq 0.1 0.1 2.0); do
python eval_multilabel_semantic.py --results-dir $RES_DIR_ML --transform "contrast" --contrast... |
c839d3681054ec4a053b77803520f2f5dedb588dedbf254368a0df567c6bdeca | Shell | 452 | 15 | #!/bin/bash
genDir=/fslgroup/fslg_spec_networks/compute
codeDir=${genDir}/code/HCP_analysis/freesurfer
dataDir=/fslgroup/grp_proc/compute/HCP_analysis/HCP_download
for subj in `cat ${codeDir}/subjids/subjids.txt`; do
mkdir -p ${codeDir}/logfiles
sbatch \
-o ${codeDir}/logfiles/output_sub-${subj}.txt \... |
1acb57818a27037026c06e347b4b26c5ed239ca479e7b78eab1d035f82ade22f | Shell | 453 | 20 | #!/bin/bash
#SBATCH --job-name="SH_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/SimNIBS_hr_%a.out"
#SBATCH --error="output_amr/SimNIBS_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module l... |
88737cb9c5acfc12c05f75c1ee9262ce93d6511efb4ba21480364a4ed80402d9 | Shell | 453 | 15 | #!/bin/bash
genDir=/fslgroup/fslg_spec_networks/compute
codeDir=${genDir}/code/NSD_analysis/freesurfer
dataDir=/fslgroup/fslg_fun_conn/compute/NSD_analysis/NSD_BIDS
for subj in `cat ${codeDir}/subjids/subjids.txt`; do
mkdir -p ${codeDir}/logfiles
sbatch \
-o ${codeDir}/logfiles/output_sub-${subj}.txt ... |
a0af86f41d7c0234830413f899aabd8efc0435b8ae4ea86ba7437a07638e5b54 | Shell | 453 | 15 | #!/bin/sh
#ffmpeg2gif input.mp4 output.gif "fps=15,scale=1920"
#copied from https://cassidy.codes/blog/2017/04/25/ffmpeg-frames-to-gif-optimization/
palette="/tmp/palette.png"
#filters="fps=15,scale=320:-1:flags=lanczos"
filters="$3:flags=lanczos"
echo $filters
ffmpeg -v warning -i $1 -vf "$filters,palettegen=stat... |
f93c8692dff2f916197d8f9eb47c1e2a2d6bc2fc38d0304d0e756634ff5cb13b | Shell | 453 | 19 | viewpoint=V1O2
for viewpoint in train1_80k
do
python3 ../train_ae.py \
--max_epochs 100 \
--batch_size 128 \
--data_dir /data/lpandey/UT_Austin_EgocentricDataset/output_64x64Squished/${viewpoint} \
--seed_val 10 \
--dataset_size 10000 \
--enc_type resnet18 \
... |
31a5b07d1cbc87146c695e9ec3e8113e532ebb7d56e15da90f6c640039098a6d | Shell | 455 | 15 | #!/bin/bash
##--------------------------------------------
## make .raw file for top snps for brant test
##--------------------------------------------
# clump top snps
cat output/nacc/ordinal_results.txt | awk '{print$2,$7}' | awk '{if (NR == 1) print "SNP P"; else print $0}' > data/tmp/ordinal_results.tmp
plink \
... |
a8b5e539bb0ec98b2d319f38596776dfc3db034b458900d365b5415e95a3d329 | Shell | 455 | 20 | #!/bin/bash
#SBATCH --job-name="GEH_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/german_hr_%a.out"
#SBATCH --error="output_bem/german_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module lo... |
c107ce9c1309ee379c9e1b8b248c22e6b85ca84a0e6fbbb68c690d6fe6071e5c | Shell | 455 | 23 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=20:00:00
#SBATCH --job-name=nbds
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/nbds_connectomes
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=("Celegans_nbds.json"
"Drosophila_nbds.json"
"MICrONS_... |
c2c872b19a40efbde3c624f7210ba04623073a37d7e883a99ea8203b97d95a5d | Shell | 455 | 20 | #!/bin/bash
#SBATCH --job-name="SWISS3_AMR"
#SBATCH -D .
#SBATCH --output="output_3shell/swiss_amr_%a.out"
#SBATCH --error="output_3shell/swiss_amr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
... |
0994ed91f4e265a7c746d3fc8a91be7af36aa5e0e3827a2e154164a14d54af71 | Shell | 456 | 19 | viewpoint=V1O1
for viewpoint in train1_80k
do
python3 ../train_vae.py \
--max_epochs 100 \
--batch_size 128 \
--data_dir /data/lpandey/UT_Austin_EgocentricDataset/output_64x64Squished/${viewpoint} \
--seed_val 0 \
--dataset_size 80000 \
--enc_type resnet18_2b \
... |
743a888c080e549ca1921aa75fff546813154e8d19a3a0f0fcae5111d81d506f | Shell | 456 | 14 | #!/bin/sh
DATADIR=/Users/ctsu0221/data/asl/fsl_course/
#DEBUG=--debug
oxasl -i ${DATADIR}/mpld_asltc --casl --iaf=tc --ibf=tis --slicedt=0.0452 \
--tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 \
--fslanat=${DATADIR}/T1.anat --senscorr \
-c ${DATADIR}/aslcalib --tr=4.8 --cmethod=single --csf=${DATADIR}... |
8ccc25941f179766ce147c04d5fa5643f1079c1d06af5f3c42536c73fb6cb34a | Shell | 457 | 20 | #!/bin/bash
#SBATCH --job-name="GER_3AMR"
#SBATCH -D .
#SBATCH --output="output_3shell/german_amr_%a.out"
#SBATCH --error="output_3shell/german_amr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
... |
8fdfd2ac3b0a9ce76eb6ac475511e0bdae79464316d1cc460b51893586475eb1 | Shell | 457 | 16 | #!/bin/sh
juliapath=`which julia`
compiled_code="./SimplicialTS/Simplicial.so"
nthreads=$1
input_file=$2
output_file_scaffold=$3
output_file_triangles=$4
output_HOindicators=$5
scaffold_flag=1 # Flag 1-> frequency, Flag 2 -> persistence
##Launching the code
time julia -J ${compiled_code} --threads ${nthreads} simp... |
862c8d29d284e8218234153ede5ff509198ea7ff7a3807269168fd014b29657e | Shell | 458 | 22 | #!/bin/bash
#SBATCH --partition cpu_short,cpu_medium,cpu_long
#SBATCH --mem=4G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --array=1-90
#SBATCH -t 00-12:00:00
#SBATCH --job-name=SimTrainingData
#SBATCH --mail-type=FAIL
export JULIA_BIN=/gpfs/scratch/asslaj01/julia-1.10.0/bin/julia
set -Eeo ... |
5e5b5ab47a71f76444f0bc432595a9269740e3ce045736924aa126091e22a2d6 | Shell | 459 | 19 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=02:00:00
Dmem=5G
threads=1
if [ $# -ne 2 ]
then
echo "Please, give these following inputs:"
echo "1) input bam file"
echo "2) output bed file"
exit
fi
input==$1
output=$2
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/bam2bed.sh $1 $2" | qsub -cwd -N ${o... |
81e6f2751168470bcce33ea285a47c7c27a33cd5e022fe3a899aa3c85bdd3986 | Shell | 459 | 20 | #!/bin/bash
#SBATCH --job-name="SNH_BEM"
#SBATCH -D .
#SBATCH --output="output_bem/SimNIBS_hr_%a.out"
#SBATCH --error="output_bem/SimNIBS_hr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module ... |
b3d2d0adf96dd0dcb75559d77a036122aca64fc83b26ff132719d5a47054d9e5 | Shell | 459 | 20 | #!/bin/bash
#SBATCH --job-name="SN_AMR"
#SBATCH -D .
#SBATCH --output="output_3shell/SimNIBS_amr_%a.out"
#SBATCH --error="output_3shell/SimNIBS_amr_%a.err"
#SBATCH --array=1-15
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
... |
772270bb3069219f654a6ee428e36542632ec96f1b3725df829e0aa414bea060 | Shell | 460 | 9 | #!/bin/sh
RES_DIR_ML="/home/webermau/rey-figure/lukas-final/final-aug_01/rey-multilabel-classifier/"
RES_DIR_REG="/home/webermau/rey-figure/lukas-final/final-reg_01/rey-regressor-v2"
for brightness in $(seq 0.1 0.1 2.0); do
python eval_multilabel_semantic.py --results-dir $RES_DIR_ML --transform "brightness" --brig... |
a874fdf703847cc56e88d7bb395eeb94b46b32b548d16ca9006f1a804de8c831 | Shell | 460 | 8 | mkdir -p Datasets/TUM_RGBD
cd Datasets/TUM_RGBD
wget https://vision.in.tum.de/rgbd/dataset/freiburg1/rgbd_dataset_freiburg1_desk.tgz
tar -xvzf rgbd_dataset_freiburg1_desk.tgz
wget https://vision.in.tum.de/rgbd/dataset/freiburg2/rgbd_dataset_freiburg2_xyz.tgz
tar -xvzf rgbd_dataset_freiburg2_xyz.tgz
wget https://vision.... |
334309b2b3ece3cc0ebe5eef3d53d6e48130964dfc380291eafe107cec575eee | Shell | 461 | 21 | #!/bin/bash
#AWS_SSH_PRIVATE_KEY_FILE=''
echo $AWS_SSH_PRIVATE_KEY_FILE
set -e
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
i=0
for publicDnsName in $(cat nodes-public)
do
i=$((i+1))
echo Starting on node ${i}: ${publicDn... |
83776f83720381ccdad067a79c99ab5e9df7c1da9a591fc559726eafdc26be07 | Shell | 462 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./ligand_contacts.py HEM 3.5 test_inputs/5ofq.pdb test_inputs/4rm4.pdb"
python3 ligand_contacts.py HEM 3.5 test_inputs/5ofq.pdb test_inputs/4rm4.pdb
echo -e "#Running python3 ligand_contacts.py... |
dc253b035287cceb6a6ecdd776579f41365602f3ee309c0f53e9d522030c3936 | Shell | 462 | 21 | #!/bin/bash
echo "Running through scripts to set up EC2 + H2O..."
echo
set -e
echo "Setting up cluster instances..."
echo
./h2o-cluster-launch-instances.py
echo "Getting latest stable build of H2O and disitributing across instances..."
echo
./h2o-cluster-download-h2o.sh
echo "Distributing AWS Credentials... |
823007c5bc8454dba971f401749986333163e84d4aa87c483ffdc707dad11551 | Shell | 463 | 8 | #!/bin/bash
wget https://www.hamamatsu.com/content/dam/hamamatsu-photonics/sites/static/sys/dcam-api-for-linux/tar-gz/DCAM-API_Lite_for_Linux_v24.4.6764.tar.gz
tar -xvf DCAM-API_Lite_for_Linux_v24.4.6764.tar.gz
ln -s ~/Desktop/octopi-research/software/drivers\ and\ libraries/hamamatsu/DCAM-API_Lite_for_Linux_v24.4.6764... |
c3aead3c09b1d67672d5228fbd8f709effd9849fbca7e626bc0c85d8350bd4d7 | Shell | 463 | 21 | #! /bin/sh
########## Path
# top level folder of ABCD dataset
ABCD_DIR=/mnt/isilon/CSC2/Yeolab/Data/ABCD
# folder of ABCD tabular data
ABCD_table_dir=${ABCD_DIR}/raw/documents/release2.0/ABCDstudyNDA
# folder of t1 imaging data
t1_data_dir=${ABCD_DIR}/raw/images
# folder of rest fMRI data
rs_data_dir=${ABCD_DIR}/ra... |
620dca2e65f2fb105142c268eaddd851a5d9e083aa922ee1347d31743d6c85b8 | Shell | 464 | 24 | #!/bin/bash
sudo apt-get install libudev1
sudo apt-get install libudev-dev
chmod 777 sdk/install.sh
cd sdk
folder="/etc/tucam/"
if [ ! -d "$folder" ]; then
mkdir "$folder"
fi
# copy the tucsen usb camera config file
cp tuusb.conf /etc/tucam
cp 50-tuusb.rules /etc/udev/rules.d
# copy the tucsen camera libraries
cp... |
1f08d2c3c284766b7cc6a2fbf74379b79ab909cfc2d5a2e21b22b807b6541c94 | Shell | 465 | 21 | #!/usr/bin/env bash
# Halt on error
set -e
NUM_ITER=1000
SEED=42000
OUTDIR="./results_ll_num_layers_effect"
# Iterate over different seeds here
for LEXP in data/LearningExp_*.txt; do
for NUM_LAYERS in 3 2 1; do
echo "Learning experiment: $LEXP";
python3 train.py "$LEXP" --seed "$SEED" --project "language-lea... |
e3553b61f7125e65132ef4f108704412e7cbf15971333ee5de909412ec6e5fd6 | Shell | 465 | 19 | #!/bin/bash
#SBATCH --job-name="SN_SINGLE"
#SBATCH -D .
#SBATCH --output="output_amr/SimNIBS_%a.out"
#SBATCH --error="output_amr/SimNIBS_%a.err"
#SBATCH --exclude=compute-3-01
#SBATCH --array=1,3,4,[6-8]
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=20
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=... |
d5dc97ad683bad73aa6e1620a8ce1604b70deecc9d6272c80e1673f2c28886f6 | Shell | 466 | 16 | #!/bin/bash
indexdir='indexes'
maindir=''
bwdir=$maindir/bigwig
conditions='d2_ESC d3_ESC d3_WT05 d3_SA01 d3_SA05'
for cond in ${conditions[@]}
do
echo ${cond}
wiggletools mean $bwdir/${cond}_*_RPGC.bw > $bwdir/${cond}_RPGC.bedgraph
LC_COLLATE=C sort -k1,1 -k2,2n $bwdir/${cond}_RPGC.bedgraph > $bwdir/${c... |
50f862009850b8469091ec13de164828e0162234dd68ef86fceb1c9cb59f86d7 | Shell | 467 | 23 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=12:00:00
#SBATCH --job-name=complexity_network
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/complexity_analysis
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
run_files=("complexity_Drosophila.py"
"comple... |
aa9a01a092b27fe28ae6ac4dcd90bbb2570b9763a75cbd45c482d940e0b6cfb1 | Shell | 467 | 13 | #!/bin/bash
#==================================================
# list IIDs in ADGC imputed using TOPMed panel
# (run in gazelle)
#==================================================
rm data/act/act_ids_adgc.txt
for i in {1..3}
do
file=$(ls /data_global/ADGC_GWAS/ADGC_NHW/ACT$i/CleanedGenotypes/ | egrep '.*.fam')
... |
33bb3a09bf9fac5bae71167e3fc5ecd4fc8a53bf3a8a46fcb32bee4ec52120b2 | Shell | 468 | 15 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ap_AAHydrophobicity test_inputs/2gb1.pdb"
./ap_AAHydrophobicity test_inputs/2gb1.pdb
mv out.pdb outputs_from_test/2gb1.out.pdb
echo "# Running ./ap_AAHydrophobicity test_inputs/4rm4.pdb test_inputs/CYP109B1.a... |
4bd24809547e47a2e3a23fcf1bada45ad2b43776893982cf97d00c1a63d55995 | Shell | 468 | 9 | #!/bin/sh
RES_DIR_ML="/home/webermau/rey-figure/lukas-final/final-aug_01/rey-multilabel-classifier/"
RES_DIR_REG="/home/webermau/rey-figure/lukas-final/final-reg_01/rey-regressor-v2"
for distortion in $(seq 0.1 0.1 1.0); do
python eval_multilabel_semantic.py --results-dir $RES_DIR_ML --transform "perspective" --dis... |
6e68a697899f07079a643869bceaa932319d98ab24396776bcd73413e428a9d3 | Shell | 468 | 9 | #!/bin/bash
# date: Jun 9, 2023
# by: zeliha gozde turan
# https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1644019928_nHYZhj3FL1O1CcJEOpzanexUpnm7&clade=mammal&org=Human&db=hs1&hgta_group=allTracks&hgta_track=hub_3671779_hgUnique&hgta_table=0&hgta_regionType=genome&position=chr9%3A145%2C458%2C455-145%2C495%2C201&hgta_... |
a24f593aa97468a5341b5997f7286e4c765733b271a3f5f43ab44b9d2391e885 | Shell | 468 | 23 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=5:00:00
#SBATCH --job-name=rc_den
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/rc_den
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=(#"rc_den_Celegans.json"
#"rc_den_Drosophila.json"
#"rc_den_MIC... |
d7a52ea5bca5c4b609299d756ab5a1f8dc4e2ae14e88dd778980d11db6a69ecc | Shell | 468 | 19 | #!/bin/bash
# 1. receive essential arguments from dag input
outdir_home=$1
indir_staging=$2
job=$3
# 2. set paths
outdir_condor=$outdir_home/$job
in_tarball=$indir_staging/all_samples_bam.tar.gz
# 3. mkdir for receiving output (log files) from HTCondor at home directories
mkdir -p $outdir_condor
# 4. tar bam files ... |
3ac2c2ffc1b0c34c8b56705b9280c6b596d7c3c67193960935089b1fe415dc0e | Shell | 469 | 14 | #!/bin/sh
DATADIR=/Users/ctsu0221/data/asl/fsl_course/
#DEBUG=--debug
oxasl -i ${DATADIR}/mpld_asltc --casl --iaf=tc --ibf=tis --slicedt=0.0452 \
--tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 \
--fslanat=${DATADIR}/T1.anat --senscorr \
-c ${DATADIR}/aslcalib --tr=4.8 --cmethod=single --csf=${DATADIR}... |
67915b0c03b126366b85830f257b6317be8f52442341f0798a0d09e71c07a943 | Shell | 470 | 21 | #! /bin/sh
########## Path
# folder of ABCD tabular data
ABCD_table_dir=${ABCD_DIR}/raw/documents/release2.0/ABCDstudyNDA
# folder of t1 imaging data
t1_data_dir=${ABCD_DIR}/raw/images
# folder of rest fMRI data
rs_data_dir=${ABCD_DIR}/raw/images
# folder of task fMRI data
task_data_dir=${ABCD_DIR}/raw/images
# re... |
7ff74d09cd60bebe1848357d112da145b1e068450ed712ac075c25e4a1f35567 | Shell | 471 | 21 | #!/bin/bash
out=$'/console.out'
ckpt_dir=$'./checkpoints/'
date=$(date +%y-%m-%d-%H-%M)
nohup \
python train_regressor.py \
--arch v2 \
--workers 10 \
--id final-reg \
--data-root ./data/serialized-data/data_232x300-seed_1 \
--results-dir ./results \
--eval-test \
--epochs 40 \
--ba... |
b04d67e486e5289d129d40e0fc4d17b1eaebef0e50fa9a1d7b128a60fc64d079 | Shell | 474 | 21 | #! /bin/sh
########## Path
# folder of ABCD tabular data
ABCD_table_dir=${ABCD_DIR}/raw/documents/release2.0/ABCDstudyNDA
# folder of t1 imaging data
t1_data_dir=${ABCD_DIR}/raw/images
# folder of rest fMRI data
rs_data_dir=${ABCD_DIR}/raw/images
# folder of task fMRI data
task_data_dir=${ABCD_DIR}/raw/images
# re... |
8cd931952000cbb20d8307ba41da93ce6e47a62aac3c1b5303c355334cf80114 | Shell | 475 | 17 | #!/bin/bash
# export ROUTES=leaderboard/data/neat_weathers.xml
# export SCENARIOS=leaderboard/data/eval_scenarios.json
python3 ${LEADERBOARD_ROOT}/leaderboard/leaderboard_evaluator.py \
--scenarios=${SCENARIOS} \
--routes=${ROUTES} \
--repetitions=${REPETITIONS} \
--track=${CHALLENGE_TRACK_CODENAME} \
--checkpoint=$... |
28ce408a58a07ff396ac500070563bf6824399a1b809d8887a36e359c0d0b91d | Shell | 476 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
39cb13047576307a33f1ae160a4723ec6c21040752230f39de858e02c35ac2c3 | Shell | 476 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
502cc36cb01242e52f33cc95269e62e7cce316c346794a67b75fc698381c07f7 | Shell | 476 | 16 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_pdb_to_fasta_ss test_inputs/5edw.pdb"
./ap_pdb_to_fasta_ss test_inputs/5edw.pdb
echo -e "Running ./ap_pdb_to_pir test_inputs/5d95.pdb A"
./ap_pdb_to_fasta_ss test_inputs/5d95.pdb A
echo -e "# Running ./ap_pdb_to_fasta_ss test_inputs/5d... |
2eee0de4d24fcc1f48b08c7649bf1a499a37c6f735d35f68b159f81004edcba8 | Shell | 477 | 15 | #!/bin/bash
#example: bash basic_benchmark.sh ../testdata/bmdata/human.fa 99 human_basic_out
infile=$1
min=$2
outdir=$3
mkdir -p $3
time orfipy --min $2 --bed b --outdir $3 --between-stops $1
time orfipy --min $2 --dna d --pep p --outdir $3 --between-stops $1
time orfm -m $2 -t "$3/orfm_d" $1 > "$3/orfm_p"
time orfm... |
ba9eaa78ac7c425d555de89a9088b903583225f1a52b7931e9fdd30283ed921e | Shell | 477 | 8 | #! /bin/bash
# run a modified GSEA script to generate list of outlier-associated genes
cd /home/siyuan/jobs/suzukii_WGS/EAA/downstream/GSEA/random_SNP/scripts/output_gene_list/all_trimmed_outliers/scripts
for env_var in Altitude Annual_mean_wind_speed Annual_Precipitation Precipitation_Seasonality Mean_Diurnal_Range M... |
fc8628e7a2ebb060fd1cd64dd6145388b656bdfa9a2913689d40cf558b142f5b | Shell | 478 | 3 | export PYTHONPATH=""
snakemake --jobs 100 --use-conda --cluster-config cluster.json --cluster "sbatch --account={cluster.account} --job-name={cluster.job-name} --output={cluster.output} --error={cluster.error} --threads-per-core=1 --ntasks={cluster.ntasks} --ntasks-per-node={cluster.ntasks-per-node} --nodes={cluster... |
8b8aead0af12f78a1260085a076e7866a51469a5f3992b199eb727230eea2eea | Shell | 480 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
c1b2f89c3943a2382fb0525813381172e9e2f5b2e2ae1790796f7fa0da245e23 | Shell | 480 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
ab54c0c9f634382356b58441c9169424f8a4d726137198a31980462e508b04d0 | Shell | 481 | 19 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=10G
threads=2
if [ $# -ne 2 ]
then
echo "Please, give these following inputs:"
echo "1) root of _*_S*_L*_R1/R2.fastq.gz files"
echo "2) root for output files"
exit
fi
input==$1
output=$2
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/mergeL... |
b9e1c7d6789f03e93e29d63f8c989dea2797113e77f16103e5c459dda23a7409 | Shell | 481 | 11 | ARGS="cohort_csv='`pwd`/tutorials/tutorial3/cohort.csv';"
ARGS="$ARGS config_path='`pwd`/tutorials/tutorial3/mappers.json';"
ARGS="$ARGS output_dir='`pwd`/results/tutorial3_mappers';"
ARGS="$ARGS data_root='`pwd`/tutorials/tutorial3/';"
ARGS="$ARGS data_root='`pwd`/tutorials/tutorial3/';"
# new arguments
ARGS="${ARGS}... |
faa8c15ff3cc6fe15d86bb778a5d666b02a1d633f39672d3116c62dab11cc0bd | Shell | 481 | 17 | #!/bin/bash
cp -rf $1/Results/DwiVolu/TensorMetrics/FA/* $1/Results/DwiVolu/TBSS/Working/
cd $1/Results/DwiVolu/TBSS/Working/
tbss_1_preproc *.nii.gz
tbss_2_reg -T
tbss_3_postreg -S
tbss_4_prestats 0.2
cp -rf $1/Results/DwiVolu/TensorMetrics/AD $1/Results/DwiVolu/TBSS/Working/
tbss_non_FA AD
cp -rf $1/Results/DwiVolu... |
106fbfddf67036494dc8ed005383d5f7a95824dd0bc49d89d9230aecb622a128 | Shell | 482 | 23 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=12:00:00
#SBATCH --exclusive
#SBATCH --job-name=correlations
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/correlation_signals
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=("corr_signals_exc.jso... |
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