sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8662ee20e2995a50453f6f898e81473b838bcfcdb850559b684a50c8438bff74 | Shell | 495 | 13 | #!/bin/bash
#SBATCH --job-name=hybrid-model_%a
#SBATCH --output=logs/hybrid-model/cross-validation_%A_%a.out
#SBATCH --error=logs/hybrid-model/cross-validation_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=12:00:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=16G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Huma... |
8a58f3287485eee3356da4b0c982adbad2c7514fe558a8b50dbd4655bf1e1f73 | Shell | 495 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
18211cea533887159e0581a2aebc42c4625de4165e1ce712ad46db9afd746196 | Shell | 496 | 18 | #!/bin/bash
# ensure paths are correct
maindir=/gpfs/scratch/tug87422/smithlab-shared/night-owls #this should be the only line that has to change if the rest of the script is set up correctly
scriptdir=$maindir/code
mapfile -t myArray < ${scriptdir}/sublist.txt
# grab the first 10 elements
ntasks=1
counter=0
while ... |
6051c9655e8047afb55f189b1ba29431c6554a75497f8ff19eba04640f5e51dd | Shell | 496 | 12 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive/... |
38b63e00e5a0bf388e1f358478bdc324b7d07de3ae275a8a2f30d3848b763358 | Shell | 497 | 12 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cogn... |
be4576a8a4cd35b25aef335030de0dd1cfccb191ccf40c7fb6d95ce636470d89 | Shell | 497 | 22 | #!/usr/bin/env bash
# We already have data so this is not needed.
# cd dataset && matlab -batch generate_lorenz_stenflo_dataset && python data.py
bash run_hidden_variants.sh
for dir in ./ dataset/; do
cp NeuralRK4_h32/*.mat 2th_h32/*.mat 4th_h32/*.mat "$dir"
done
python plot.py
python learn_missing_physics_com... |
ed74161aa75a8c31eafa4ab79fff16967396479bfe3e28b49299e753fb98d9dd | Shell | 497 | 13 |
# To run samples:
# bash run_example.sh {file_to_run.py} {num_gpus}
# where file_to_run = example to launch. Default = 'fsdp_tp_example.py'
# num_gpus = num local gpus to use (must be at least 2). Default = 4
# samples to run include:
# sequence_parallel_example.py
# tensor_parallel_example.py
# fsdp_tp_example.py
... |
1597a0355e78fdd7b99db147d61a90ac75639cac6603e024211195675be514a0 | Shell | 498 | 35 | #!/bin/bash
# batch build all bigneuron related plugins
# by Zhi Zhou
svn up
for mydir in $(ls -d */); do
echo
echo $mydir
echo ===============================
cd $mydir
if [ -f *.pro ]; then
for mypro in $( ls *.pro ); do
qmake $mypro
make
done;
else
for mysubdir in $(ls -d */); do
echo... |
bc039f95553b6f2ff4c816892e5b7f203ada190886d2d2809f5ca4f95c948260 | Shell | 498 | 18 | #!/bin/bash
#SBATCH --job-name=hmds_fish
#SBATCH --partition=debug
#SBATCH --array=1-7
#SBATCH --cpus-per-task=1
#SBATCH --time=24:00:00
#SBATCH --output=logs/fish%a_%j.out
#SBATCH --error=logs/fish%a_%j.err
# --- Environment ---
source /home/wenlab/miniconda3/etc/profile.d/conda.sh
conda activate /home/wenlab/minicon... |
2108cc5b015d0b5abbcc7716c21903220a90ab5dbbe41256bddf0448bf1261c0 | Shell | 499 | 18 | #!/bin/bash
tools_dir=$(realpath $(dirname $(command -v $0)))
[[ -d $tools_dir/pkg/fsl ]] && rm -rf $tools_dir/pkg/fsl
mkdir -p $tools_dir/pkg
pushd $tools_dir/pkg > /dev/null
# download fsl
wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
# install fsl to pkg dir
python fslinstaller.py -d ${tools_dir}/p... |
e39b0361d7a541f4536cdf69f0603b1c6c2ac018bff7873b66e00480999ff726 | Shell | 499 | 14 | #!/bin/bash
# Download TF Lite model from the internet if it does not exist.
TFLITE_MODEL="model_opt.tflite"
TFLITE_FILE="Midas/Model/${TFLITE_MODEL}"
MODEL_SRC="https://github.com/isl-org/MiDaS/releases/download/v2/${TFLITE_MODEL}"
if test -f "${TFLITE_FILE}"; then
echo "INFO: TF Lite model already exists. Skip ... |
4e714309e7d0911e6493153689296cf6df6c66517f063d5364b7936ad52dea8e | Shell | 501 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
56cbf97b51889379b7d304e17af41ae63d3b7e39fa47af843262dbf8478bbf67 | Shell | 501 | 23 | #!/bin/sh
DIR=$(dirname "$0")
echo "Run tests from directory $DIR"
DEMO=./Polyhedron_3
for f in $DIR/good/*.js; do
if ! $DEMO --no-debug-scripts $f 'qtscript:quit()'; then
echo "Error with file $f"
exit 1
fi
done
echo "All good tests have correctly finished."
for f in $DIR/bad/*.js; do
i... |
a73cfb564327e42f23deebc9d98606a11fb46c9e5858295a9cd83ceb37af4149 | Shell | 501 | 20 | cd ./data/shinobi_behav
datalad get ./
cd ./data/shinobi
git checkout event_files
datalad get ./
cd ..
scp -r yharel@elm.criugm.qc.ca:/data/neuromod/DATA/games/shinobi_beh ./
# Additional lines to setup gym environment
cd shinobi/stimuli
# export aws etc...
datalad get ./
conda activate shinobi_env
python3 -m retro.im... |
60203cf8174c8067618c9afdfd9d3f345e63f25157f279fd6a5b5822da229a4a | Shell | 503 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
d93d6790f5a201b6650a4a1cebf9809cf1d7a7b8c2593ef4eadd410ae3cc245f | Shell | 503 | 7 | #!/usr/bin/env bash
# Run the pipeline (ReadsPipelineSpark) on small data in GCS.
. utils.sh
time_gatk "ReadsPipelineSpark -I gs://broad-spark-eval-test-data/small/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O gs://broad-spark-eval-test-data/small/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf -R gs://broad-spark-eval-test-da... |
f36286d92cc3b0d8da9b2e0666994f21615e40b0f168de14b66345b424793152 | Shell | 503 | 13 | set -e
if [[ "$COVERAGE" == "true" ]]; then
# # Need to run coveralls from a git checkout, so we copy .coverage
# # from TEST_DIR where nosetests has been run
# cp $TEST_DIR/.coverage $TRAVIS_BUILD_DIR
# cd $TRAVIS_BUILD_DIR
# Ignore coveralls failures as the coveralls server is not
# very reliable... |
780ed463af2748d0e8975f2f018c8cb173584aae33906e5e4e2ef39ae521f675 | Shell | 504 | 34 | #!/bin/sh
# Mac os x intermediate between applescript and neurondemo
echo -e "\033]0;neurondemo\007"
NRNGUI="neurondemo"
source set_nrnpyenv.sh
if test "x$1" != x ; then
if test -f "$1" ; then
dname=`dirname "$1"`
cd "${dname}"
arg1=`basename "$1"`
shift
${NRNGUI} "$arg1" "$@"
nex=$?
else
cd "$1"
s... |
1388392db86ee9587d22f23f4188185110ffec91df174b13a3896436962bb40d | Shell | 505 | 17 | #!/bin/bash
if command -v python3 &>/dev/null; then
echo Python 3 is installed
if command -v pip &>/dev/null; then
echo pip is installed
sudo pip install -r requirements.txt
else
sudo apt-get install python3-pip python3-dev build-essential
sudo pip install -r requirements.txt
fi
else
echo Python3 is not in... |
57c7e43a7828bda744fa9cae9f1e483ba7b422f05095a7e4064d050972b42e2e | Shell | 505 | 18 | #!/bin/bash
BED=/storage/nmmsv/reference_TRF/hg19/hg19_ver13.bed
DISEASE=/storage/nmmsv/reference_TRF/disease/hg19_disease_thresh.bed
READLEN=150
OUT=/storage/nmmsv/analysis/GangSTR-analyses/genome_wide/str_info/hg19_ver13_strinfo_pop_pad3.bed
POPULATION=/storage/resources/datasets/ENA-illuminia-150/ENA-illumina-150.s... |
8a101d5145ed18a07823e2f9abb75e75dae0d3c5f0e52757c4ab022dc263e09f | Shell | 505 | 19 | #!/bin/bash
SCRIPT=$1
ARG=${@:2}
AA=( "$@" )
## assume the last passed argument is a sample ID or something equivalent
TAG=${AA[-1]}
## in case the last argument is a path, we only want the sample ID
TAG=`basename $TAG`
GROUP=`bugroup -w | grep "\b${USER}\b" | cut -d" " -f1`
CPUS=16
RAM=64000
QUE="normal"
WDIR=`p... |
23c86b99c6f759834659ef5172e5040dc1d43b6d8fb9198dd7928572e18aa64f | Shell | 506 | 25 | #!/bin/bash
#conda activate ldsc
outdir=outMarkerP_LDscore
indir=dxMarkerPeak
path_ldsc=ldsc
path_resource=ldsc_ph/resources
path_data=ldsc/data
path_outAnno=$path_data/$outdir
chrs=`seq 1 22`
group=$1
chr=$2
bed=$path_data/$indir/$group"_dxMarkerP_ctUniqueP.bed"
ls $bed
annot_file=$group.$chr.annot.gz
bim=$... |
70c8ac5f85a8e8eac72dfc53d3f92282614a64cb1768fce554af445fc37fae4e | Shell | 506 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate XGBoost
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
80cf9e56c8159cb35b322ef1394974d9009db973422b2ebc44bdba22aa8469d9 | Shell | 506 | 27 | #!/bin/bash
cat /etc/os-release
lsb_release -a
echo "=> Current dir:"
echo $PWD
echo "=> Install prerequisites..."
curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.1/install.sh | bash
source ~/.bashrc
export NVM_DIR="$HOME/.nvm"
[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh" # This loads nvm
nvm ins... |
916fb5055fd966720472421504ce0df7367f549e87c278c3d3ac8fd9658b5d68 | Shell | 506 | 19 | #!/bin/bash
# ensure paths are correct.
maindir=/gpfs/scratch/tug87422/smithlab-shared/night-owls #this should be the only line that has to change if the rest of the script is set up correctly
scriptdir=$maindir/code
mapfile -t myArray < ${scriptdir}/sublist.txt
# grab the first 10 elements
ntasks=2
counter=0
whil... |
3c3c29b178e33ae2abd667cad85759876a354de7056ff6d9bfd280d6d5ba6826 | Shell | 507 | 21 | # 2020-05-12 Ji Young Lee
###Check
Struc=../md.pdb
PSFfi=' ..\/md.psf '
Traje=' ..\/sim.dcd '
Selec='all '
Step=1
Start=0
Head='CRYST1 85.328 96.807 93.491 90 90 90'
###Check
sed '1,1d' $Struc > __test ## Check!!!
echo "$Head " > t0.pdb
cat __test >> t0.pdb
cp 0chlcmpall.tcl __... |
61e28856e54376a052c78172438c22cede9053dfae5b4b5298d5fedfe1b399b7 | Shell | 507 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
c739f6635ec1c46162c5075863b03e5f41e2f3b276e5cea7092ddcbb9f8db3e4 | Shell | 507 | 11 | #!/bin/sh
### Launch the code for the times 0-5 and using 5 cores
### and save the magnitude of the projected violating triangles \Delta_v at the level of edges
### on the file "edges_projection.hd5"
codepath="../High_order_TS/simplicial_multivariate.py"
filename="./../Kaneko_CLM/trial_N50_T240_r175_eps012_008_03_0068... |
eb6acdb9b8dcad7200fe5def35a4c8b5b9ed84a8b8f5b8943ab2cfa73f122652 | Shell | 507 | 20 | #!/bin/bash
if [ "$1" == "" ] || [ "$2" == "" ]
then
echo "ERROR: Usage: \"$0\" \"INPUT_DATA_DIR\" \"OUTPUT_DIR\""
exit 1
fi
INPUT_DATA_DIR=$1
OUTPUT_DIR=$2
NAME_IMAGE_VERSION="antonioguj/bronchinet:stable_torch" # CHANGE WHEN TESTING OTHER OWN-BUILT DOCKER IMAGES
if [ ! -d "$OUTPUT_DIR" ]
then
mkdir -p ... |
a0d7127e4ae4c5ae5c83c275ad76ed49c8184c08181cde5e8d60c0bef09fc6dd | Shell | 508 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
047799a8653af4e1c46964ada55c56eb879bb0408eab02461ce63c1ad17bc2ab | Shell | 510 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
3f3a30cab805f81931820c3a211c02e2a416c727a012ab96396eecc66dcc9674 | Shell | 510 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
1a1f5ecdaf87ee539d4ac64cc413f1ebf40bad8f3f92a5a69cb52de5ff4488a0 | Shell | 511 | 7 | #!/usr/bin/env bash
# Run the pipeline (ReadsPipelineSpark) on genome data in HDFS.
. utils.sh
time_gatk "ReadsPipelineSpark -I hdfs:///user/$USER/q4_spark_eval/WGS-G94982-NA12878-no-NC_007605.bam -O hdfs://${HDFS_HOST_PORT}/user/$USER/q4_spark_eval/out/WGS-G94982-NA12878.vcf -R hdfs://${HDFS_HOST_PORT}/user/$USER/q... |
60f87ec426c6b394d578f1bbd671019f303e1805221b08bff2dd46c07ce74ddb | Shell | 511 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate XGBoost
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
a1e553a22b62f9ae047c7c3fab6471eac23000dd49ca305129f9aef2ca11da91 | Shell | 511 | 14 | python mape_plots.py \
--minimum-waso-minutes 5 \
--absolute \
-d ./results/LogReg-tr-healthy \
-d ./results/LogReg-tr-clinical \
-d ./results/RandomForest-tr-healthy \
-d ./results/RandomForest-tr-clinical \
-d ./results/LSTM-tr-healthy \
-d ./results/LSTM-tr-clinical \
--extra-data... |
20903a774eca37070e7551828d00b797b56f74cf7b9466cb90092b33f71f2419 | Shell | 512 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
34f150347ca18411af25219258bef9b67acbf35865ce14f6440466bcd99e85d7 | Shell | 513 | 18 | #!/bin/bash
#SBATCH --job-name=symbolic-model_%a
#SBATCH --output=logs/symbolic-model/estimate_ov_%a.out
#SBATCH --error=logs/symbolic-model/estimate_ov_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
module load Julia
path2script=scr/analysis/fi... |
aaceb045383df19f2405411f8b70dccb93cfdee4ff3c81eaa077b1f088ec45ae | Shell | 513 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
252ed27718b5db47a2571fee2688fbd328122d35c8ade57a7d11f84c340b7752 | Shell | 514 | 19 | #!/bin/bash
# Change the list according to your local conda/virtualenv env.
CONDA_ENVS="py27-np16 py27-np18 py34-np110 py35-np112 py36-np114"
COMPRESS_METHODS="zlib gzip bz2 xz lzma lz4"
for i in $CONDA_ENVS
do
. activate $i
# Generate non compressed pickles.
python create_numpy_pickle.py
# Generate ... |
26a7f9682992b2d2b984b1f0e117b90e5d5eb4ff79599680bdcaa78adfb21233 | Shell | 514 | 18 | #!/bin/bash
#SBATCH --job-name=hmds_fish
#SBATCH --partition=debug
#SBATCH --array=1-7
#SBATCH --cpus-per-task=1
#SBATCH --time=24:00:00
#SBATCH --output=logs/fish%a_%j.out
#SBATCH --error=logs/fish%a_%j.err
# --- Environment ---
source /home/wenlab/miniconda3/etc/profile.d/conda.sh
conda activate /home/wenlab/minicon... |
4366e875a7cd2b77c63cc378d675ec9382ae2ee753aaef6bf4687b150397f46c | Shell | 514 | 21 | #!/bin/bash
#SBATCH --job-name=simulate-sessions
#SBATCH --output=logs/simulate-sessions_%A.out
#SBATCH --error=logs/simulate-sessions_%A.err
#SBATCH --time=00:5:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=80G
# Run the Julia script
cd /home/fs0/jdf650/scratch/DPhil-Human-fMRI-OptimalPolicy/
# Parse arguments
source s... |
9377a5210c248611c378bf31f9f5de0180073e0d1298bed6c5a4381a9be30fad | Shell | 514 | 13 | #!/usr/bin/env bash
set -euo pipefail
mkdir -p examples/homology/celegans_dmelanogaster/raw
cd examples/homology/celegans_dmelanogaster/raw
wget -c https://ftp.ensembl.org/pub/release-115/fasta/caenorhabditis_elegans/pep/Caenorhabditis_elegans.WBcel235.pep.all.fa.gz
wget -c https://ftp.ensembl.org/pub/release-115/f... |
8ae507d34493f00f8028a7761c44b5f90f84f5203bb79831418c7a8447109a71 | Shell | 516 | 15 | conda create -n NeNe -c conda-forge python=3.8 -y
conda activate NeNe
pip install bio-embeddings
pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 --index-url https://download.pytorch.org/whl/cpu
pip install 'transformers[torch]'
pip install sentencepiece
pip install tqdm==4.64.1
pip install biopython==1.8... |
3e9d452055e51df23597b201c562b21663202d1026cb495e70f62ff7a1dffa23 | Shell | 517 | 18 | #!/bin/bash
# If you need to add or remove from the repo root please change NUM_ITEMS_SHOULD_BE
# Please take care to only add files or directories to the repo root unless they are
# required to be in the repo root, otherwise please find a more appropriate location.
NUM_ITEMS_SHOULD_BE=43
NUM_ITEMS=$(ls -la | wc -l)... |
6d8458a9b3fc0b866aa625d3f850e2656db03d0fa2cf11c1fc3c6a03762c7288 | Shell | 517 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
de0bd1702347c7bb4a500e2c4e5c31bfcdc976de19d9d9c329f3a2d80966abe5 | Shell | 517 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
f8e73c9810a76806f61b075b1eb765c0a2f2a345ca672c5e82bae3120ee9285a | Shell | 517 | 10 | #!/bin/sh
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_CBIG_fMRI_Preproc2016
# remove useless stable projects
rm -r Standalone_CBIG_fMRI_Preproc2016/stable_projects/brain_parcellation/Kong2019_MSHBM
rm -r Standal... |
d299a6f3b0f322eca878e97d378561ecb03d9ce6b48b53ac4aafc22b25065bfd | Shell | 518 | 13 | #!/bin/bash
for i in {25..27}
do
echo $i
var=0;
for j in {1..16}
do
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_c_exe_scripts.sh /global/project/projectdirs/m2043/BigNeuron/zhi/taiwan_16k_valid_batch_run/anisosmooth/runVAA3D_all/runVAA3D_${i}_part${j}.c /global/pro... |
fd4caf7acbc32c02b9c2b39f7ff5272ffd7ee516bdcfb55d41df039b8e0f0b80 | Shell | 518 | 15 | conda create -n NeNe -c conda-forge python=3.8 -y
conda activate NeNe
pip install bio-embeddings
pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 --index-url https://download.pytorch.org/whl/cu121
pip install 'transformers[torch]'
pip install sentencepiece
pip install tqdm==4.64.1
pip install biopython==1... |
47bef24ed49fd8702afc5c598f97e31c3ba0aba12e2d3725ef163a9e1df0be36 | Shell | 520 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
860935de67c2cdf8981035a1faa98ea163413804f56b41fa78c37c5f14de5c50 | Shell | 521 | 12 | #!/bin/bash
for i in {25..27}
do
var=0;
for j in {1..16}
do
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_c_exe_scripts.sh /global/project/projectdirs/m2043/BigNeuron/zhi/taiwan_16k_valid_batch_run/nopreproprcessing/runVAA3D_all/runVAA3D_${i}_part${j}.c /global/projec... |
91d933dd7dee923903ca78e308f559a75dfdd1413e46a266948ba52d24a04b9e | Shell | 522 | 17 | #!/bin/bash
# Setup directory for running a minimal DREAM synthetic 3 dataset
# The original DREAM data is subset to exomes on chromosome 6
set -eu -o pipefail
mkdir -p cancer-syn3-chr6
cd cancer-syn3-chr6
wget -c https://s3.amazonaws.com/bcbio_nextgen/dream/cancer-syn3-chr6-input.tar.gz
tar -xzvpf cancer-syn3-chr6-in... |
f642e1956e622bcbf8861e9dc75048a56be278a1492e05e38bb654d626865c06 | Shell | 523 | 9 | #!/usr/bin/env bash
# for untargeted attacks, use the following commands
python tangent_attack_hemisphere/attack.py --gpu 0 --norm l2 --dataset CIFAR-10 --all_archs
python tangent_attack_semiellipsoid/attack.py --gpu 0 --norm l2 --dataset CIFAR-10 --all_archs
# for untargeted attacks, use the following commands
pytho... |
7130e15bf46b588fb646ba9d0d5abb8a2de08388c474f8c5029f6cf462008e7b | Shell | 524 | 12 | #!/bin/bash
for i in {25..27}
do
var=0;
for j in {1..16}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/taiwan_16k_valid_batch_run/anisosmooth/runVAA3D_all/runVAA3D_${i}_part${j}.c /lust... |
057789681c5d824dcb7ab8779487c0a6e4e55399d1d919abda198ecc2ff6957a | Shell | 525 | 28 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_chopper
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 02:00:00
#SBATCH -v
#SBATCH -o run_chopper.%j.out
#SBATCH -e run_chopper.%j.err
module purge
module load tools/Singularity/3.9.1
PROJECT_DIR=/lustre/project/m2_jgu-funcpoll
## ... |
11815caa20566a47fb2c70afae3ea9de4a34dd43a5d9776e965aa8f0065672c7 | Shell | 527 | 12 | #!/bin/bash
for i in {1..27}
do
var=0;
for j in {1..7}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/gaussiansmooth_set1/runVAA3D_all/runVAA3D_${i}_part${j}.c /lus... |
9c4d87954eb526fd06361048c7c4813a80024c03144aedeadc1bc8182387aa3a | Shell | 527 | 12 | #!/bin/bash
for i in {1..27}
do
var=0;
for j in {1..8}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/gaussiansmooth_set2/runVAA3D_all/runVAA3D_${i}_part${j}.c /lus... |
1ba978b0a1cc099094ce5479e88d492c171fa7bc81b24c47eaeee955506f4875 | Shell | 528 | 12 | #!/bin/bash
for i in {1..24}
do
var=0;
for j in {1..16}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/taiwan_16k_valid_batch_run/gaussiansmooth/runVAA3D_all/runVAA3D_${i}_part${j}.c /lu... |
765fe4cb93c00512f7a13d450b7393dc3d6271aa1aadca4ba9e5f0b2c4adb8d9 | Shell | 528 | 15 | #!/bin/bash
# point to working directory
cd /Path/to/personal/working/directory
# Execute qsiprep in the container with the required bind mount
apptainer exec \
-B /Path/to/personal/working/directory:/Path/to/personal/working/directory \
-B "${TMPDIR:-/tmp}:${TMPDIR:-/tmp}" \
--pwd "$TMPDIR" \
/Path/to/Wrapper... |
593e324f8ec1869d926d19d535db75a813248eb06eb0fbc9b2ba52134eb80725 | Shell | 529 | 23 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N makeATAC
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="r4_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
exp... |
aa2b01b1198e577364002ec14b6de788f537e2ecd04e065e5c6d0ea21855c54b | Shell | 529 | 16 | #!/bin/bash
# Vagrant shell provisioning script https://www.vagrantup.com/docs/provisioning/shell.html
set -e -x
/usr/bin/apt-get -qq update
/usr/bin/apt-get install -q -y build-essential docker.io python-setuptools
/usr/bin/apt-get -y autoremove
/usr/bin/apt-get clean
/bin/systemctl start docker.service
/usr/sbin/... |
6064015c68105f0f470581c13487bb51c420cb15c62ed5be15b6d1a8d1bc00f7 | Shell | 530 | 44 | #! /bin/bash
[ $# -lt 3 ] && { echo 'Usage :
$1 = MNI152 image
$2 = mask
$3 = resultFolder
$4 = lower threshold for mask
$5 = upper threshold for mask'; exit 1; }
fileName() {
name=$(basename $1)
name=${name%%.*}
echo -n $name
}
low_thr=$4
if [[ $4 == '' ]];
then
low_thr=0
fi;
low_thr=$4
if [[ $... |
8cde5966db31a60288b040f7ad14cfd912dc40b34a3e25d901fa62d0735888b3 | Shell | 530 | 13 | #!/bin/bash
for i in {1..27}
do
echo $i
var=0;
for j in {1..7}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/anisosmooth_set1/runVAA3D_all/runVAA3D_${i}_part${j}.c... |
3618fa378d53ac4d4c25ff6daadb0d27de2686ae5993b3858afb90b8e6b12a67 | Shell | 531 | 13 | #!/bin/bash
for i in {1..27}
do
var=0;
echo $i
for j in {1..8}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/anisosmooth_set2/runVAA3D_all/runVAA3D_${i}_part${j}.... |
7dfed16f0f6c5169e0108ddc272089901c31314ffaaa630f127a79115a5f5f81 | Shell | 531 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
b896649dadc363327bfb09cc851387f39f1eeee5cf6800856c8b127b2223fabf | Shell | 531 | 11 | #This is a simple scoring script to calculate pDockQ
#1 Rewrite the predicted pdbfile to contain two chains (A and B)
PDBDIR=./test/ #Path to predicted structure
ID=1ay7 #Name of predicted structure
L1=96 #Length of first chain of predicted structure
#Rewrite
python3 ./src/rewrite_af_pdb.py --pdbfile $PDBDIR/unrelaxed_... |
4f6ea201625ddd33ee8b8a5e1b84ccec31d9609c56d8dfc5daf53ba5332a5a88 | Shell | 533 | 16 | export CXX=g++-7;
rm -rf build; python setup.py install --test=coordinate
python -m unittest coordinate_test
rm -rf build; python setup.py install --test=coordinate_map_key
python -m unittest coordinate_map_key_test
rm -rf build; python setup.py install --test=coordinate_map_cpu
python -m unittest coordinate_map_cpu... |
5d581e47364fcbf6991fe75d8092ffcacb20c00c670f9368afe0dfdf524f2b74 | Shell | 533 | 11 | #!/bin/bash
cd /lustre/atlas/proj-shared/nro101/BigNeuron/first2000/images/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
sh /lustre/atlas/proj-shared/nro101/BigNeuron/gen_bench_job_text_scripts.sh 2 /lustre/atlas/proj-shared/nro101/BigNeuron/first2000/images/$filename/$filename /lustre/atlas/proj-sh... |
7a907f63def1d68c1692f847d335d50d87a824c5f4a2bd0c567db69e4a8d3b2f | Shell | 533 | 19 | #!/bin/bash
# This script is used to create a phylogenetic tree with teleost nonapeptide receptor sequences
# MAFFT version 7.526
# IQTREE version 2.0.3
path_seq="Data/01.Telost_tree_receptors/in/sequences_receptors.fa"
folder_out="Data/01.Telost_tree_receptors/out/"
# Create directory
mkdir ${folder_out}/tree_recep... |
c4ef8292efa3e207e7ec5a2f336287965e2b4c1c09dcc90dc47b66cb412e4797 | Shell | 533 | 23 | #!/bin/bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
declare -A SKIP=(
["101:04"]=1
["101:05"]=1
["101:12"]=1
["103:12"]=1
)
for sub in 101 103 104 105; do
for s... |
06ec0b92afc1ede6c388851af5ff4ed8f72a9bd72559ad002238d138deb65a4e | Shell | 534 | 18 | #!/bin/bash
# shellcheck disable=SC2154
export SETUPTOOLS_SCM_PRETEND_VERSION="${halfpipe_version}"
# Fetch the git-annex branch from the source repo
git remote set-url origin "$(realpath "${RECIPE_DIR}/../..")"
git fetch origin git-annex:git-annex
git annex init
# Setup hardlinking to pull directly from your local h... |
36c858aab520a445b0569d28cb4b74d01ca318b22f6754447f745f75eb7a7d5f | Shell | 534 | 7 | #!/usr/bin/env bash
# Run the pipeline (ReadsPipelineSpark) on small data in HDFS.
. utils.sh
time_gatk "ReadsPipelineSpark -I hdfs:///user/$USER/small_spark_eval/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O hdfs://${HDFS_HOST_PORT}/user/$USER/small_spark_eval/out/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.vcf -R hdfs:///use... |
9bec0dbe1a1d87fdbdb9ad032ecca5e99dd7e2112bf9a8a218f7c6493679ced3 | Shell | 534 | 19 | #!/bin/bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
mapfile -t myArray < "${scriptdir}/sublist.txt"
# grab the first n elements
ntasks=1
counter=0
while [ $counter -lt $... |
016d206f67716927a2dba04a743df46cd50d58edaf0dd81c057c8fc0a8a66b5e | Shell | 535 | 23 | #!/bin/bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
declare -A SKIP=(
["101:04"]=1
["101:05"]=1
["101:12"]=1
["103:12"]=1
)
for sub in 101 103 104 105; do
for s... |
5a48b3208671a4732c6526faed09b4c90efc312d6c262b7c8ff085c1a5d81ee1 | Shell | 535 | 20 | #!/bin/bash
data=$1
prfpath=$2
spmpath=$3
biascorrpath=$4
echo ""
echo "------------------------------------------------------------------------------"
echo "| Performing bias field correction using SPM12"
echo "------------------------------------------------------------------------------"
matlab -nosplash -nodispla... |
dc82a35376d8d9a1f4195ceddf3e74dd2899ee726e8665efffab7068a1c5dbed | Shell | 536 | 19 | #!/bin/bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
mapfile -t myArray < "${scriptdir}/sublist.txt"
# grab the first n elements
ntasks=1
counter=0
while [ $counter -lt $... |
f189f5b424fcdda6ffd353e931033d37ffd5e8d3318a11994ecfe411d235f524 | Shell | 537 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
0cff49ef108a3402dce177c40a275683e8c5cc61ecb4ebe86095f720f9493c77 | Shell | 538 | 19 | #!/bin/bash
REF_SEP=PATH/TO/CHROM/SEPARATED/REF/ # Folder containing chrom separated reference genome (chr1.fa chr2.fa chr3.fa ...)
OUT=PATH/TO/OUT.bed # Output file
TRF=trf # Path to TRF executable (if trf is not added to path)
THREADS=4 # Number of threads
MAX_CHR_NUM=22 # Maximum chr number (other than sex chroms)... |
74875cb931d0636fad50840bfaa1b17dee94337b34be5894d6378c8498f60653 | Shell | 539 | 23 | #!/bin/sh
# This is assumed to be running from the root of the repo
echo "[before] running in: $PWD"
# For debugging
echo $CI_COMMIT_BRANCH
echo $CI_DEFAULT_BRANCH
python --version
git branch
# Needed for Sphinx (make in build-base) and pysam (build-base + others)
# apt-get bzip2-dev zlib-dev xz-dev openblas-dev linux... |
408ac585dd9f9746a12eae93c2777d31c5eca711586943be825cec8dd6cc9b96 | Shell | 540 | 25 | #!/bin/bash
#SBATCH --time=00-00:30:00
#SBATCH --mem=80G
#SBATCH --cpus-per-task=20
module load picard
# input the sample name
sample=$1
# input gvcf directory
gvcfdir=$2
# input chromosome list
chromosomes=($(cat $3))
for chr in ${chromosomes[@]}; do
# read in the gvcf files
gvcfs=($(ls ${gvcfdir}/${sample}... |
62fee8b47b77ce3c81e842356c55830f033edb2c11905cacca7cf30d806d564c | Shell | 540 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
e796cdb06c20ac00fa7665e18978dbdac6277d499fb495d8bbb6f09c593599f7 | Shell | 540 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
fcb0daa7cc8665c864b6f7507c35ff7fb39591fd785588b3cddd25381e6e0386 | Shell | 540 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
1d346466c45945de482189e19fdc667570d865a0e52300fb1e9c14e34ed55e60 | Shell | 542 | 13 | #!/bin/bash
for i in {1..27}
do
echo $i
var=0;
for j in {1..7}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/nopreproprcessing_set1/runVAA3D_all/runVAA3D_${i}_part... |
cd157329ed40b8e6345c9b9edb16582debae701cb8f8cac994d470eb28798067 | Shell | 542 | 19 | #! /bin/bash
cd .helm/adhoc &&
kubectl apply -f pvc-log-volume.yml \
-f secret-siibra-explorer.yml \
-f configmap-siibra-explorer.yml \
-f deployment-redis.yml \
-f service-redis.yml && \
cd ../..
DEPLOYMENT_NAME="prod"
VERSION=$(jq -r '.version' package.json)
helm \
install \
--set image.ta... |
3344ac9a30ab39047eb4450a55732963e4193fb6b9bc9f1cbfe34db72f89e525 | Shell | 543 | 25 | #!/bin/bash
#SBATCH --job-name=multinode-example
#SBATCH --nodes=2
#SBATCH --ntasks=2
#SBATCH --gpus-per-task=1
#SBATCH --cpus-per-task=4
nodes=( $( scontrol show hostnames $SLURM_JOB_NODELIST ) )
nodes_array=($nodes)
head_node=${nodes_array[0]}
head_node_ip=$(srun --nodes=1 --ntasks=1 -w "$head_node" hostname --ip-a... |
7fbd473984d3c8960d83f446613898ab1e82a4d7497c579cec73e07481727698 | Shell | 543 | 13 | #!/bin/bash
for i in {1..27}
do
var=0;
echo $i
for j in {1..8}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/nopreproprcessing_set2/runVAA3D_all/runVAA3D_${i}_par... |
a9f68349688e72c9bfd2f9a01da596490d18577c977a81b022bef1aa9607f315 | Shell | 544 | 14 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
#conda activate new_autogluon
conda activate gpu_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Co... |
44872f833ed4a58e417dace659793b68fba67bd46182d8fb73539d2f7e364a6a | Shell | 545 | 14 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
#conda activate new_autogluon
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Co... |
e1fec87ab515823673c2c7643199f2aaf9c56f5416fc9628d7dc75f2ffd06727 | Shell | 545 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/bigneuron_annotation_consolidated_20150715/gold166/
for foldername in `ls -d checked*`
do
cd $foldername
for subfolder in $(ls -d */)
do
cd $subfolder
for swcfile in $(ls *.swc)
do
... |
21962afd9ae59f420729f4f18f2bf0186bbd925222bb081e7440b4524de9f83e | Shell | 546 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
56f5b6cf35d58fb142c87f73f1d649db1d503bda9fd36f3042ca0223ca0ec07e | Shell | 546 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
885f14f4f22e00770a08181c509f7f4fc36ddb2f240a14d919a74a2734975486 | Shell | 546 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cog... |
8a440db465823e3ff9e6d6bdbf3f962cb293d9f4fc1367a9a18e15537e9d9a99 | Shell | 546 | 24 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_quast_multi
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 01:00:00
#SBATCH -v
#SBATCH -o run_quast_multi.%j.out
#SBATCH -e run_quast_multi.%j.err
module purge
PROJECT_DIR=/lustre/project/m2_jgu-funcpoll
src/quast-5.3.0/quast.py --l... |
23b905889a1603a057748717549c4812462c6f505f0cc2b4b8c92003ed5470b4 | Shell | 547 | 16 | #!/bin/bash
source /etc/profile.d/modules.sh
export SUBJECTS_DIR=/data/project/sleep_ENIGMA_harmonization/data/Juelich_FreeSurfer
module avail freesurfer
module load freesurfer/7.4
# Check if the input argument is provided
if [ -z "$1" ]; then
echo "Error: No subject ID provided."
exit 1
fi
recon-all -s su... |
d44d2721092651c892bfb016bfabbd4e6b188cdb34d9862d0dc707f1a568d241 | Shell | 549 | 21 | #!/bin/bash
while getopts ":i:o:h" opt; do
case $opt in
i) infile="$OPTARG" ;;
o) outfile="$OPTARG" ;;
h) echo "Usage: $(basename "$0") [-i infile] [-o outfile]" >&2; exit 0 ;;
\?) echo "Unknown option: -$OPTARG" >&2; exit 1 ;;
:) echo "Missing argument for -$OPTARG" >&2; ex... |
b40c5d4536f3417f71ef3c5336f15f8e78565d7802b3e8fd4c8fd23327c2d0dd | Shell | 551 | 14 | #!/bin/bash
source /home/h.bi/miniforge3/etc/profile.d/conda.sh
conda deactivate
#conda activate new_autogluon
conda activate gpu_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_C... |
b6418ada43039a143c2efe2c42976287178cbe2c8d4429b1d506364a192ef415 | Shell | 551 | 19 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
FC_mean_file=$1
y_file=$2
krr_folds=$3
perm_seed_start=$4
perm_num=$5
outdir=$6
group=$7
scripts_dir=`dirname "$(readlink -f "$0")"`
LF=${outdir}/logs/PFM_perm_start_${perm_seed_start}.txt... |
2551e44fab87f9996edae97a4bf53e582142e9689dc8309cf4e5527336a3c0a7 | Shell | 552 | 22 | #!/bin/bash
SERIES=$1 ## GSE123456
if (( $# != 1 ))
then
>&2 echo "USAGE: ./run_starsolo.sh <series_id>"
>&2 echo
>&2 echo "(requires bsub_starsolo.sh, starsolo_10x_auto.sh, and non-empty /fastqs directory)"
exit 1
fi
## job array submission here
./bsub_starsolo.sh $SERIES starsolo_10x_auto.sh `pwd`/fastqs
... |
2b9379f00c36b72218e2e447478c5adb47cd9c0efa5cd5b0fdab7ce239931593 | Shell | 552 | 17 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download ImageNet10 dataset https://image-net.org (first 10 classes of ILSVRC2012 train/val)
# Example usage: bash data/scripts/get_imagenet10.sh
# parent
# ├── yolov5
# └── datasets
# └── imagenet10 ← downloads here
# Make dir
d='... |
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