sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f482ab3a29545ab54df5c6708a96691a6c1455827afb8fbbe5e9d9eb53837795 | Shell | 449 | 22 | #!/bin/bash
# usage -> bash update_mailmap.sh <previous-release>
# by default, will use the latest tag
set -ux
ROOT=$( git rev-parse --show-toplevel )
MAILMAP=$ROOT/.mailmap
LAST=$(git describe --tags `git rev-list --tags --max-count=1`)
RELEASE=${1:-$LAST}
IFS=$'\n'
for NAME in $(git shortlog -nse $RELEASE.. | cu... |
fc071e11faa5f5dfd732cf61fb97859cbcade4c4d4e909cabda809dab13e1168 | Shell | 449 | 15 | #!/bin/bash -l
#SBATCH --job-name=model2loc
#SBATCH --time=24:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
source /gpfs/bbp.cscs.ch/home/pokorny/ToposampleKernel/bin/activate
python -u run_SSCx_model_building_order2_local_per_pathway.py $1 $2 $3
... |
299466a25211efda481985abb1150ce0122cf857af234c44e1d8a533e9253057 | Shell | 450 | 17 | #!/bin/bash
ver=$(fgrep '#define VERSION ' gffcompare.cpp)
ver=${ver#*\"}
ver=${ver%%\"*}
pack=gffcompare-$ver
macpack=$pack.OSX_x86_64
echo "preparing $macpack.tar.gz"
echo "-------------------"
/bin/rm -rf $macpack
/bin/rm -f $macpack.tar.gz
mkdir $macpack
make clean
make release
cp LICENSE README.md gffcompare trmap... |
664bc8a910cf27d9d0a696885aef7d2ae9992c270c7b563246897c6bfdc275c2 | Shell | 450 | 15 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
shopt -s expand_aliases
me=$(whoami)
#alias myqstat="qstat -u $me | grep "${1}" | wc -l"
alias myqstat="qstat -f | grep -C 1 ${me} | grep ${1} | wc -l"
status=$(myqstat)
if [ $status -ne 0 ]; th... |
f327b846b27d6d1bccea540474956c4fe89e38d122b06bba3c9c1a1e2ed2100d | Shell | 451 | 21 | for i in $(find src/ tests/ include/ apps/ -regex ".*\.\(tpp\|hpp\|cpp\|c\|h\)$"); do
if ! grep -q Copyright $i; then
echo "Adding license to $i"
cat config/licenseHeader.txt $i >$i.new && mv $i.new $i
fi
done
for i in $(find integration_tests/ | grep "\.py"); do
if ! grep -q Copyright... |
9ce76a25752bd9484baddc1440a1911e42f695057120e64848fb047613624e56 | Shell | 452 | 27 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_busco
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 24:00:00
#SBATCH -v
#SBATCH -o run_busco.%j.out
#SBATCH -e run_busco.%j.err
module purge
module load bio/BUSCO/5.4.3-foss-2021b
PROJECT_DIR=/lustre/project/m2_jgu-funcpoll
INPUT=... |
d8028d10b2a6e036f7823350b9c84aaf7673271169d4e38e63183cd2949d71ad | Shell | 452 | 17 | #!/bin/sh
OUTPUT_DIR=/local1/ephys/tsts
SPECIMEN_ID=$1
CELL_NAME=$SPECIMEN_ID
CELL_DIR=$OUTPUT_DIR/$CELL_NAME
INPUT_JSON=$CELL_DIR/pipeline_input.json
OUTPUT_JSON=$CELL_DIR/pipeline_output.json
LOG_FILE=$CELL_DIR/log.txt
echo $CELL_DIR
mkdir -p $CELL_DIR
python generate_pipeline_input.py --specimen_id $SPECIMEN_ID... |
bb23bed025774e0332499e9c036e4a4a16ba8eaae7689407c0715397e0efd8a4 | Shell | 453 | 23 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_nanoplot
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 02:00:00
#SBATCH -v
#SBATCH -o run_nanoplot.%j.out
#SBATCH -e run_nanoplot.%j.err
module purge
module load lang/Python/3.12.3-GCCcore-13.3.0
PROJECT_DIR=/lustre/project/m2_j... |
651860290f7aa252b34c97cffafee3be9f17a2df4b0ea9b84bbc1c21507111d2 | Shell | 454 | 27 |
for dir in */; do
if [[ -d "$dir" ]]; then
# Commands to execute for each directory
echo "Processing directory: $dir"
cd "$dir"
#pwd
g++ python_main_ipsc_baseline.cpp -shared -fPIC -Ofast -o pycppipsc
python3 createData.py
cd test21
#pwd
pyth... |
712a20ab476af07e55a34df4b11a350045c70ad3837ae38aff6ab16c532d33f0 | Shell | 454 | 17 | #!/usr/bin/env bash
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
python ind_eval.py \
--gpu 0 \
--result_dir 'data/Example_train/results/' \
--target_data_dir 'data/Example_eval' \
--save_dir 'data/Example_eval/results/' \
--batch_size 256 \
--num_workers 4
# If no GPU device i... |
a53b51a0e89c99f1b26d793d6bb5a1167af012f2fefeb875e464bedbc3b41ea4 | Shell | 454 | 31 | cd c:/nrn
rm -f nrncyg.zip
zip -r nrncyg.zip \
bin/as.exe \
bin/cat.exe \
bin/cc1.exe \
bin/cpp.exe \
bin/cpp0.exe \
bin/cygiconv-2.dll \
bin/cygintl-1.dll \
bin/cygintl-2.dll \
bin/cygncurses6.dll \
bin/cygpath.exe \
bin/cygreadline5.dll \
bin/cygwin1.dll \
bin/echo.exe \
bin/gcc.exe \
bin/grep.exe \
bin/ld.exe \
bin/... |
f4726d514f36d2a6f19e4eca726353489bae3062cdc5fee61efc9e3be848d26e | Shell | 455 | 23 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_minimap2
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 04:00:00
#SBATCH -v
#SBATCH -o run_minimap2.%j.out
#SBATCH -e run_minimap2.%j.err
module purge
module load bio/SAMtools/1.14-GCC-11.2.0
PROJECT_DIR=/lustre/project/m2_jgu-funcp... |
2b4bb2605c7579fbeb66568120819e15bca647248708a9f5ea3efd693c0e5553 | Shell | 456 | 15 | #!/bin/bash -l
#SBATCH --job-name=model2midr
#SBATCH --time=24:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
source /gpfs/bbp.cscs.ch/home/pokorny/ToposampleKernel/bin/activate
python -u run_SSCx_model_building_order2_midrange_per_pathway.py $1 $2... |
428b0f6585b80d320840f1070952d69140508e10c7c1a567729932354ab38065 | Shell | 456 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=47
sta_i_batch_KM=1
end_i_batch_KM=51
n_batch_KM=1
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_KM in $(eval echo "{$sta_i_batch_KM..$end_i_batch_KM..$n_batch_KM}")
do
... |
c12f6f1e312248bee0339676b1dc8dc2004aefb62965fabe2521bcf51f56fdf2 | Shell | 456 | 20 | #!/bin/tcsh
set ANTSPATH=$argv[1]
set pointset = $argv[2]
set patid = reg_out
set tmpPath = $argv[3]
set WARPPTS = ${ANTSPATH}/antsApplyTransformsToPoints
######## apply warp - structural images
set CMD=" ${WARPPTS} -d 3 -i ${pointset} -o ${tmpPath}/${patid}_syn.csv -t ${tmpPath}/reg_out1InverseWarp.nii.gz"
ec... |
d9cb143b05615444fac6a83cea43c1070c6c6ccef39f88edfd944e271078713a | Shell | 456 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_anisosmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_anisosmooth/... |
799c72e62a7901e7fb6d148727d5ff91f261d7c41a0147188f03c1fc0f8ff697 | Shell | 457 | 20 | #!/usr/bin/env bash
CONFIG=$1
GPUS=$2
NNODES=${NNODES:-1}
NODE_RANK=${NODE_RANK:-0}
PORT=${PORT:-29500}
MASTER_ADDR=${MASTER_ADDR:-"127.0.0.1"}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
python -m torch.distributed.launch \
--nnodes=$NNODES \
--node_rank=$NODE_RANK \
--master_addr=$MASTER_ADDR \
--np... |
c6a53b6842421b54a0a70277f9d7be183ecaf2de9209d1e8181df95c332c0c0c | Shell | 457 | 12 | #!/bin/bash
#SBATCH --job-name=ucb-model-%a
#SBATCH --output=logs/ucb-model/cross-validation_%A_%a.out
#SBATCH --error=logs/ucb-model/cross-validation_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-Hyb... |
f31b5ae2c9e15954c678b4a0053e9385b658a7c0e2940a0edb8405c536686976 | Shell | 457 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=24
sta_i_batch_KM=1
end_i_batch_KM=16
n_batch_KM=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_KM in $(eval echo "{$sta_i_batch_KM..$end_i_batch_KM..$n_batch_KM}")
do
... |
3a1e3fa5a45a4035a4c295af317235d264a4a96759d4215cee208b3032cf0e0d | Shell | 458 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_anisosmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_anisosmoot... |
69392d1b013d9385feac46e6c24fbc9a591984b6e48f39acfad53eed4b34a42c | Shell | 458 | 14 | rm -rf test_installation
mkdir test_installation
cd test_installation
wget https://files.rcsb.org/view/1XDN.pdb
cat 1XDN.pdb | grep -v ATP > receptor.pdb
cat 1XDN.pdb | grep ATP > ligand.pdb
# Remove terminal phosphate
cat ligand.pdb | grep -v "O1G" | grep -v "PG" | grep -v "O2G" | grep -v "O3G" > ligand2.pdb
cd ../
... |
3d7723a345c2f1f1145b16a1e5e90ec380cb1440284c0ca06ccb35222e181ced | Shell | 459 | 12 | #!/bin/bash
# Reason for docker application called MPI_Abort(compute, 59): (last question)
# https://github.com/pmodels/mpich/blob/main/doc/wiki/faq/Frequently_Asked_Questions.md
# --mount type=bind,source=./docker_tunnel,target=/openCARP/PIE-Model-Experiments/calibration,readonly
# -v ./docker_tunnel:/openCARP/PIE-M... |
7e287181009ec8556a363a5e6a63cad3d5a07417602de6213927473b43df8f94 | Shell | 459 | 20 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_repeat_modeler
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 36:00:00
#SBATCH -v
#SBATCH -o run_repeat_modeler.%j.out
#SBATCH -e run_repeat_modeler.%j.err
module purge
module load bio/RepeatModeler/2.0.2a-foss-2020b
PROJECT_DIR=/lus... |
b33dd5564613ab834a1757b698b901d8155c68f61949cc8e7d13218e93b8ed04 | Shell | 459 | 14 | #!/bin/bash
#SBATCH --job-name=adni_conv
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=16G
#SBATCH --time=12-24:00:00
#SBATCH --output=slurm_%j.out
module load anaconda3
conda activate clinicaEnv
export FREESURFER_HOME=/DIR/TO/freesurfer/6.0.0/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export PATH="DIR/TO/mricron... |
c18e56dd8e0f174e23fd25994a754cb545aea054fe250b63bc3c5791a57fe890 | Shell | 459 | 10 | #!/bin/bash
for i in {1..27}
do
j=16
# for j in {1..16}
# do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 921 100 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/taiwan_16k_valid_batch_run/gaussiansmooth/pbs_all/taiwan16_gaussian_${i}_part${j}.pbs /lus... |
07081e8d7db72048fb203c741486fbd0be4246483b60c54795c6ccd7516a1f78 | Shell | 460 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=47
sta_i_batch_Kir=1
end_i_batch_Kir=51
n_batch_Kir=1
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_Kir in $(eval echo "{$sta_i_batch_Kir..$end_i_batch_Kir..$n_batch_Kir}")
do
... |
5b80c945d68184e3aff003551510b8d48f74ab4fd0d501ad296f188c69c9a819 | Shell | 460 | 4 | # Estimate mean volumes and mean surface values inside ROI
/data/project/sleep_ENIGMA_insomnia/Tools/CAT12.8.1_r2040_R2017b_MCR_Linux/standalone/cat_standalone.sh -m /data/group/sysmed/TOOLS/MCR/v93 \
-b /data/project/sleep_ENIGMA_insomnia/Tools/CAT12.8.1_r2040_R2017b_MCR_Linux/standalone/cat_standalone_get_ROI_value... |
2e42bdeca3fe9a71fa0b547260946829c831224c97beed6c5ba0ac3021fae308 | Shell | 461 | 23 | #!/bin/bash
#SBATCH -c 20
#SBATCH --mem=60G
#SBATCH -t 00-06:00:00
# load the necessary modules
module load cesga/system miniconda3/22.11.1-1
source activate /mnt/netapp1/Store_CSIC/home/csic/eye/eba/gadma2
# read the arguments
boot_folder=$1
best_moments=$2
output_folder=$3
if [ ! -d ${output_folder} ]; then
mk... |
4025febd32c7b954450b6111c1d11e2294fe7f05123cc812fd4d9dabc05b4cf3 | Shell | 461 | 21 | #!/bin/bash
set -x
GPUS=$1
exp_name=medvit_cls_exp
time=$(date "+%m%d_%H%M%S")
save_root_dir=../${exp_name}/${time}
if [ ! -d ${save_root_dir} ]; then
mkdir -p ${save_root_dir}
echo save root dir is ${save_root_dir}.
else
echo Error, save root dir ${save_root_dir} exist, please run the shell again!
ex... |
49461ae27e45e0382d67bf9472e2eca991937013609dc7cb7bd9651b627861c6 | Shell | 461 | 10 | #!/bin/bash
for i in {1..27}
do
#for j in {1..16}
j=16
# do
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_pbs_scripts.sh 921 200 /global/project/projectdirs/m2043/BigNeuron/zhi/taiwan_16k_valid_batch_run/nopreproprcessing/pbs_all/taiwan16_nopre_${i}_part${j}.pbs /glob... |
e41cd6f7813dac8ee9832485443a8bccc73b6ad1ca689c6a9d06fae150021138 | Shell | 461 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=21
sta_i_batch_KM=1
end_i_batch_KM=16
n_batch_KM=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_KM in $(eval echo "{$sta_i_batch_KM..$end_i_batch_KM..$n_batch_KM}")
do
... |
25e01aece84fe4bbc0aeca7184f6e203e9508379beb486d015b342cb3533a766 | Shell | 462 | 10 | #!/bin/bash
for i in {1..27}
do
# for j in {1..8}
# do
j=8
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 150 20 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/gaussiansmooth_set2/pbs_all/janelia13_set2_gaussian_${i}_part${j}.pbs /... |
4ae06ea7ae54d693a712452c6c10073eec4fc3b66bf17711f465b73fc61569d3 | Shell | 462 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_gaussiansmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_gaussians... |
69b3253121c8df1c726fb028c725d11269fa4f1818dfc8a2b69ee2a15d2202c8 | Shell | 462 | 10 | #!/bin/bash
for i in {1..27}
do
# for j in {1..7}
# do
j=7
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 299 30 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/gaussiansmooth_set1/pbs_all/janelia13_set1_gaussian_${i}_part${j}.pbs /... |
742915044e9da6c994f6aee02a6c7842d44d72867ef8a4c996dbc8b1a3c2fa48 | Shell | 462 | 17 | #!/bin/bash
##
## Gencode, release 43 / assembly GRCh38
##
## 09th May 2023
## Izaskun Mallona
mkdir -p ~/indices
cd $_
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.primary_assembly.annotation.gtf.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GR... |
b3a04c9453f8e488275aa4620ea6c084a856c0979aead41e1f7662543b905813 | Shell | 462 | 10 | #!/bin/bash
for i in {1..27}
do
# for j in {1..16}
# do
j=16
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 921 100 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/taiwan_16k_valid_batch_run/anisosmooth/pbs_all/taiwan16_aniso_${i}_part${j}.pbs ... |
b33abffa8a16d13c90a55552f0d1a1b81207b23779f940091e25ae33e3ae7fc7 | Shell | 463 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=24
sta_i_batch_Kir=1
end_i_batch_Kir=11
n_batch_Kir=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_Kir in $(eval echo "{$sta_i_batch_Kir..$end_i_batch_Kir..$n_batch_Kir}")
do
... |
57a014d4bc405cc9d416f2045ef609483db353603602f73e57c7846750f4e153 | Shell | 464 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=21
sta_i_batch_KM=1
end_i_batch_KM=16
n_batch_KM=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_KM in $(eval echo "{$sta_i_batch_KM..$end_i_batch_KM..$n_batch_KM}")
do
... |
8f6bc34e4d97da8fd510da355aa2422c1c587564f9f0c6bfedd3cb494fc82a3e | Shell | 464 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_gaussiansmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_gaussia... |
0f6a7b297378d299df4ea09993bdfbc0199c9f6844f0cc65b62e82664b20aca6 | Shell | 465 | 20 | #!/bin/tcsh
set ANTSPATH=$argv[1]
set pointset = $argv[2]
set patid = reg_out
set tmpPath = $argv[3]
set WARPPTS = ${ANTSPATH}/antsApplyTransformsToPoints
######## apply warp - structural images
set CMD=" ${WARPPTS} -d 3 -i ${pointset} -o ${tmpPath}/${patid}_rigid.csv -t [${tmpPath}/${patid}0GenericAffine.mat, 1... |
25083f9e73d36a200f6116ab408b7863d226dd9272609a0f882eadbf7fbc75c6 | Shell | 465 | 15 | #!/bin/bash
# para for taskmng Ntask
Ntask=111;#110;#35;#1;#105;
npertask=16;#1772#3;#105;#1;
slurmfile="./slurm/step3_tri_3model_multiple_node.sl"
# loop for submit task
for ((itask=1; itask<=$Ntask; itask++)); do
# for ((itask=1; itask<=2; itask++)); do
sed -i "s/Ntask=[0-9]\+/Ntask=$Ntask/" "$slurmfile"
s... |
7224e8bb99bd25a13b3b32b07f4098e2d8d0a721fcdd5b7ae382602743303b67 | Shell | 465 | 10 | #!/bin/bash
for i in {1..27}
do
# for j in {1..8}
# do
j=8
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 150 20 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/anisosmooth_set2/pbs_all/janelia13_set2_aniso_${i}_part${j}.p... |
bd3d989a7212c5fb5cb30c5e39f60fd4f01df484bb59351cef1ca91949244abd | Shell | 465 | 12 | #!/bin/bash
cat .github/workflows/header.md > "COVID 19/fechas.md"
git log --shortstat -1 README.md
git ls-tree -r --name-only HEAD COVID\ 19/*.csv | while read filename; do
fecha=$(git log -1 --format="%aD" -- "$filename")
echo "| $fecha | $filename |" >> "COVID 19/fechas.md"
done
git config --global user.e... |
1278df076611cc4af29344ff74afd7c27bfee1970ddaceee5b0af785e5b2094b | Shell | 466 | 21 | #!/bin/bash -e
echo "Building and installing netneurotools"
python -m build
if [ "$INSTALL_TYPE" == "setup" ]; then
python -m pip install .
elif [ "$INSTALL_TYPE" == "sdist" ]; then
python -m pip install dist/*.tar.gz
elif [ "$INSTALL_TYPE" == "wheel" ]; then
python -m pip install dist/*.whl
else
false
fi
p... |
6c0d7f64f1033f5bffadfa36d503b9a5018652af90aced0cbf8aa33d5502a2f7 | Shell | 466 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=16
sta_i_batch_Kir=1
end_i_batch_Kir=6
n_batch_Kir=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_Kir in $(eval echo "{$sta_i_batch_Kir..$end_i_batch_Kir..$n_batch_Kir}")
do
... |
b667a843457e0e5e038fd92585b19f8a4f6b8258b3213aa7c10c32b765deb1a7 | Shell | 466 | 11 | #!/bin/bash
for i in {1..27}
do
j=7
# for j in {1..7}
# do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 299 30 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/anisosmooth_set1/pbs_all/janelia13_set1_aniso_${i}_part${j}.... |
8109a045a9a401fa843e1008b762c2ae2b68f0cc009d0f9ff91904c67ccff567 | Shell | 467 | 21 | #!/bin/bash
DIR="/ZPOOL/data/projects/night-owls/bids/sub-103/ses-02/func"
cd "$DIR" || { echo "Directory not found"; exit 1; }
shopt -s nullglob
for f in *run-3*; do
target="${f/run-3/run-2}"
if [[ -f "$target" ]]; then
if mv -f "$f" "$target"; then
echo "Moved $f → $target"
el... |
3947590aa1b0f894a1b0d078fbb945c3061e755fe733c522773fc4765f277a81 | Shell | 468 | 22 | #!/bin/bash
set -euo pipefail
list_file="$1"
outfile="$2"
echo "*** cat-bgen-wrap.sh ***"
echo "[info] list file: $list_file"
echo "[info] outfile: $outfile"
echo "[info] getting files..."
INFILES=($(cat "$list_file"))
echo "[info] merging chunks"
cat-bgen -g ${INFILES[@]} -og "$outfile"
echo "[info] create an inde... |
9b443b8d9e9a9e5344e9a6d9599360138491afa3fc8886e20551befc5e9a2a95 | Shell | 468 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_nopreproprcessing/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_noprep... |
a04141003fa23302d69ce227ebd741cf00acb27be9b0a83eea11f3c40b0f2913 | Shell | 468 | 18 | #!/usr/bin/env bash
# helper script to change ownership to $USER of built container,
# and moving file to the appropriate directory in repository
set -e
if [[ $(/usr/bin/id -u) -ne 0 ]]; then
echo "Must run script with sudo or as root"
exit
fi
# exit on errors
trap 'exit' ERR
# change ownership to $USER, mov... |
94a8819cf0b2f278ec9f25e2149c05984d73a33b5bc018d34337e0dc1621d9d2 | Shell | 469 | 18 | #!/bin/bash
# ensure paths are correct
maindir=/gpfs/scratch/tug87422/smithlab-shared/night-owls #this should be the only line that has to change if the rest of the script is set up correctly
scriptdir=$maindir/code
mapfile -t myArray < ${scriptdir}/sublist.txt
ntasks=9
counter=0
while [ $counter -lt ${#myArray[@]... |
080b6d0625e24b673ad0915b4271378ce42d80f5df0c18f7bf7070f95cb07a6b | Shell | 470 | 25 | #!/bin/bash --login
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=192
#SBATCH --time=04:00:00
#SBATCH --job-name='LFPy Circuit'
#SBATCH -o output.out
#SBATCH -e error.out
module load StdEnv/2023
module load python/3.13.2
module load cmake/3.31.0
source /project/def-etayhay/venvs/lfpy2/bin/activate
module load mpi4py/4... |
40bf8f950afb8610227c45ef324b664743d75a28c96168ec9896bc787e462abf | Shell | 470 | 20 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=21
sta_i_batch_Kir=1
end_i_batch_Kir=11
n_batch_Kir=6
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_batch_Kir in $(eval echo "{$sta_i_batch_Kir..$end_i_batch_Kir..$n_batch_Kir}")
do
... |
c04ff45e297e4f82ceb6dd8abc97bf1129e0ce6a27707977c61bb5c018287e58 | Shell | 470 | 29 | #!/bin/sh
# Mac os x intermediate between applescript and modlunit
echo -e "\033]0;modlunit\007"
MODLUNIT="modlunit"
if test "x$1" != x ; then
for i in "$@" ; do
if test -f "$i" ; then
cd `dirname "$i"`
arg1=`basename "$i"`
${MODLUNIT} "$i"
else
cd "$i"
for j in *.mod ; do
${MODLUNIT} "$j"
d... |
c6121a5c8627f4f4de1b2dab7930e8e8b6f558d6a6a7509687fa5462396015c1 | Shell | 470 | 14 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_nopreproprcessing/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_nopr... |
27c25c7deaa88130741323cc8222e124d46460d86c7825a62428132b22533f3f | Shell | 475 | 10 | #!/bin/bash
for i in {1..27}
do
for j in {1..7}
do
# j=8
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 1000 100 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/nopreproprcessing_set2/pbs_all/janelia13_set2_nopre_${i}_part$... |
1fc1d055d2e3c77c1ef9cc1b3d0cae3869494972f329c8cfc423d914274d4186 | Shell | 476 | 26 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_flye_hq
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 08:00:00
#SBATCH -v
#SBATCH -o run_flye_hq.%j.out
#SBATCH -e run_flye_hq.%j.err
module purge
module load bio/Flye/2.9.1-GCC-11.2.0
PROJECT_DIR=/lustre/project/m2_jgu-funcpoll
##... |
3e3de0cf32684c88ec929ee0d45819a6bbb262e15cde4abd6d11839ba937178d | Shell | 476 | 19 | #!/bin/bash
conda activate cyclegan_ulf
python train.py \
--data_path ../data/CycleGAN/ULF/train/ \
--label_path ../data/CycleGAN/HF/train/ \
--batch_size 2 \
--patch_size 128 128 128 \
--netG resvit \
--name cyclegan_model_1 \
--checkpoints_dir ../models/ \
--input_nc 2 \
--output_... |
5412c2e1a79c5645699fd2ad3e36ad4fc38f9a0ac64073bdcb91afa3894c67df | Shell | 476 | 11 | #!/bin/bash
for i in {1..27}
do
# j=7
for j in {1..6}
do
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_pbs_scripts.sh 1000 100 /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/janelia_13k_batch_run/nopreproprcessing_set1/pbs_all/janelia13_set1_nopre_${i}_part... |
68042fdc552be7636db76d6d9ff60db2555a82b35d500ea8e207bbd0a86bf443 | Shell | 478 | 9 | #!/bin/bash
for i in {1..22}
do
/global/homes/z/zhizhou/bigneuron/BigNeuron_bench_test_LBNL_v1/gen_bench_job_scripts.sh $i /global/homes/z/zhizhou/bigneuron/BigNeuron_bench_test_LBNL_v1/testing_data/images/test2/00039.FruMARCM-M002235_seg001.lsm.tif.c3.v3draw.uint8.v3draw /global/homes/z/zhizhou/bigneuron/Big... |
6fdb93262aa45851de75c45b98f5cc56737eada0c6bf25e88b1201735d91b439 | Shell | 478 | 8 | #!/bin/sh
echo "\n\n[rebuildPortalAssets.sh] Downloading latest npm package from internal npm registry..\n\n"
rm -rf ./node_modules
rm -f ./static/external_assets/bundled.js
npm install aibs-portal-assets --save --registry http://dev_resource:4873
rm -f ./node_modules/aibs-portal-assets/dist/index.html
cp ./node_module... |
753031519dd27417c9c39e15792fd8a76d43dfaf9ed88a0c7ab606e0eea315db | Shell | 478 | 14 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/img_anisosmooth/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/reconstructions_for_img_anisos... |
b4f038a6e5140d0fe60d281415636c41ad93e25ec3df94ef38f0c9538539d2da | Shell | 478 | 17 | #!/usr/bin/env bash
set -e
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
echo "SCRIPT_DIR: ${SCRIPT_DIR}"
echo "=> Create production bundle..."
cd ${SCRIPT_DIR}/../label_studio/frontend
npm ci && npm run build:production
cd ${SCRIPT_DIR}
MANAGE=${SCRIPT_DIR}/../label_studio/manage.py
... |
21d9bcf753ea9b728d0daf2e38aba2377a259a540796067727a01d5da8d5262f | Shell | 479 | 19 | #!/bin/bash
# change to the dir of the script
cd $( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# change to the dir to the project
cd ../..
title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
upload_dataset_config=AI/upload_dataset.yam... |
bb00db6ed07c128c244ee9b0c8883b04d9cb4408e0b8b90580ad5b49b714a3e5 | Shell | 479 | 22 | #!/usr/bin/env bash
CONFIG=$1
CHECKPOINT=$2
GPUS=$3
NNODES=${NNODES:-1}
NODE_RANK=${NODE_RANK:-0}
PORT=${PORT:-29500}
MASTER_ADDR=${MASTER_ADDR:-"127.0.0.1"}
PYTHONPATH="$(dirname $0)/..":$PYTHONPATH \
python -m torch.distributed.launch \
--nnodes=$NNODES \
--node_rank=$NODE_RANK \
--master_addr=$MASTER_A... |
2b8fdc327e16b997764d77ce8ae69d49e3ed0d5220276b996a6ff2b54d0eeb22 | Shell | 480 | 18 | #! /bin/bash
step=1
## Run T1
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist.txt
for sub in $(cat $sublist)
do
T1IMAGE=${sour_dir}/${sub}/t1.nii.gz
if [[ -f ${T1IMAGE} ]]... |
e48a4240dc8031cae4158a277acddb3987161abed6ba1d375e64486dd1bd3d5e | Shell | 480 | 19 | #!/bin/bash
export SUBJECTS_DIR=... # Set your SUBJECTS_DIR here.
fsgd_base_dir=... # Set your fsgd_base_dir here.
for hemi in lh rh; do
for smoothness in 10; do
for meas in volume thickness area; do
for tail in pos abs; do
glmdir=${SUBJECTS_DIR}/${hemi}.${meas}.${smoothness}_increase.glmdir
... |
7a282b5ce2ca85480620bc0cea280e19fd45f0c01ad155c2e29d449c5a53516a | Shell | 481 | 13 | #!/bin/bash
#SBATCH --job-name=hybrid-model_%a
#SBATCH --output=logs/hybrid-model/estimate_%A_%a.out
#SBATCH --error=logs/hybrid-model/estimate_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=01:00:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-HybridMode... |
ab1764397f6f7632e88662d717c2b1fae4be9b8c4094d9c59945cefefe3de55a | Shell | 482 | 28 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${FastqPath}
OutPath=${FastpPath}
#####
make_dir ${OutPath}
#####
fastp \
--in1 ${DataPath}${FASTQ1} \
--in2 ${DataPath}${FASTQ2} \
--out1 ${OutPath}${FASTP1} \
--out2 ${OutPath}${FASTP2} \
--html ${OutPath}${ID}.report... |
cee08211ce39bf9b5b06d07a27a8032b24315661c2c5a7f5146c38771496a89b | Shell | 483 | 15 | #!/usr/bin/env bash
npw=$(ps aux | grep ProcessWorker.py | grep -vw grep | wc -l)
echo "" && echo "There are ${npw} videos being processed now."
if [[ ${npw} -eq 0 ]]
then
echo ""
echo "To check if all videos have been processed, you can restart the "
echo "analysis in the Batch Processing Multiple Files GUI, selecti... |
d470d9df643a09426cdc938584575ed1d674b5cf430638fa48901fda418cb949 | Shell | 483 | 7 | #!/usr/bin/env bash
# Run the pipeline (ReadsPipelineSpark) on genome data in GCS.
. utils.sh
time_gatk "ReadsPipelineSpark -I gs://broad-spark-eval-test-data/genome/WGS-G94982-NA12878-no-NC_007605.bam -O gs://broad-spark-eval-test-data/genome/out/WGS-G94982-NA12878.vcf -R gs://broad-spark-eval-test-data/genome/huma... |
eff0f628414e65a0235aaa33168f9d4b38f6fe95da5c59e4e4fcd58f06d606d1 | Shell | 483 | 21 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_repeat_modeler_soft
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 36:00:00
#SBATCH -v
#SBATCH -o run_repeat_modeler_soft.%j.out
#SBATCH -e run_repeat_modeler_soft.%j.err
module purge
module load bio/RepeatModeler/2.0.2a-foss-2020b
... |
4d63623151bc373c08f533cd1c134d92807874fe22db8b23bb9349b708529f69 | Shell | 484 | 22 | #!/usr/bin/env bash
CWD=`pwd`
id=$1
GENOTYPE_DIR=$2
SAVE_DIR=$3
HASEDIR=$4
STUDYNAME=$5
cd $GENOTYPE_DIR
for i in $(cat ${SAVE_DIR}/files_order.txt ); do
zcat $i.dose.gz | gawk '{split($1,a,"->");if(a[2]=="'$id'"){$1="";$2="";gsub(" ","",$0);gsub(" ","\n",$0);print $0; exit}}' >>${SAVE_DIR}/${id}.txt
done
python... |
6e2baa1643887e5298689c7ddf278ce2fbd4ca3328874caca77cc9436fbe8857 | Shell | 484 | 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/... |
907390f357f690845745a6b187de229dd0c9597445e6ba61ac29f272fbf2f55b | Shell | 484 | 17 | #!/bin/bash
readonly URI_REGEX='postgres:\/\/(.+):(.+)@(.+):(.+)\/(.+)'
[[ $DATABASE_URL =~ $URI_REGEX ]]
export POSTGRE_USER="${BASH_REMATCH[1]}"
export POSTGRE_PASSWORD="${BASH_REMATCH[2]}"
export POSTGRE_NAME="${BASH_REMATCH[5]}"
export POSTGRE_HOST="${BASH_REMATCH[3]}"
export POSTGRE_PORT="${BASH_REMATCH[4]}"
exp... |
819c1ac601cbad158ab3573b94d2f3ec6706a427cc6a0c0f72af5bfdb674825a | Shell | 485 | 8 | #!/bin/bash
for i in {1..164}
do
echo $i
/lustre/atlas2/nro101/proj-shared/BigNeuron/Script_Vaa3D_svn_ORNL/script_MPI/gen_bench_c_exe_scripts.sh /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/bigneuron_annotation_consolidated_batch_run/gold166/runVAA3D_all/runVAA3D_gold166_$i.c /lustre/atlas2/nro101/proj-sh... |
a6428e39e9e8458fdd65b4e79b515a81f0fad3da2f0624410a852e16e785c413 | Shell | 485 | 8 | #!/bin/bash
for i in {1..164}
do
echo $i
/global/project/projectdirs/m2043/BigNeuron/Script_Vaa3D_svn_LBNL/script_MPI/gen_bench_c_exe_scripts.sh /global/project/projectdirs/m2043/BigNeuron/zhi/bigneuron_annotation_consolidated_batch_run/gold166/runVAA3D_all/runVAA3D_gold166_$i.c /global/project/projectdirs/m... |
cedbd5b1c94e90413633f657317874e89ec70c150df701be418be1968bda081a | Shell | 485 | 16 | #!/bin/bash
# Signing the package with an identified developer certificate means the
# installer does not have to lower the security settings on their machine.
# The information in this file is not private since the installer may obtain
# with
# pkgutil --check-signature /path/to/package.pkg
# "$1" The package to be ... |
29862480fe082fdcfa03c5d7574cf701b51fa90e99bc4d66c786895a71a83293 | Shell | 486 | 33 | #!/bin/sh
# Mac os x intermediate between applescript and nrngui
echo -e "\033]0;nrngui\007"
NRNGUI="nrngui"
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"
shift
${NRN... |
490e0c889a504ccf4c4f72684f958ef04d460f38b2951401853ac622964324c1 | Shell | 486 | 17 | #!/bin/sh
# Mac os x intermediate between applescript and mos2nrn
echo -e "\033]0;NEURON launched from browser\007"
if test "$1" = "" ; then
echo "The purpose of mos2nrn is to unzip, build, and launch
models downloaded from the ModelDB model database at
http://senselab.med.yale.edu."
echo "Drop a nrnzip (or zip) f... |
f463c9b74c57eb06570c4d5cae4b854e72c16ae0e2ce776b20325c5b691cd509 | Shell | 486 | 7 | #!/usr/bin/env bash
# Run the pipeline (ReadsPipelineSpark) on exome data in GCS.
. utils.sh
time_gatk "ReadsPipelineSpark -I gs://broad-spark-eval-test-data/exome/NA12878.ga2.exome.maq.raw.bam -O gs://broad-spark-eval-test-data/exome/NA12878.ga2.exome.maq.raw.vcf -R gs://broad-spark-eval-test-data/exome/Homo_sapien... |
f8e440d0d8119b9b5bdc58beb358fef4b7083bbf7e2d23a084a5bb76ce2d4e0e | Shell | 486 | 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... |
3f2ad1342ccfdddc3c662110d9e2b5023a9dd74302eecb3f0b3df62c494b97e0 | Shell | 487 | 27 | #!/bin/sh
# Mac os x intermediate between applescript and nrnivmodl
echo -e "\033]0;mknrndll\007"
NRNIVMODL="nrnivmodl"
if test "x$1" != x ; then
if test -f "$1" ; then
dname=`dirname "$1"`
cd "${dname}"
files=""
while test $# -gt 0 ; do
files="$files "`basename "$1"`
shift
done
${NRNIVMODL} $files... |
55dfb8c5ae36555567e132b451253bf02008a2cba14e7102b1df88cc042338f8 | Shell | 488 | 18 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 1-00:00
#SBATCH -p medium
#SBATCH --mem=64G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_aggregate_influence_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_aggregate_influence_%j.err
start=$(date +%s)
cd /home/ab714/bancpipeline
source /home/ab714/bancpipeline/o2/o2_env.sh
u... |
ed7922c60ff990fd6c9e3bce1641426e86fabb5ddffde587af71e612e3c5d1bb | Shell | 488 | 17 | #!/bin/bash
export SUBJECTS_DIR=... # Set your SUBJECTS_DIR here.
fsgd_base_dir=... # Set your fsgd_base_dir here.
fsgd_file=${fsgd_base_dir}/fsgd_increase.tsv
for hemi in lh rh; do
for smoothing in 10; do
for meas in volume thickness area; do
mris_preproc --fsgd ${fsgd_file} \
--cache-in ${meas... |
f39c2e4488463ac5003865ab02cff4a49f48f1b5a6bad73d71009770f179291e | Shell | 488 | 13 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate julearn
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
python3 /data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive... |
18b4fb9919b85578dfd5d342ea52452122d0e06061c8092fd8b944d3a87b0d19 | Shell | 489 | 9 | #!/usr/bin/env bash
# ensure a valid job identifier
jobID="$*" # concatenate all input into a variable
jobID=$(echo "$jobID" | tr [:space:] ,) # replace spaces with commas
jobID=$(echo "$jobID" | tr -s ,) # squeeze series of commas to single
jobID=${jobID#,}; jobID=${jobID%,} #... |
ddf7e0e1b59394c77a714d72118853d00af06c63f4f74db9622c1a996be6d071 | Shell | 489 | 16 | cli_arg=$1
OMPI_VERSION_STRING=$cli_arg
if [ -z "$cli_arg" ]; then
path=$PATH
OMPI_VERSION_STRING=$([[ $path =~ openmpi-[0-9]+\.[0-9]+\.[0-9]+ ]] && echo $BASH_REMATCH)
fi
if [ -z "$OMPI_VERSION_STRING" ]; then
echo "Open MPI not found in PATH and no version string provided as argument."
exit 1
fi
OM... |
e9bb58c0f4521a0071f4505f58519ffbd86f10ce8d246b9a4268f394f07d37bd | Shell | 489 | 14 | #!/bin/bash
# Download low confidence regions from UCSC genome browser
CENTROMERES=https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz
SDS=https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/genomicSuperDups.txt.gz
mkdir -p files/UCSC_files
cd files/UCSC_files
wget $CENTROMERES
wget $SD... |
8537791c34072f50530b43a3d66949fa3ca171356b2bf32b8236efd28224ecdf | Shell | 490 | 13 | #!/bin/bash
source /p/project/cinm-7/bi1/miniconda3/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 /p/project/cinm-7/bi1/ENIGMA_Sleep_Cog_Predicti... |
92ba81181345f02e84f5128105cdf39239dedd65686c82927436ce4b5127f268 | Shell | 490 | 16 | #!/bin/bash
#hg19: /storage/resources/dbase/human/hg19/chromFa/ \
# New hg19: /storage/nmmsv/ref_genome/hg19/chromFa/ \
#hg38: /storage/nmmsv/ref_genome/chromFa/
# mm10: /storage/nmmsv/ref_genome/mouse/mm10
# mm9: /storage/nmmsv/ref_genome/mouse/mm9
#maximum chr number (other than sex chroms) human:22, mouse:19
./chr... |
fd0cce0ed0a530499e9b7019cee737de14d4f5a43f091ccb3c99223e83acab09 | Shell | 490 | 14 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/img_nopreproprcessing/
for filename in `ls -d *`
do
cd $filename
echo $filename
for file in `ls *.swc`
do
mv $file /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/reconstructions_for_img_... |
035be3e5f92fdcca798fba1b3f3884aa947dd21488d6af1fd14066ee0416d092 | Shell | 491 | 12 | #!/bin/bash
# This script is used to run the MethylCnT pipeline for ChIP-Seq data.
chipr -i 04-analysis/ANA01-mCT_construsts/peaks/*pA* \
-o 04-analysis/ANA01-mCT_construsts/peaks_replicates/all_pA.broadPeak
chipr -i 04-analysis/ANA01-mCT_construsts/peaks/*gDNA*pA* \
-o 04-analysis/ANA01-mCT_construsts/peak... |
26833ffccf07e2ad4460eafd5e5dd562fc1719a8fde57a8ec223182f300f4e89 | Shell | 491 | 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... |
e032b1b40cc2053bdb2bd63984931565a64aaf7ab1e69956517c842d49f78a17 | Shell | 491 | 7 | cp /net/ostrom/data/bcc/charliew/annotationFiles/c2.cgp.v2023.2.Hs.symbols.gmt .
cp /net/ostrom/data/bcc/charliew/annotationFiles/c2.cp.v2023.2.Hs.symbols.gmt .
cp /net/ostrom/data/bcc/charliew/annotationFiles/c5.go.bp.v2023.2.Hs.symbols.gmt .
cp /net/ostrom/data/bcc/charliew/annotationFiles/c5.go.cc.v2023.2.Hs.symbols... |
a08353da23806c179de9b9c5aeee0b4a9823ef35412462c0f72780dc657666a3 | Shell | 492 | 15 | #! /bin/bash
export SUBJECTS_DIR=$1
SUBJECT=freesurfer
## Calculate LGI
recon-all -s ${SUBJECT} -localGI
## Calculate ROI measure
for curr_parc in Schaefer.300Parcels.7Networks 500.aparc
do
for hemi in lh rh
do
mris_anatomical_stats -mgz -cortex ${SUBJECTS_DIR}/${SUBJECT}/label/${hemi}.cortex.label -f ${SUBJECT... |
fb0273da3ff111c6596e437f037cd3130f25530e7705b5df0c2f95997331587e | Shell | 492 | 21 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Detect the platform
echo "Installing dependencies. You might be prompted for your sudo password."
OS="$(uname)"
cas... |
9866317d517d1ecfa7afd9f3cc692826d06e8743a5fc4feb292f3feff30200d0 | Shell | 493 | 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/... |
b37916a51438265802aac116396031fe158daf82052e243d0969a0607a1cc843 | Shell | 493 | 27 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
DataPath=${FastqPath_A}
OutPath=${FastpPath_A}
#####
make_dir ${OutPath}
#####
fastp \
--in1 ${DataPath}${FASTQ1_A} \
--in2 ${DataPath}${FASTQ2_A} \
--out1 ${OutPath}${FASTP1_A} \
--out2 ${OutPath}${FASTP2_A} \
--html ${OutPath}... |
3ed0bccf0f23f098ef04327abaa93d5e9774288d6d681fe26a268cbe56c7ed19 | Shell | 494 | 13 | #!/bin/bash
#SBATCH --job-name=linear-model-%a
#SBATCH --output=logs/linear-model/cross-validation_%A_%a.out
#SBATCH --error=logs/linear-model/cross-validation_%A_%a.err
#SBATCH --array=1-20%20
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human... |
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