sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b9ee18b9d7fdf584b575aab9b2f431269a3c3fc7be78accd17facf0aa7d57d01 | Shell | 711 | 37 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_full_p40
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/... |
efa916e597f1c4c097676947a759fe6f9a5490e30c6c7e051627bda86a7655fc | Shell | 711 | 11 | #!/bin/bash
for S in {0..87}; do
echo $S
python ../../examples/run_zsssl.py --config /figures/motion/config_zsssl_navi.yaml --mode test --checkpoint /examples/2024-05-22_zsssl_0.7mm_21-dir_R2x2_vol1_scan1_kdat_slice_040_norm-kdat-1.0_navi_ResNet2D_ResBlock-12_kernel-3_ADMM_08_lamda-0.050_Adam_lr-0.000500_MixL1... |
d2721157401d2bc8122ac5a14b2a23390e398296cdfb3961eb266ff8b9cd8a30 | Shell | 713 | 19 | #!/bin/bash -l
#SBATCH --job-name=struct_comp
#SBATCH --time=5:00:00
#SBATCH --account=proj142
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
#SBATCH --out=logs/%j.txt
#SBATCH --err=logs/%j.txt
module purge
module load unstable
#source /gpfs/bbp.cscs.ch/home/pokorny/ReWiringKerne... |
06cc7c8bff1cedc53a86b987b498ac6a05eeda5802cf7bba4ea2b46d36f60084 | Shell | 715 | 27 | # config_path=configs/blood_config.yaml
config_path=configs/multi_gene_196kb_blood.yaml
model_type=MultiGene
seed=0
# for fold in 0 1 2; do
for fold in 0; do
for random_weights in 0 1; do
sbatch slurm_train_gtex_random_weights.sh $config_path $fold $seed $model_type $random_weights
done
done
#for t... |
5e6693fb942ef65da30c0bcb12b0dfc7a27762ddfcaeeee80d5ed482ff530030 | Shell | 717 | 20 | #!/bin/bash
# Jo Lynne Rokita (D3b), Run Jin (D3b), and Stephanie Spielman (CCDL)
# Run survival analysis
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Plot survial curves of subtypes in HGG/DMG samples
Rscript -e "rmarkdown::render('surviva... |
4ff7241a07251c77922f12ee330b734f1b0164d51f67a41cd097e64152bf55e0 | Shell | 718 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%... |
ab25b99e6d0060b064c29e4d9691c6f4fa0c657c0a87d8afe34b56b01d0b4b6a | Shell | 719 | 25 | #!/usr/bin/env bash
set -e
fs_subjects_dir=$1
fs_subject_id=$2
output_gm_mask=$3
# merge lh.ribbon.mgz and rh.ribbon.mgz to create a gm mask, and delete temporary files
output_dir=$(dirname "${output_gm_mask}")
mkdir -p "${output_dir}"
# make a temp dir in output dir
temp_dir=$(mktemp -d -p "${output_dir}")
mri_con... |
0554bb725781a0d30ffef14f100a04ed9a862c0b8b77f146a7f47d84c4e9d340 | Shell | 721 | 15 | ############## Maleckar 2008 ##########################################################
MODEL_FILE_CPU="Maleckar2008.c"
MODEL_FILE_GPU="Maleckar2008.cu"
COMMON_HEADERS="Maleckar2008.h"
COMPILE_MODEL_LIB "Maleckar2008" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
###############################################... |
318add2a173327eea46e9ba215760f81bdb9b284eea17caedf0b129af412dabf | Shell | 721 | 47 | #! /bin/bash
set -e
pf_agg() {
local m=$1
shift 1
sleep 20
python -m rscvp.statistic.$m \
-D 250916,250917,250918,250919,251018,251019 \
-A YW102,YW102,YW071,YW071,YW109,YW109 \
-P ,,,,, \
"$@"
}
# ----- width ----- #
pf_agg csv_agg.main_pf_agg \
-H pf_width \
--trunc-session \
-s close \
... |
6ee054dafced29d2afef2a3bb191df02ac8733b70567ad31d67d8f859f971ef2 | Shell | 722 | 23 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
e524c935a568a7a4619c019ea2075a61e27a7b12732ca5f6be00c2f5af397435 | Shell | 723 | 36 | #!/usr/bin/env bash
set -e
# === Argument parsing ===
EPI=$1
T1=$2
T1BRAIN=$3
OUT=$4
WMSEG=$5
EPI2T1MAT=$6
T12EPIMAT=$7
if [[ $# -ne 7 ]]; then
echo "Usage: $0 <epi.nii.gz> <T1.nii.gz> <T1_brain.nii.gz> <output_epi_reg.nii.gz> <wmseg.nii.gz> <epi2t1.mat> <t12epi.mat>"
exit 1
fi
# === Run epi_reg ===
epi_reg --ep... |
1117b2496a56ff09ccda92b7b1378f82a768a020b275ca0fef3c311ced9c6b31 | Shell | 725 | 14 | #!/bin/bash
bash ./tools/dist_train.sh configs/SimIPU/SimIPU_r50_scratch_nyu.py 2 --work-dir nfs/saves/SimIPU/scratch_nyu
bash ./tools/dist_train.sh configs/SimIPU/SimIPU_r50_supervise_imagenet_nyu.py 2 --work-dir nfs/saves/SimIPU/supervise_imagenet_nyu
bash ./tools/dist_train.sh configs/SimIPU/SimIPU_r50_kitti_50e_ny... |
b675917887adde8e72c0e1016647fe4378eebeb12acc7f74d922cda49f76ace8 | Shell | 728 | 25 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
4fd24c05f7c18c47e7b69f77aa071f1f ${pref}_0
7059a4e90b6670b2d814e44e2bc7d429 ${pref}.histo
c3233e107bb6b42d0c979707f156264c ${pref}.query
EOF
echo "Counting 22-mers on ${nCPUs} CPU" && \
cat seq10m.fa | $JF count --matrix seq10m_matrix_22 -... |
c68d3903498f76d6372d6f521a379384e89e437504caa36bea60024fbf274f9c | Shell | 728 | 33 | #!/bin/bash
# Check if the correct number of arguments is provided
if [ "$#" -ne 1 ]; then
echo "Usage: $0 <path_to_directory>"
exit 1
fi
# Get the directory path argument
path=$1
# Check if the directory exists
if [ ! -d "$path" ]; then
echo "Error: Directory $path not found."
exit 1
fi
# Check if ... |
af38caaaf9ddb6714a6027e9bee6b9eb9ccf76620c9aeadfbfe9cd9eb81320fd | Shell | 733 | 28 | #!/bin/bash
# Written originally Chante Bethell 2019
# (Adapted for this module by Candace Savonen 2020)
#
# Run `00-subset-files-for-chordoma.R` and
# `01-Subtype-chordoma.Rmd` sequentially.
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_... |
67409f55d1b53d8f31f40848687764189d19f5cc3c3ce3ebf734854147ceaac3 | Shell | 737 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%... |
e37bc10aed2a1759aabebfb0551d30456bbd2425e13d4c2f61ec9cb185b0a1b2 | Shell | 738 | 47 | #! /bin/bash
set -e
spatial_agg() {
local m=$1
shift 1
sleep 10
python -m rscvp.statistic.$m \
-D 250916,250917,250918,250919,251018,251019 \
-A YW102,YW102,YW071,YW071,YW109,YW109 \
-P ,,,,, \
"$@"
}
# ----- si ----- #
spatial_agg csv_agg.main_spatial_agg \
-H si \
--trunc-session \
-s clos... |
0b4d82e95cd28248bf1ca7364eda03498b9ef56dcf893a17a6ff2665b40ac178 | Shell | 739 | 31 | #!/usr/bin/env bash
# NB: this is a convenience script; under normal circumstances
# validation files will be built as required by CMake.
cmd="${0##*/}"
function usage {
echo "usage: $cmd SCRIPTDIR [DESTDIR]"
exit 1
}
if [ $# -gt 2 -o $# -lt 1 ]; then usage; fi
scriptdir="$1"
if [ ! -d "$scriptdir" ]; then
... |
68c391c92ba9d34c10c408287320a90d32aa7235876fc4ccbc3051c473137225 | Shell | 739 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_spirals_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME... |
43cf178aa9afde7e09619f3c51dc347125dfd61d0107d2a2c88b3b435b0e51c7 | Shell | 740 | 26 | IMAGE="acrumley/setbp1-shiny:0.1.1"
SIF="setbp1-shiny_0.1.1.sif"
if [[ ! -f "$SIF" ]]; then
echo "$SIF not found — pulling image..."
singularity pull docker://$IMAGE
else
echo "$SIF already present."
fi
singularity exec \
--cleanenv \
--containall \
--bind run:/run,var-lib-rstudio-server:/var/... |
d46283cf3f35da7cdd446c5b34632983b5ca50f95d9c201219ca9ff23ffb1570 | Shell | 740 | 11 | #$ -M chef.maximiliano@gmail.com # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -pe smp 1 # Specify parallel environment and legal core size
#$ -q long # Specify queue
#$ -N merge_fastq # Specify job name
run1_dir=/afs/crc/group/TIMELab/N... |
a42eca6888d7c13a59b72827d512e3628549fbdbc2d50af7253245c59c5c1258 | Shell | 742 | 25 | #!/bin/bash
# Bethell and Taroni for CCDL 2019
# Run the dimension reduction plotting pipeline. Samples will be colored by
# user-specified variable. It will be broad_histology by default.
set -e
set -o pipefail
COLORVAR=${COLOR:-broad_histology}
# This script should always run as if it were being called from
# the... |
c907bdd340fd694ff318fdb20511c2cb0c4663860898371db07fa83bb2b8ce77 | Shell | 742 | 22 | #!/bin/bash
REGION=$(sed -n "${SLURM_ARRAY_TASK_ID}p" /path/to/regions.txt) #A simple lookup table of the GTEx v8 brain region used in our T-SEM pipeline to store prefixes
OUTDIR=/path/to/univ_outputdir
WEIGHTS=/path/to/weights/${REGION}.pos
WEIGHTS_DIR=/path/to/weights
REF_LD_BASE=/path/to/LDREF/1000G.EUR.
for chr ... |
5d11ab58b05f79f28237070be9f25ebd5840fdea3934555a31358de277c0f338 | Shell | 743 | 35 |
#!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_p0
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/minic... |
410362cd6af5dde8d7e457315d141bfc9cb83154158cefda4e8a01f3a64aa515 | Shell | 744 | 16 | # =======================================================================================
# Bash script to convert a set of frames stored in .png to video animation in .mp4
# Author: Lucas Berg
# =======================================================================================
#!/bin/bash
# Variables
FILENAME="f... |
c2dedd42424cce299d323e176faf37455ddf1863ddf1aeab917ec90cea2ca6d1 | Shell | 744 | 34 | #!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_p40
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/minic... |
304e51a8ef7df3e3bc40e838e5ac5e8974be2c964bb5d15184852f21c9d1e0da | Shell | 745 | 35 |
#!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_p10
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/min... |
87faa0bbd3381cf3ba603cc4ae6aba84d599ca0e0b1b755df6aefae2af67b045 | Shell | 745 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_dev_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/$JOB_NA... |
aa3ff4efa83b692e2e5c6405c91abce6bfdf9c18011311e41650be35d37a58b0 | Shell | 745 | 35 |
#!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_p30
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/min... |
b2101aac31fa57bc4978f1fd3b46add62afecb800e93a8446cd22d924125fc96 | Shell | 745 | 35 |
#!/bin/bash
#SBATCH --mem=32G
#SBATCH -c 16
#SBATCH -t 00:02:00
#SBATCH --error=/err/path
#SBATCH --output=/out/path
#SBATCH -p gpuq
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=infer_p20
module load cuda11.8/toolkit/11.8.0
nvidia-smi
date
# Activate the Miniconda base environment
source {your_conda_directory}/min... |
8b5e7a590352e4857e2591636c59f8111ddd19d628a461674648cd098e43a01f | Shell | 747 | 45 | #! /bin/bash
set -e
set -x
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/concat_etl.log"
export NO_COLOR=1
# Redirect all script output (stdout and stderr) to the log fil... |
2023946e9106a7fea52017d72ba6cfd635113d18afc8aa988fe5b807a7ac96ac | Shell | 748 | 10 |
#!/bin/bash
# main analyses
cp ~/two_axes/code/run_babs_qsirecon/qsirecon_json_files/mrtrix_singleshell_ss3t_ACT-hsvs_pyafq_dti.json ~/input/PNC/derivatives/babs_qsirecon_pyafq_act_v2/analysis/code
cp ~/two_axes/code/run_babs_qsirecon/qsirecon_json_files/mrtrix_multishell_msmt_ACT-hsvs_pyafq_dti.json ~/input/HCPD/der... |
304fc22e295a0c4217df40005398a3fc65f833e8eb84036866fa07bb30df726a | Shell | 754 | 46 | #! /bin/bash
set -e
set -x
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/concat_etl.log"
export NO_COLOR=1
# Redirect all script output (stdout and stderr) to the log fil... |
09024d4c0b816a0864c27adac5502a36670324b785f1b9e1c757db7353193f7c | Shell | 755 | 45 | #! /bin/bash
set -e
set -x
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/concat_etl.log"
export NO_COLOR=1
# Redirect all script output (stdout and stderr) to the log fil... |
3750d6bab9782ee83de1b74c355b09e0e74417b50ff4f7120c3a92575eb0e46a | Shell | 758 | 36 |
#!/bin/bash
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate babs
########################
# HCPD - noddi
########################
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/babs_noddi
babs-merge --project-root $PWD
########################
# HCPD - mapmri
###########... |
5a846a13d6b99892e89823527a7a6aade2875f871bcf93585457d2a73140b948 | Shell | 759 | 30 | rm -f tensor_benchmark_sycl
: "${COMPUTECPP_PACKAGE_ROOT_DIR:?Need to set COMPUTECPP_PACKAGE_ROOT_DIR}"
echo "COMPUTECPP_PACKAGE_ROOT_DIR is set to: "$COMPUTECPP_PACKAGE_ROOT_DIR
${COMPUTECPP_PACKAGE_ROOT_DIR}/bin/compute++ \
tensor_benchmarks_sycl.cc \
benchmark_main.cc \
-I ../../ \
-I ${COMPUTECPP_PACKAGE_ROO... |
294e465c1b38d65f29cb03378f2dd0c106b2603ca88880f12fb372cfccc61443 | Shell | 760 | 33 | #!/bin/bash
set -e
set -o pipefail
# This script checks that all python files in the docker image match
# requirements.txt
# run from this file location but move up to root
cd "$(dirname "${BASH_SOURCE[0]}")"
cd ..
req_diff=/tmp/package_diffs.txt
## diff will exit code 1 with differences, so we need to pass true
... |
6c5b2624e8ad84186303f80e47ac63f2dd0d523e7f5588cc8d363d86f170273c | Shell | 760 | 22 | #!/bin/bash
file="$1"
XMLSTARLET=$(which xmlstarlet)
BASE64=$(which base64)
ZLIBFLATE=$(which zlib-flate)
if [[ -z $XMLSTARLET ]]; then echo "xmlstarlet not found"; exit 1; fi
if [[ -z $BASE64 ]]; then echo "base64 not found"; exit 1; fi
if [[ -z $ZLIBFLATE ]]; then echo "zlib-flate not found"; exit 1; fi
count=$($XM... |
4da37d0048d9750078bc159fc6426d2119a2e4ea231c1e9ef95b2d8771e9d4f1 | Shell | 762 | 14 | #!/bin/bash
mkdir MyIcon.iconset
sips -z 16 16 Icon1024.png --out MyIcon.iconset/icon_16x16.png
sips -z 32 32 Icon1024.png --out MyIcon.iconset/icon_16x16@2x.png
sips -z 32 32 Icon1024.png --out MyIcon.iconset/icon_32x32.png
sips -z 64 64 Icon1024.png --out MyIcon.iconset/icon_32x32@2x.png
sips -z 128 1... |
59182a3d87c8874b52c62bef75f5971e73b9dd8ed5a0f53fcc21efdd100bd845 | Shell | 765 | 16 | ############## CRN ##############################
MODEL_FILE_CPU="courtemanche_ramirez_nattel_1998.c"
MODEL_FILE_GPU="courtemanche_ramirez_nattel_1998.cu"
COMMON_HEADERS="courtemanche_ramirez_nattel_1998.h"
COMPILE_MODEL_LIB "courtemanche_ramirez_nattel_1998" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
#####... |
c15b7ed32825c9b750f285d2154083f40bde2007d53fe83870e077c5629dd37d | Shell | 765 | 15 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
path_to_metadata=./metadata_from_past_runs/wandb_export_FinalPape... |
45f150648ba07ccdf80e2f4178b673795d6a7290c9f3fc397b20d10dbd6e94ee | Shell | 771 | 28 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
8bfdd1b137b73ebfed05d0496bbddd0c ${pref}.histo
9418b1a2e05a2526a81ae9b1200ed5df ${pref}_Q.histo
768e261fc7d7ede192f4a0eeae6e839f ${pref}_LU.histo
EOF
echo "Counting 10-mers on ${nCPUs} CPU"
$JF count --matrix seq10m_matrix_10 -m 10 -t $nCPUs \
-... |
88ea3ae7845413a2550348e06ff9ddf5944b8fb3ff563f2723010143048e3856 | Shell | 772 | 13 | #!/usr/bin/env bash
# Check any git submodule remotes for updates, and print difference with current Arbor repo state to `diff.log`
git submodule foreach 'git describe HEAD --tags' | tee current_state_of_git_submodules_in_arbor_repo.log
git submodule foreach 'git fetch'
git submodule foreach 'git describe `git log --b... |
b548b839497bd5f684db0c99ea0a9be78b746dc22dcc56e0987d4915ba970060 | Shell | 772 | 33 | #!/bin/bash
#SBATCH --job-name=prepare_thr
#SBATCH --output=./slurm_out/prepare_thr.out
#SBATCH --error=./slurm_out/prepare_thr.err
#SBATCH --time=00:10:00
#SBATCH --mem=16Gb
#SBATCH -c 4
#SBATCH -p cpu_p
#SBATCH --qos=cpu_normal
# To run this file:
# cd ./reproduce/synleth/
# sbatch ./scripts/01_prepare_thr.sh
# Se... |
f7d26c77bda4a1303d378bd2f6772fac709bbbced8c524c48757b88369e46666 | Shell | 774 | 18 | !#/bin/sh
data_root=data
echo "Parsing UniProt data and creating the DataFrame"
python gendata/uni2pandas.py -sf $data_root/uniprot_sprot.dat.gz -o $data_root/swissprot_exp.pkl
echo "Adding interactions data to the DataFrame"
python gendata/ppi_data.py
echo "Creating FASTA file for diamond database"
python gendata/p... |
e0cdea3ae72cad836a7e005226d3177e44875b3218010cea4b581b66a9c0e5e8 | Shell | 776 | 28 | #!/bin/bash
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# This option controls whether on not the step that generates the LGAT only mutation
# files gets run -- it will be turned off in CI
SUBSET=${OPENPBTA_SUBSET:-1}
# Generate JSON file with... |
c6c7b57f1a0d97eeb43ee9e953f7a0970a74a1a17ffcd3f4de6921b8d0d429a2 | Shell | 777 | 16 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
path_to_metadata=./metadata_from_past_runs/wandb_export_FinalPape... |
158b3aa69d8a38ed8fc5c8842c1ab02e90f8ad4d1edc624b87c81d5b3215196e | Shell | 779 | 32 | #!/usr/bin/env bash
set -euo pipefail
# Post-processing for FreeSurfer's mri_synthseg
# Create a white-matter mask from specified labels
if [[ $# -ne 2 ]]; then
echo "Usage: $0 <synthseg_input_img> <wm_output_name>"
exit 1
fi
SYNTHSEG_INPUT_IMG=$1
WM_OUTPUT_NAME=$2
# Basic checks
if [[ ! -f "$SYNTHSEG_INPUT_IMG... |
b6b6dbf3b154b2545fcd123dbe33a64c6ca55869cf9df01f919a609d2578be63 | Shell | 779 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmil/... |
58cef8ce6cdf7d86481d52885dbac887bc92b444bd8685dc33625ed63730aada | Shell | 781 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_dev_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaron... |
c7b0bea002127625303dc5d8afbfb117a611c3b88422f448aa5a4dbe6a0c4a9d | Shell | 781 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_spiral_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmil... |
414aae04c30c5347b2b88509bce1a64d18a24d6dca255d3ba339e7e57e417556 | Shell | 782 | 23 | #!/bin/bash
if [ "$#" -ne 1 ]; then
echo "Command requires 1 argument (input dir). Destination dir will be a \'pred\' subfolder of it. Only run within nnUNet enviroment"
exit 1
fi
dataset_id="001"
inpDir=$1
outDir1=$inpDir"/pred_nnUnet"
outDir2=$inpDir"/pred_nnUnetResM"
outDir3=$inpDir"/pred_nnUnetResL"
merg... |
903a979fcb6867e484e3f78399bd14b01763f54d3c321eccec6a8118ba306bb3 | Shell | 782 | 29 | #! /bin/sh
cd tests
. ./compat.sh
if [ -z "$BIG" ]; then
echo "Skip big test"
exit 77
fi
sort -k2,2 > ${pref}.md5sum <<EOF
f52abd3e2a7cc5089cc8f32cb607c4c5 ${pref}_16.histo
EOF
# $JF count -m 31 -s 4000000000 -o ${pref}_31 -c 4 -p 253 -C -r -t $nCPUs --timing ${pref}_31.timing \
# seq30g.fa && \
... |
434a11a0804208fd504b29f671b7a6212f8f94d5b9e1ca295e4d06da048d2b6c | Shell | 783 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_cifar10_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmi... |
efc4608af82f717c7ea01b7be77f46c6f54c4ebaccff89d5a9ca2b719540a7f4 | Shell | 783 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_spiral_dev_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaro... |
d77e9f481dd6da1f179025b1725ad5f6d58de382660b36377a7f11d160a6b78c | Shell | 784 | 28 | #!/bin/bash
# Validate input parameters
if [ "$#" -lt 2 ]; then
echo "Usage: $0 <gpu_ids> <output_path> [additional_args]"
exit 1
fi
# Convert output path to absolute path
outpath="$2"
if [[ "$outpath" != /* ]]; then
outpath="$(pwd)/$outpath"
fi
# Create output directory
mkdir -p "$outpath"
echo "Runnin... |
a081a77fe2bed40a6145549a94403c30e3b7c53064c54b17df95fc5b4785c606 | Shell | 785 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_cifar10_dev_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aar... |
7b4958e3325cb9bfd37ae1e41759a7dd151e0123eea4cb8692d0c71acd155abb | Shell | 787 | 20 | #!/bin/bash
# This study uses a single heuristic file that should be consistent across all subjects
# because they all get scanned with the exact same sequence
# This also only runs in an interactive bash instance, not in slurm
# Monica tried setting it up to run through slurm and it appeared to convert the data okay
#... |
39473fa8d2dfe663690cb49419a0b1354c2dd1ea79f067f703214e6acd2163cb | Shell | 790 | 28 | #!/usr/bin/env bash
# Mention here where your remote datasets are
# raw dataset url (either GIN or openneuro)
# for DEMO use: git@gin.g-node.org:/cpp-lln-lab/CPP_visMotion-raw.git
URL_RAW=''
# derivatives sibling url
# for DEMO use: git@gin.g-node.org:/cpp_brewery/CPP_visMotion-derivatives.git
URL_DER=''
# derivati... |
41eb6db4bc0e17a56d57cd9b09c1116e46fbbb8d09fbc2f2432834205e9a54ab | Shell | 791 | 22 | #!/bin/bash -l
#SBATCH --job-name=conn_rewire
#SBATCH --partition=prod
#SBATCH --nodes=5
#SBATCH --tasks-per-node=18
#SBATCH --cpus-per-task=4
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --out=logs/%j.txt
#SBATCH --err=logs/%j.txt
module load archive/2023-07 parquet-conv... |
ab2493eb7b7bb833d4f4c584e82e0721a2196effeed7f4fc1255a3525cad8d65 | Shell | 791 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_EIANN_mnist_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/batch... |
d4572290378d03fff4a7ec01ece5e1180ddd0dfc53eb7097ad3d067d8b5aa413 | Shell | 791 | 25 | #!/usr/bin/env bash
set -e
# === Argument parsing ===
DWI_NIFTI=$1
DWI_BVEC=$2
DWI_BVAL=$3
OUTPUT_DIR=$4
if [[ $# -ne 4 ]]; then
echo "Usage: $0 <DWI.nii.gz> <DWI.bvec> <DWI.bval> <output_dir>"
exit 1
fi
mkdir -p "$OUTPUT_DIR"
mrconvert "$DWI_NIFTI" "$OUTPUT_DIR/dwi4denoise.mif" -fslgrad "$DWI_BVEC" "$DWI_BVAL" ... |
64e1ef3a0383dc0460f44604cb944303fa740c3a63158e58ca574ba4bf556eff | Shell | 799 | 31 |
#!/usr/bin/env bash
set -euo pipefail
export SUBJECTS_DIR=/Applications/freesurfer/7.3.2/subjects
mri_dir=/Users/bo/Desktop/grid_cell_model/raw_meg_data
subjects=("19" "20" "21" "22" "23" "24" "25") # 想并行几个就写几个
max_jobs=7 # 同时跑多少个 recon-all
running_jobs=0
for sub in "${subjects[@]}";... |
5963d15bf76f0d4b7c55c5f4919e7ca9a2951ba0ea0a1dd2e933da14fee78ddc | Shell | 800 | 34 | #!/bin/env bash
#Change PROT below to match your system
#NR determines number of clusters plotted
NR=5
PROT=cGNSRV
function calcDihed () {
local ip=$1
local ir=$2
out_dir1=s1${PROT}_phipsi
out_dir2=s2${PROT}_phipsi
xtc1=../cluster_traj/s1${PROT}/cluster${ir}.xtc
xtc2=../cluster_traj/s2${PROT}/cluster$... |
eb019f1b39af62de2e4782078d0c196077d02d8825fdd17d8a8fecf8841061eb | Shell | 800 | 27 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_extended_EIANN_mnist_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EI... |
4d417663ff848f76e68ea707077825a27c5d612287024e78853f898481aeb3cf | Shell | 801 | 23 | #!/bin/sh
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your o... |
c31872e101f2f9312f9728d9f8d8a7e5ad6c591fa74d9d86357cc42cabaf4795 | Shell | 801 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /global/cscratch1/sd/aaronmil/logs/EIANN/"$JOB_NAME".%j.o
#SBATCH -e /global/cscratch1/sd/aaronmil/logs/EIANN/"$JOB... |
676e593f400c359ee5b855e3a0e091f71b0170e78df64e3e15f64c108fa09af3 | Shell | 803 | 50 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
5ad6ad80eb066eba36947ebc47f144b2e0a6ad99a1963a8412d333bf761ab483 | Shell | 804 | 23 | #!/bin/bash
#SBATCH --mem=140G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=30:0:0
#SBATCH --gres=gpu:v100l:1
#SBATCH --array=185-200
cd $project/moralization_temporal
module purge
module load python/3.10 scipy-stack
source ~/venv2/bin/activate
year=$(($SLURM_ARRAY_TASK_ID * 10))
model='bert-bas... |
679700395eaaa5c0645ea27840ef9c0f219adc1c4d8274d7eda599bfa70b9845 | Shell | 806 | 26 | #!/usr/bin/env bash
# Usage: ./make-methylation_pipeline_manifest.sh 14455_p1
sample=$1
ASD=/net/eichler/vol28/projects/autism_genome_assembly/nobackups
fn=$(echo $sample | cut -f1 -d'_')
sex=$(grep $sample $ASD/sample_info.tab | cut -f2)
mo_sr=/net/eichler/vol28/projects/autism_genome_assembly/nobackups/data/Illumin... |
ad3d68409607a5ff42fce63caa860f3d720ed10c7573156a6ed925198346a493 | Shell | 809 | 29 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_EIANN_mnist_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAM... |
d04a9c630cfcc62c228d8da3399d96f4c6661db11bf7c9fa92ee31318b22ba68 | Shell | 809 | 28 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_ddd_pars_model_train_start
#SBATCH --output=logs/gnn_ddd_pars_model_train_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
if [ "$#" -ne 1 ]; then
echo "Usage: $0 <name>"
exit 1
fi
# Get the path from t... |
8142d8a8e472bc8e96501de66adc035594d60abdf1e0dbcdb437e3bc794f8500 | Shell | 811 | 33 | #!/usr/bin/env bash
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
TESTDIR="$SCRIPTPATH/.."
if [[ $# -eq 1 ]]; then
pushd tmp_$(basename $1 .json)
else
pushd .
fi
file=$(find . -maxdepth 1 -name '*.json')
# check for uniq json-file
cnt=$(echo $file | wc -w)
if [[ $cnt -ne 1 ]]; then
echo "Need one *.json file... |
1aa3357e299266cbe014d0399b344092b18b4f5f9b8279802b3c2731760721eb | Shell | 812 | 26 | #!/bin/bash
# Sample commands to deploy nuclio functions on GPU
set -eu
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
FUNCTIONS_DIR=${1:-$SCRIPT_DIR}
nuctl create project cvat --platform local
shopt -s globstar
for func_config in "$FUNCTIONS_DIR"/**/function-gpu.yaml
do
func_ro... |
1ec1ecbd0854b6c077b6440c59ea5cc73f243e47408446d5e951bf2f942984c4 | Shell | 812 | 25 | #!/bin/bash
# PNC
cd /cbica/projects/luo_wm_dev/input/PNC/derivatives/babs_qsirecon_pyafq_act_v2/analysis/code
datalad save -m "add custom recon"
datalad push --to input
datalad push --to output
# HCPD
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/babs_qsirecon_pyafq_act_v2/analysis/code
datalad save -m "... |
43eec9db877946c84e6c534d999acd0e516e3e4b2aae111611219edfc44ff421 | Shell | 812 | 17 | #!/bin/bash
#SBATCH --job-name=mC # Job name
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=name@org # Where to send mail
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=8gb ... |
773dc91e86c0ab62c11402881e8351248b02be4a3bf6c2995907feda11678b9c | Shell | 818 | 29 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_extended_EIANN_mnist_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmil/logs/EIANN... |
92a72f9d7023efd4c183116094d0859ac70e867c5f05a0e4a2ae4caa512f4736 | Shell | 820 | 16 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
path_to_metadata=./metadata_from_past_runs/wandb_export_FinalPape... |
9774fcea9d27e6c23ea905f5722a6f8088681d3dde003d7d31432f8f744d4928 | Shell | 820 | 25 | #!/usr/bin/env bash
set -e
# === Argument parsing ===
DWI_NIFTI=$1
DWI_BVEC=$2
DWI_BVAL=$3
OUTPUT_DIR=$4
if [[ $# -ne 4 ]]; then
echo "Usage: $0 <DWI.nii.gz> <DWI.bvec> <DWI.bval> <output_dir>"
exit 1
fi
mkdir -p "$OUTPUT_DIR"
mrconvert "$DWI_NIFTI" "$OUTPUT_DIR/dwi_raw.mif" -fslgrad "$DWI_BVEC" "$DWI_BVAL" -for... |
45162884ed7714ffb441bbf13ce1c0d402c6d0fc8570358316f0c60e51805e05 | Shell | 822 | 16 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
path_to_metadata=./metadata_from_past_runs/wandb_export_FinalPape... |
081b900e30c4edfaa20747e7ca5831916d58b6161de8140f9d6b7273fc1b466c | Shell | 824 | 27 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=export_eve_start
#SBATCH --output=logs/export_eve_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=short
# Ensure the "logs" directory exists
mkdir -p logs
ml R
Rscript -e "devtools::install_github('EvoLandEco/eve')"
Rscri... |
a156d05beb49fcc100c2bd9443750e96c46a917430f8e902799fcc695ed32c6d | Shell | 825 | 33 | #!/bin/bash
#SBATCH --time=00:59:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gnn_emp_gnn
#SBATCH --output=logs/gnn_emp_gnn-%j.log
#SBATCH --mem=16GB
#SBATCH --partition=gpu
ml R
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Check if the correct number o... |
e496ab0d5de636bfe540ba3fae9bb6ebe7fed6753096828228d46bed72b695c5 | Shell | 825 | 18 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
ded3925fe6bbaca10accc10d1bde11b5 ${pref}_m100_2M_ordered
ded3925fe6bbaca10accc10d1bde11b5 ${pref}_m100_2k_ordered
ded3925fe6bbaca10accc10d1bde11b5 ${pref}_m100_2k_disk_ordered
EOF
head -n 10001 seq1m_0.fa | time $JF count -t $nCPUs -o ${pref}_m100_2... |
de8e62366d0e124706816051fc66d75350191fb828ec9d9ccb9e89f8df6df3ed | Shell | 828 | 37 | #!/bin/bash
export LD_LIBRARY_PATH=/software/plink-ng/zlib-1.2.8
export PATH=~/Software/shellfish:~/Software/plink-ng:$PATH
DAT=data
~/Code/flashpca/flashpca --bfile ${DAT} \
--ndim 100 \
--numthreads 8 2>&1 | tee log
# smartpca won't accept missing phenotypes so make some up
awk '{print $1, $2, $3, $4, $5, "... |
914938804a644c078dd5fa4997b94577457c3c5a6dab89e6fa1b86d4bd486dcc | Shell | 829 | 28 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$2"
export JOB_NAME=optimize_EIANN_mnist_hot_start_"$LABEL"_"$DATE"
export CONFIG_FILE_PATH="$1"
export HISTORY_FILE_PATH="$3"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /scratc... |
17d8e2a8e9ccc4efdbdf1d887097835968a8868a4aa7e96059f9cb05754ce37d | Shell | 832 | 25 | #!/bin/bash
#
# import-fs-ribbon.sh <freesurferDir> <analysisDir> <vaso_t1>
#
# - imports ribbon file from freesurfer
# - tranaforms it to func space
# - makes values compatible with LAYNII
freesurferDir=$1
analysisDir=$2
vaso_t1=$3
export FSLOUTPUTTYPE=NIFTI
mri_convert ${freesurferDir}/mri/ribbon.mgz ${analysisDir... |
b4b539205ce47283dc10b5ceaecb3898b70671cae06fe148c1990361cbef6095 | Shell | 832 | 31 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_ddd_pars_start
#SBATCH --output=logs/gnn_ddd_pars_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Ensure the script is called with the necessary argument for 'name'
if [ "$#" -ne 1 ]; then
echo "Usage: $0... |
160050abce883886b80d45e148b0ee85527e27eee7fa608a18d08e3f9610f945 | Shell | 835 | 29 | #!/bin/bash
# qc files wrapper
# submit this with `./get_qc_files_wrapper.sh`
datasets=( "PNC" "HCPD" "HBN")
for dataset in "${datasets[@]}"; do
# make dataset-specific logs folders
logs_dir="/cbica/projects/luo_wm_dev/two_axes/code/logs/datalad/${dataset}/"
if [ ! -d ${logs_dir} ]; then
mkdir... |
6dcb3b00a3055c6d82b7d2101cc14529060d92fea3aedcf2d189a4f8dbf496dc | Shell | 836 | 25 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
5c5d07dfb4e3de89b7fe4c72c714b921 ${pref}.stats
dbe881e4649406321d0e481da08eab5c ${pref}_L.dump
c3233e107bb6b42d0c979707f156264c ${pref}.query
7059a4e90b6670b2d814e44e2bc7d429 ${pref}.histo
EOF
echo "Counting 22-mers on ${nCPUs} CPU" && \
$JF coun... |
396eb6d0f65d93ed89c92d199a2b34d753e02b509c3352bd235e3457b76b59ac | Shell | 839 | 31 | #!/bin/bash
# set variables
datasets=("PNC" "HCPD" "HBN")
tract_list="/cbica/projects/luo_wm_dev/input/tract_list/tract_list.txt"
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
tract_count=${#inputarray[@]}
# submit job array for each dataset
for dataset in "${datasets[@]... |
db557fd88715e1b274df43fc1981064995b2dd3ecf5b91a68ab3b75e5037fccc | Shell | 839 | 26 | #!/bin/bash
# Description: Launch Jupyter Lab on HPC and print SSH tunnel instructions.
# --- Set critical variables
readonly IPADDRESS=$(hostname -I | tr ' ' '\n' | grep '10.211.4.')
readonly PORT=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')
# --- Print user ... |
813a593a0992918de51e47b99def4a1a37ad051214dc3d72c5ee975eb54ad0ea | Shell | 843 | 33 | #!/bin/bash
#SBATCH --job-name=run_KR4SL
#SBATCH --output=./slurm_out/run_KR4SL.out
#SBATCH --error=./slurm_out/run_KR4SL.err
#SBATCH --time=48:00:00
#SBATCH --mem=64Gb
#SBATCH -c 4
#SBATCH --gres=gpu:1
#SBATCH -p gpu_p
#SBATCH --qos=gpu_normal
# To run this file:
# cd ./reproduce/synleth/
# sbatch ./scripts/02_run_KR... |
884218b17302e1eba574e62513cdc47623bbf868d5cb8233e6c867c187e28a47 | Shell | 847 | 29 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_extended_EIANN_cifar10_10_epochs_"$DATE"
export CONFIG_FILE_PATH="$1"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio240068p/aaronmil/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio240068p/aaronmi... |
0078ddfdef5c5a22db3461a7b84a38f6baf6f679fa60fe97b7b5d34818cced64 | Shell | 850 | 9 | echo 'Run simulation'
module purge
module load Python/3.9.6-GCCcore-11.2.0
time srun -A ec12 --time=4-20:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/.local/bin/nrniv FFI_BS_separate_241106a_IPSG0_dep0.hoc &
time srun -A ec12 --time=4-20:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-nod... |
1e7a0e26ad401df9cfa1a4eeed221c90c44b01c2764181c9503080f65d313b25 | Shell | 853 | 22 | #!/bin/bash
# =====================================================================================================================
# This script is responsible for tuning the PMJ delay parameters
# =====================================================================================================================
#... |
497879da028b574f5993f92908d08db5c48bb1306b30a14ad91e28649081d253 | Shell | 855 | 9 | echo 'Run simulation'
module purge
module load Python/3.9.6-GCCcore-11.2.0
time srun -A ec12 --time=4-20:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/.local/bin/nrniv FFI_BS_separate_241106a_IPSG0_dep10.hoc &
time srun -A ec12 --time=4-20:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-no... |
c4bab941a00ca5476155f6f8c5d46c6f39772ac3ae109ff9c4292b665d2a9639 | Shell | 855 | 33 | #!/usr/bin/env bash
#####################################################################
# Example script for computing the variant effect sequence class scores
# given Sei chromatin profile variant effect predictions
# Usage:
# sh 2_varianteffect_sc_score.sh <ref-fp> <alt-fp> <output-dir>
# ... |
2d95a0b2478d7e8dab15245956009ef7ad1a7d6642a002405c8bdcc12d3a1842 | Shell | 856 | 31 | #!/bin/bash
set -e
set -x
subj=$1
algo=$2
mnitracksdir=$3
#try to stop python/numpy from secretly using extra cores sometimes
export OPENBLAS_NUM_THREADS=1
export MKL_NUM_THREADS=1
scriptdir=/home/ubuntu
mkdir -p ${mnitracksdir}
subjdir=${mnitracksdir}/mnitracks_${subj}_${algo}
numtracks=5M
bash ${scriptdir}/ru... |
c1f754180c6853e7a8ec249b845a83ec86ea4e93c0cb665e3ef90df78199aa0a | Shell | 856 | 36 | #!/bin/bash
#
# fs_recon-all_on-brain-extracted.sh <anatFileName> <subjectsDir> <subject>
#
# - runs freesurfer recon-all on high-res data that has already been brain extracted
anatFileName=$1
subjectsDir=$2
subject=$3
echo "mris_inflate -n 100" > expert.opts
recon-all -i ${anatFileName} \
-hires \
... |
c8642e0659933186a33b89911e28b53fd1332d10e4885052ed3c6234787c0593 | Shell | 856 | 32 | #!/usr/bin/env bash
set -e
fs_subjects_dir=$1
fs_subject_id=$2
output_matrix=$3
output_inverse_matrix=$4
# tkregister2 --mov "${FS_OUTPUT}/mri/orig.mgz" \
# --targ "${FS_OUTPUT}/mri/rawavg.mgz" \
# --regheader \
# --reg junk \
# --fslregout "${OUTPUT_DIR}/freesurfer2st... |
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