sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
69ef95cf47396e7d29f983f95216622b1e279b35229c84ec592a9c78c4358e5e | Shell | 925 | 35 | # converts DICOM images into niftis and places them in the corresponding directories.
if [[ $copyRaw -eq 1 ]] && [[ $origDataDir -eq 0 ]]; then
echo "Cannot copy data. Please specify path in the config file."
exit 1
fi
if [[ $(command -v module) ]]; then
module load mricron
fi
if [[ $(command -v dcm2nii) ]]; then... |
3039dcca71d48fffb61f1905817b50675c067787cc9ef4c20c6492116976026f | Shell | 929 | 31 | #!/usr/bin/env bash
echo "Run this script with your conda env activated"
echo "Invoke the script like this: "
echo "./debug_openmm.sh | tee -a debug.log"
echo "Then send us debug.log"
set -euo pipefail
date
which -a python
conda info -a || echo "no conda"
mamba info -a || echo "no mamba"
micromamba info || echo "n... |
9ee91888287f3c1caa662c9c2332dcc8e80d4b0d984e4981ce445dae4b56b5c4 | Shell | 932 | 18 | # assumes you are in the nnunet repo!
# prepare raw datasets
python nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset999_IntegrationTest_Hippocampus.py
python nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset998_IntegrationTest_Hippocampus_ignore.py
python nnunetv2/dataset_conversion/... |
4ab722f8b3560ce05e226da51ab1a41919d73fdf446ca3caa5904834844a39c7 | Shell | 938 | 42 | #!/bin/bash
#
# Process a directory of input scans. Each scan should be named "<UID>.nii.gz".
#
if [ $# -ne 2 ]
then
echo "Wrong number of arguments."
exit 0
fi
INPUT_FILE_DIR=$1
SUBJECT_DIR=$2
MNI_TEMPLATE_FILE=/mnt/nas/Data_Neuro/mni_templates/MNI152_T1_1mm.nii.gz
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURC... |
6a409442180ebf0433fc83031bace4daa34514d0c43f984cacf6f313dff442c8 | Shell | 941 | 33 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
BIN="python train_net.py"
OUTPUT="inference_test_output"
NUM_GPUS=2
IMS_PER_GPU=2
IMS_PER_BATCH=$(( NUM_GPUS * IMS_PER_GPU ))
CFG_LIST=( "${@:1}" )
if [ ${#CFG_LIST[@]} -eq 0 ]; then
CFG_LIST=( ./configs/quick_schedules/*inference_acc_test.yaml )
fi... |
160144b745adf97a18453ab86e265903149507388b3bcba9726fdef07ffcac11 | Shell | 944 | 32 | #!/usr/bin/env bash
set -euo pipefail
IN_DIR="genotype_sample_files" # folder with *.raw.vcf.gz
OUT_DIR="genotype_sample_files" # can be same as IN_DIR
MAX_JOBS=4 # how many samples in parallel
mkdir -p "${OUT_DIR}"
filter_sample() {
local idx="$1"
local SAMPLE="SRR${idx}"
... |
2cea74af17a50fb1b7d60fe3efe3f437d856ef849ebd764fd560d30e9ce12fe7 | Shell | 952 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP210_PD_NP19-91_SN_bulk.u.STAR
#SBATCH -o ASAP210_PD_NP19-91_SN_bulk.u.STAR.out
#SBATCH -e ASAP210_PD_NP19-91_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/raqu... |
3a09590ca3bb8fecdc5bcde628014dc83da9c2170b4e851535f0bc9066b0b7b4 | Shell | 952 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
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#SBATCH -o ASAP194_PD_NP22-55_SN_bulk.u.STAR.out
#SBATCH -e ASAP194_PD_NP22-55_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/raqu... |
a419cf551b94ab0fb17fa736b57bb698f1c516d61b27530f211caee230cce9d4 | Shell | 952 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -t 10:00:00
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#SBATCH -o ASAP212_PD_NP21-04_SN_bulk.u.STAR.out
#SBATCH -e ASAP212_PD_NP21-04_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/raqu... |
e8dc4cedf29db579390cef31f9b1c5d9169f7344981c2c956eb7947836c7ecf7 | Shell | 952 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP177_PD_NP21-57_SN_bulk.u.STAR
#SBATCH -o ASAP177_PD_NP21-57_SN_bulk.u.STAR.out
#SBATCH -e ASAP177_PD_NP21-57_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/raqu... |
030ae70be5d6282c96de0c73bdb9474ccd1a2dc68556cea1f15543f3aafa25f6 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP178_PD_NP21-208_SN_bulk.u.STAR.out
#SBATCH -e ASAP178_PD_NP21-208_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
0f82c4abf398de4bf26917e5ca06efc0b6bae53d7c62c9a834834880bc010474 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -o ASAP228_PD_NP19-91_PFC_bulk.u.STAR.out
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ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
26a2f1343521d6da06a4edb4e3af4406add9446c6bf5506d58ec8c50877c9e98 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP204_PD_NP21-04_AMY_bulk.u.STAR.out
#SBATCH -e ASAP204_PD_NP21-04_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
2e3f3d886124dc72425ca3a85171de1576efb8d4d12147636fdb189ac5993b64 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP173_PD_NP21-57_PUT_bulk.u.STAR.out
#SBATCH -e ASAP173_PD_NP21-57_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
32bc1e448187732a38d00a3e372b77ad509380025e9672e944b90b96e768b67e | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP192_PD_NP22-55_PFC_bulk.u.STAR
#SBATCH -o ASAP192_PD_NP22-55_PFC_bulk.u.STAR.out
#SBATCH -e ASAP192_PD_NP22-55_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
33f2cf79356c74bcf11bef7698f26fa15cf5c0e5ce60fb0260370fe1bc62c917 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP179_PD_NP21-217_SN_bulk.u.STAR
#SBATCH -o ASAP179_PD_NP21-217_SN_bulk.u.STAR.out
#SBATCH -e ASAP179_PD_NP21-217_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
40d2c77528ad0dd03d8eaf004dfae7142403a452e1c0dd05bcf72eddd251d8f6 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP209_PD_NP17-232_SN_bulk.u.STAR
#SBATCH -o ASAP209_PD_NP17-232_SN_bulk.u.STAR.out
#SBATCH -e ASAP209_PD_NP17-232_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
58500dc01a6f10197a292e6dbddf7dcbaef9b477e5c7c6eed9d3d3a177fb4a9f | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP190_PD_NP21-57_AMY_bulk.u.STAR.out
#SBATCH -e ASAP190_PD_NP21-57_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
6f0566138cf1f2943fc1dac66d3ed45ca63e14ec50d9859bcf4f34db9f0211fb | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP216_PD_NP19-91_PUT_bulk.u.STAR.out
#SBATCH -e ASAP216_PD_NP19-91_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
724ed63f78f4ebd453951f6fbdb0418dbbf6ece7542b08a7ae72bde7d9dd1133 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP208_PD_NP16-285_SN_bulk.u.STAR
#SBATCH -o ASAP208_PD_NP16-285_SN_bulk.u.STAR.out
#SBATCH -e ASAP208_PD_NP16-285_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
7397deb735ecfd543ee5a89f513794218e4e663595708d4e24f41884c9c97d9e | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP211_PD_NP19-137_SN_bulk.u.STAR
#SBATCH -o ASAP211_PD_NP19-137_SN_bulk.u.STAR.out
#SBATCH -e ASAP211_PD_NP19-137_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
8ec85d7b0d19e13764a3370b3e60adc7e5537890c16e6f81f012328b4ebbe621 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP193_PD_NP22-55_PUT_bulk.u.STAR.out
#SBATCH -e ASAP193_PD_NP22-55_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
97081a09c7cf1025424227b49a2881117f382f6afbe30e7d433b3dc63c7bb02d | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP207_PD_NP23-21_AMY_bulk.u.STAR
#SBATCH -o ASAP207_PD_NP23-21_AMY_bulk.u.STAR.out
#SBATCH -e ASAP207_PD_NP23-21_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
9aa4807ff7415911525a33432c674a1199e4b50506c01c96ba179ee47c37f1a1 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP222_PD_NP21-04_PUT_bulk.u.STAR.out
#SBATCH -e ASAP222_PD_NP21-04_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
b6b084f0f00f779ee2b57d7ce4c872820bcf38a9fcb70624dc5428d954fb7707 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP156_PD_NP21-57_PFC_bulk.u.STAR.out
#SBATCH -e ASAP156_PD_NP21-57_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
bdecd9645fd9ec1aeecffcca85193293269a6cba812cef50c97251ec256065fb | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP225_PD_NP23-21_PUT_bulk.u.STAR
#SBATCH -o ASAP225_PD_NP23-21_PUT_bulk.u.STAR.out
#SBATCH -e ASAP225_PD_NP23-21_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
dded6fa118c9324dcd2ef10e621dbde82dd48844fcc53b2013d9fadd6fa9c6d8 | Shell | 958 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP195_PD_NP22-55_AMY_bulk.u.STAR.out
#SBATCH -e ASAP195_PD_NP22-55_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backup/r... |
13f97367b5cb793f172b521355e1857ac5ee5a789f72332f56c1668e1600d617 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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ml purge
ml GCC/10.2.0 STAR/2.7.8a
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23035a54b59b96a1611a7cda82fde357c9514c7c9a86280deb6de38a927d934f | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
26849f360602690aa56b85ba3aa3ba3aabd99e1a4e4049aa34e7dfc3bb926875 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
50f8cb4a276e89e62afc0cca41f3de8acde210bac87163fc5760af7e7790b8f0 | Shell | 964 | 11 | #!/bin/bash
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ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
6bab479f30f4e7ef98e99ef45d8c4c4c625654052ce18f1df484004502d5591e | Shell | 964 | 11 | #!/bin/bash
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
6c4de5014a1936ae95b57ebc3ed8807de29e62034138da5a569d965ad008ce35 | Shell | 964 | 11 | #!/bin/bash
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
7a0e479158a773304daa39e7458ac1c87661ef483ba3b869c4c95728297f3b77 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
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#SBATCH -o ASAP164_PD_NP21-217_PUT_bulk.u.STAR.out
#SBATCH -e ASAP164_PD_NP21-217_PUT_bulk.u.STAR.err
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
9800783948b078f68973daa76b52690de06d9d7cc137167501e03c378650f52f | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP158_PD_NP21-217_PFC_bulk.u.STAR
#SBATCH -o ASAP158_PD_NP21-217_PFC_bulk.u.STAR.out
#SBATCH -e ASAP158_PD_NP21-217_PFC_bulk.u.STAR.err
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
a8ce963bb9491436d590cf8601dbcf7ec49657d1c44706ff13a9e0bab72a3936 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP191_PD_NP21-208_AMY_bulk.u.STAR
#SBATCH -o ASAP191_PD_NP21-208_AMY_bulk.u.STAR.out
#SBATCH -e ASAP191_PD_NP21-208_AMY_bulk.u.STAR.err
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
b540b0cee532d58b452a6809981f02c5a5df46c4d85791165e3cacbd063374c8 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
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#SBATCH -J ASAP226_PD_NP16-285_PFC_bulk.u.STAR
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ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
b74f2d9ac0ce2748dc0e64e92188d2c6233e49a2668da5f5f083583cb0e4b085 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
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#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP214_PD_NP16-285_PUT_bulk.u.STAR
#SBATCH -o ASAP214_PD_NP16-285_PUT_bulk.u.STAR.out
#SBATCH -e ASAP214_PD_NP16-285_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
b8dd1e482fbf26f709811c70b202603555c015f7acc691bf2043b5ce8910ab0a | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP159_ctrl_16-119_PFC_bulk.u.STAR
#SBATCH -o ASAP159_ctrl_16-119_PFC_bulk.u.STAR.out
#SBATCH -e ASAP159_ctrl_16-119_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
d6967c2e546aafc38462845e336f03b04cb48894f8263bd359a6c1273c1c715d | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP220_PD_NP19-137_PUT_bulk.u.STAR
#SBATCH -o ASAP220_PD_NP19-137_PUT_bulk.u.STAR.out
#SBATCH -e ASAP220_PD_NP19-137_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
e1c2845694c320b6ea3a57a7656005b268b52b1ee8f7c93835e51280067ab139 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP227_PD_NP17-232_PFC_bulk.u.STAR
#SBATCH -o ASAP227_PD_NP17-232_PFC_bulk.u.STAR.out
#SBATCH -e ASAP227_PD_NP17-232_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
fd56dfa78fd6f8293ca9c407fe4e10ee32998f9f18f7a0b5d543d10113cbc757 | Shell | 964 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP196_PD_NP16-285_AMY_bulk.u.STAR
#SBATCH -o ASAP196_PD_NP16-285_AMY_bulk.u.STAR.out
#SBATCH -e ASAP196_PD_NP16-285_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/backu... |
978304a8ded4c9037f5bca42366944e4190f45060f864285a53f5b41700c3d92 | Shell | 967 | 14 | #git checkout master scratch.slurm slurmQI.sh
#dos2unix scratch.slurm slurmQI.sh
#bash slurmQI.sh $PWD/TKSB
DATADIR=$1
RUNCMD=qualimap
PARAMFILE=scratch.slurm
CPU=20
CURRENTEPOCTIME=`date +%s`
WRITEDIR=$RUNCMD.$CURRENTEPOCTIME.results
mkdir $DATADIR/$WRITEDIR
for i in $DATADIR/*sort*bam ; do echo $i; j=$(basename $i); ... |
2958554b5253d20e011ec849c4fd96199ffdccb91641823815fb9b5c2cbc83ee | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP180_ctrl_NP16-119_SN_bulk.u.STAR
#SBATCH -o ASAP180_ctrl_NP16-119_SN_bulk.u.STAR.out
#SBATCH -e ASAP180_ctrl_NP16-119_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
2da371402e81509e1fbd5f01cab0965b58e088bcbc488355e9267dacc81cc13c | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP230_ctrl_NP21-04_PFC_bulk.u.STAR
#SBATCH -o ASAP230_ctrl_NP21-04_PFC_bulk.u.STAR.out
#SBATCH -e ASAP230_ctrl_NP21-04_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
536ee9fce7fa4a7a047783dbfa4c74ed98561a3cbb8db74cdbac193f66e14d83 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP223_ctrl_NP22-37_PFC_bulk.u.STAR
#SBATCH -o ASAP223_ctrl_NP22-37_PFC_bulk.u.STAR.out
#SBATCH -e ASAP223_ctrl_NP22-37_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
586b038aede23c6784c0e58c78413bdb74573a6b3060f35e323904e5edceb309 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP218_ctrl_NP22-37_PUT_bulk.u.STAR
#SBATCH -o ASAP218_ctrl_NP22-37_PUT_bulk.u.STAR.out
#SBATCH -e ASAP218_ctrl_NP22-37_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
6b4b025257e2e51babac19eedee3a016d959ddda318a347dd775b949e7d092c9 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP167_ctrl_NP17-20_PFC_bulk.u.STAR
#SBATCH -o ASAP167_ctrl_NP17-20_PFC_bulk.u.STAR.out
#SBATCH -e ASAP167_ctrl_NP17-20_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
6f7a6ee8ff344718f21d518986147de7888e26a17fafc3614a4bca5150cb2b8f | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP200_ctrl_NP22-37_AMY_bulk.u.STAR
#SBATCH -o ASAP200_ctrl_NP22-37_AMY_bulk.u.STAR.out
#SBATCH -e ASAP200_ctrl_NP22-37_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
7d3a6a8d6f65f647e32db3beceefb706a07aeaca5d0b1a4b790584d8e55acfaa | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP172_ctrl_NP18-46_PUT_bulk.u.STAR
#SBATCH -o ASAP172_ctrl_NP18-46_PUT_bulk.u.STAR.out
#SBATCH -e ASAP172_ctrl_NP18-46_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
8b0df90bf63f13068dcd111cd4c32ab976cba3af03c13842546eae339e9a44e7 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP203_ctrl_NP19-218_SN_bulk.u.STAR
#SBATCH -o ASAP203_ctrl_NP19-218_SN_bulk.u.STAR.out
#SBATCH -e ASAP203_ctrl_NP19-218_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
939d07d98ffba6d1a9f1ebf44db60032c46e3b314fd5b75ec8d2bef911d92e51 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP219_ctrl_NP22-75_PUT_bulk.u.STAR
#SBATCH -o ASAP219_ctrl_NP22-75_PUT_bulk.u.STAR.out
#SBATCH -e ASAP219_ctrl_NP22-75_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
a28b9f33fc85bb4c30d99c3f01ab39562f77f7f473058c2ef252aa3276d2339c | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP170_ctrl_NP17-20_PUT_bulk.u.STAR
#SBATCH -o ASAP170_ctrl_NP17-20_PUT_bulk.u.STAR.out
#SBATCH -e ASAP170_ctrl_NP17-20_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
af1b3752168a112aec85a5e88cbcf83bfe3ef953b5f23d14e305bfa49d4d7c42 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP201_ctrl_NP22-75_AMY_bulk.u.STAR
#SBATCH -o ASAP201_ctrl_NP22-75_AMY_bulk.u.STAR.out
#SBATCH -e ASAP201_ctrl_NP22-75_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
b222cf4c1fa15b2012001c7324f8e7a24ac2064ab504a0ff66feb7401acbe8df | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP161_ctrl_NP18-46_PFC_bulk.u.STAR
#SBATCH -o ASAP161_ctrl_NP18-46_PFC_bulk.u.STAR.out
#SBATCH -e ASAP161_ctrl_NP18-46_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
cf49b59b66862299e13dae438972c91a34ac9aaa9738b0790e9dd4bdd7ae3fec | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP181_ctrl_NP16-293_SN_bulk.u.STAR
#SBATCH -o ASAP181_ctrl_NP16-293_SN_bulk.u.STAR.out
#SBATCH -e ASAP181_ctrl_NP16-293_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
cfccd62a1f9d7322b9832409a100d3e898ed549e7d002cc8470b2b520c16a54c | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP231_ctrl_NP23-21_PFC_bulk.u.STAR
#SBATCH -o ASAP231_ctrl_NP23-21_PFC_bulk.u.STAR.out
#SBATCH -e ASAP231_ctrl_NP23-21_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
dad48eb5f7d75b16a3dfa69fbf0867df82a6f2b33cb52a42ee6664ba425d7490 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP224_ctrl_NP22-75_PFC_bulk.u.STAR
#SBATCH -o ASAP224_ctrl_NP22-75_PFC_bulk.u.STAR.out
#SBATCH -e ASAP224_ctrl_NP22-75_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
ed12ae61847217e425afab46cee75a03cb068116aed8763d684863846b06db08 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP175_ctrl_NP16-284_SN_bulk.u.STAR
#SBATCH -o ASAP175_ctrl_NP16-284_SN_bulk.u.STAR.out
#SBATCH -e ASAP175_ctrl_NP16-284_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
f75d322882f3af4850c0d7caa53f40bc341631530526e9d9bae61866da41dcd9 | Shell | 970 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP184_ctrl_NP18-148_SN_bulk.u.STAR
#SBATCH -o ASAP184_ctrl_NP18-148_SN_bulk.u.STAR.out
#SBATCH -e ASAP184_ctrl_NP18-148_SN_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson/ba... |
04935b90f19e9e7e6f2214e0b4bf0632b60ace80d89a1e8e3756706b5cb89b16 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP168_ctrl_NP16-284_PUT_bulk.u.STAR
#SBATCH -o ASAP168_ctrl_NP16-284_PUT_bulk.u.STAR.out
#SBATCH -e ASAP168_ctrl_NP16-284_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
143ad087fbbcb35e753e0c21c88e633daefff89f25ab9d6aad93377bdec966fc | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP166_ctrl_NP16-293_PFC_bulk.u.STAR
#SBATCH -o ASAP166_ctrl_NP16-293_PFC_bulk.u.STAR.out
#SBATCH -e ASAP166_ctrl_NP16-293_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
198b786fe68207903c04e300f730c8b69fcbccb56bacc04dfd41e31d6117b522 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP176_ctrl_NP18-148_PUT_bulk.u.STAR
#SBATCH -o ASAP176_ctrl_NP18-148_PUT_bulk.u.STAR.out
#SBATCH -e ASAP176_ctrl_NP18-148_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
24ba218e24427d158a0734c44cdeba7a84e9d6084c2c09945863355d43ecb35d | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP186_ctrl_NP16-119_AMY_bulk.u.STAR
#SBATCH -o ASAP186_ctrl_NP16-119_AMY_bulk.u.STAR.out
#SBATCH -e ASAP186_ctrl_NP16-119_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
25c25f48dedc0e9fa40230133537e937742bc66e16ec7be1a3f0243a808ce83a | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP165_ctrl_NP16-284_PFC_bulk.u.STAR
#SBATCH -o ASAP165_ctrl_NP16-284_PFC_bulk.u.STAR.out
#SBATCH -e ASAP165_ctrl_NP16-284_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
4b94e0d596b65f7fd7022e44266166c98861ed5d1327d4e3f35bb5afed3b7fb3 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP189_ctrl_NP18-148_AMY_bulk.u.STAR
#SBATCH -o ASAP189_ctrl_NP18-148_AMY_bulk.u.STAR.out
#SBATCH -e ASAP189_ctrl_NP18-148_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
505e655c926bed5b0b7822e43e8d473f762c6f299d1d1eca8ba217882d2b8456 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP199_ctrl_NP19-218_AMY_bulk.u.STAR
#SBATCH -o ASAP199_ctrl_NP19-218_AMY_bulk.u.STAR.out
#SBATCH -e ASAP199_ctrl_NP19-218_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
5f0802542dfab3cecfefc15d66ec11aaadf844361a90191fca25bf3a53dee4e9 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP162_ctrl_NP18-148_PFC_bulk.u.STAR
#SBATCH -o ASAP162_ctrl_NP18-148_PFC_bulk.u.STAR.out
#SBATCH -e ASAP162_ctrl_NP18-148_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
83134d6001f192b4faba0f13fe47082156e7057a4073c6fe4f62ad6b2a4f0f7b | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP221_ctrl_NP19-218_PFC_bulk.u.STAR
#SBATCH -o ASAP221_ctrl_NP19-218_PFC_bulk.u.STAR.out
#SBATCH -e ASAP221_ctrl_NP19-218_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
8c8eec20ad8948c5eb5d5e3fa213e3b3f021cb7b29e40dead89a351c038bbfa6 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP217_ctrl_NP19-218_PUT_bulk.u.STAR
#SBATCH -o ASAP217_ctrl_NP19-218_PUT_bulk.u.STAR.out
#SBATCH -e ASAP217_ctrl_NP19-218_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
a7dee0f162530d95d6c4ed6c0f4a413ea356c2bdb7f07c76e20f9e6285ae8ba2 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP229_ctrl_NP19-137_PFC_bulk.u.STAR
#SBATCH -o ASAP229_ctrl_NP19-137_PFC_bulk.u.STAR.out
#SBATCH -e ASAP229_ctrl_NP19-137_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
c520c4b366ea2f42b1608bbc0fe34f1f65f37ef625412b31e750145ab5464915 | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP174_ctrl_NP16-119_PUT_bulk.u.STAR
#SBATCH -o ASAP174_ctrl_NP16-119_PUT_bulk.u.STAR.out
#SBATCH -e ASAP174_ctrl_NP16-119_PUT_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
fa2a0553dba919174d4c8a69f05fcf7118283dbe95991b6ea36709e76bd358ad | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP188_ctrl_NP16-293_AMY_bulk.u.STAR
#SBATCH -o ASAP188_ctrl_NP16-293_AMY_bulk.u.STAR.out
#SBATCH -e ASAP188_ctrl_NP16-293_AMY_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
febf5561ded754ea2dcb4502cb580d8cfbee84c248feee7da66e74a20d9fc22c | Shell | 976 | 11 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 10:00:00
#SBATCH -J ASAP160_ctrl_NP17-216_PFC_bulk.u.STAR
#SBATCH -o ASAP160_ctrl_NP17-216_PFC_bulk.u.STAR.out
#SBATCH -e ASAP160_ctrl_NP17-216_PFC_bulk.u.STAR.err
ml purge
ml GCC/10.2.0 STAR/2.7.8a
STAR --genomeDir /scale/gr01/shared/jjakobsson... |
e8ccb3956c538d3a09f68aa65454b2f2a0322790468d1400fd02e9dc1a3ed1b0 | Shell | 982 | 43 | #!/bin/sh
set -eu
method="$1"
script_name="$2"
cp -r /app/* /work
cp -r /snakebids /src
script="'${script_name}' tests/data tests/result participant -c1 --skip-bids-validation"
case "$method" in
"setuptools" )
python -m venv .venv
.venv/bin/python -m pip install --no-color .
PATH=".venv/b... |
874d1a72c9c8aed22a31288d117c7cdb728448e9f15035fd10d7f5e88653f654 | Shell | 984 | 31 | #!/bin/bash
# current working directory of this script
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# locate raw and processed data directories
while IFS='' read -r line || [[ -n "$line" ]]; do # loop over lines
for i in $(echo $line | sed "s/,/ /g"); do # loop over comma separation
eval $i
do... |
ac99f2f5638b50bcb03de2eb5b8da08c4691ea0222c6066ac3bbf56e05aef29c | Shell | 992 | 21 | #!/bin/sh
# This script downloads the test data used in tutorials and examples
set -e
# curl wrapper with retries + fail-fast + timeouts so a transient network blip
# on CI doesn't break the build. `-f` makes HTTP errors non-zero (so we retry /
# fail loudly instead of silently writing an error page to the output file... |
35d0e4f637717fa3221a0f17f81ed839981a27322176d051f371236a91799383 | Shell | 999 | 33 | #!/bin/bash
# This script removes carets, spaces, and underscores from the input plain-text file "subject" at the specified path.
# Usage: ./remove_carets_spaces.sh /path/to/subject
input_file="${1}"
if [[ -z "$input_file" ]]; then
echo "Usage: $0 /path/to/input_file"
exit 1
fi
subject_dir=$(dirname `realpat... |
b22aa13aaa578c8665f918559009d634161bfc539a4ba193c6ce2a9f72c8d07d | Shell | 1,005 | 26 | # intra task realignment
mkdir $workingDir/intraTask
for f in $workingDir/intraBlock/*.nii*; do
x_dim=$(fslinfo $f | grep -w dim1 | cut -f3)
z_dim=$(fslinfo $f | grep -w dim3 | cut -f3)
t_dim=$(fslinfo $f | grep -w dim4 | cut -f3)
fslmaths $f -roi 0 $x_dim 0 125 0 $z_dim 0 $t_dim $workingDir/intraTask/$(basename ... |
332c1d376b52e35bd26609e12cf50aca8fbf8345241729d3be80b091e45c4c0e | Shell | 1,017 | 31 | for relcrit in 5; do
for confsel in `seq 1 3`; do
tmpScriptName="tmpAllSubjects$relcrit$confsel"
# create temporary script forwarding part number and number of parts
echo "relcrit=$relcrit;confsel=$confsel;">$DIR/scriptTemplates/$tmpScriptName.m
# wait for script to be created
while [ ! -f $DIR/scriptTe... |
b69491c78ac2534c2396e817af2610ff543f39b62f2a1c6f110d00c7de3058b3 | Shell | 1,020 | 9 | #!/bin/sh
mex $5 '\def\Link#1.a.b.c.{\expandafter\def\csname tex4ht\endcsname{\expandafter\def\csname tex4ht\endcsname{#1,html}\input tex4ht.sty }}\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\HCode '$2'.a.b.c.\input ' $1
me... |
003319979320a73f3a47ee99ad360e1befa029a2aa2b849877457fcea9fc24b8 | Shell | 1,022 | 28 | #!/bin/bash
# -----------------------------------------------------------------------
# WORC Installation
# -----------------------------------------------------------------------
# Install requirements: git, cmake, build-essential
echo -e "Installing git, pip, build-essential, graphviz, ipython and jupyter notebook ... |
3ce566119c378cdcf3bd6d5f6e9c80d109516f3869aa52fdda6e37984e2d07d1 | Shell | 1,023 | 9 | #!/bin/sh
tex $5 '\def\Link#1.a.b.c.{\expandafter\def\csname tex4ht\endcsname{\expandafter\def\csname tex4ht\endcsname{#1,html}\input tex4ht.sty }}\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\HCode '$2'.a.b.c.\input ' $1
t... |
f63dd558a9eeca4ec020cf34724bbbb607e2662d4df317e583c97d206335d809 | Shell | 1,027 | 30 | # cuts dummy scans at the beginning of each data acquisition block according to the specifications in the config file.
echo "preparing task scans..."
for f in $taskVolumes; do
size_curr=$(fslval $f dim4)
filename=$(echo $f |rev | cut -d '/' -f1 | rev)
if [[ $size_curr -ge $(expr $numTaskVolumes + $skipVolumesTask) ... |
5dc194efc1e6f1b65cc7a947f4d707b5131acd737cf003bac09d3a0d010e2034 | Shell | 1,037 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips.sh
#SBATCH --account=def-zeighami
#SBATCH --time=168:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=150G
#SBATCH --output=slurms/output_f2_raven_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_%j.out
#SBATCH... |
c92581cc1dcf26aede934ac994aee25f69cda8b346f5b5d6b0ccabb2aecce01b | Shell | 1,042 | 23 | #!/usr/bin/env bash
# This script is used to run the gear locally for debugging purposes.
# It mounts the local directories to the docker container and runs the gear.
# The gear is run in the bash shell so that you can interact with the container.
# Assumes that API_KEY is set in the environment and added to config.j... |
28999c09c97ffbf7a1fd12d8684b1eaa8fd678d3068b5163035cae15b2e23e99 | Shell | 1,048 | 22 | #!/bin/bash
#SBATCH --job-name=test_f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=144:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=150G
#SBATCH --output=slurms/output_f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5_%j.ou... |
20ff4336d2795f7bf7e809fbe9cb91cb2f65075c28c00f096bf3a94822b335d9 | Shell | 1,049 | 31 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
set -ex
ldconfig # https://github.com/NVIDIA/nvidia-docker/issues/854
script_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
. "$script_dir/pkg_helpers.bash"
echo "Build Settings:"
echo "CU_VERSION: $CU_VERSION" #... |
ff902d2251617da84569aefff04717ad2e3a56781f045c9a2d4ce5dddcc631d2 | Shell | 1,050 | 38 | #!/bin/bash
# source laminarEEGfMRI.sh to make available
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# utility functions
lef_volume_masker_3000_tm () {
python $DIR/toolboxes/MRI-Volume-Masker-3000-TM/vol2mask.py
}
lef_clean_logs () {
if [ "$1" == "-h" ]; then
printf "Usage: `basename $FUNCNAME` \nm... |
b33c5ccc602cda420cc0f7f99f546eab15450c3846859794b02f2b0f0ff0e9b3 | Shell | 1,054 | 25 | #!/bin/bash
# current working directory of this script
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# locate raw and processed data directories
while IFS='' read -r line || [[ -n "$line" ]]; do # loop over lines
for i in $(echo $line | sed "s/,/ /g"); do # loop over comma separation
eval $i
do... |
a01f0df0bba26b3fffe23b74aa93721f39ae69abb816a7cc4512fe7892c0591c | Shell | 1,060 | 30 | #!/bin/bash
# Anoushka Joglekar
# April 2020
fastqDir=$1;
mmOut=$2;
progPath=$3;
genomeFa=$4;
numThreads=$5;
## Create a fastq guide
for i in $(ls $fastqDir/*.fastq.gz) ; do echo $i | awk -v path=$(realpath $i) \
'{n=split($1,a,/\/|.fastq/); print a[n-1]"\t"path}' ; done > Misc/fastqGuide
## Running minimap2 over al... |
3ff488b325264a0ae7c50323ed6267f7c571b7cbb2a41081e61f7ad7a4b397e1 | Shell | 1,062 | 9 | #!/bin/sh
xetex -no-pdf $5 '\def\Link#1.a.b.c.{\expandafter\def\csname tex4ht\endcsname{\expandafter\def\csname tex4ht\endcsname{#1,html}\input tex4ht.sty }}\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\HCode '$2'.a.b.c.\input ' $1
... |
7970402fee8249bae54c44ad11c5c360a040a333f2540f1abb90b201c299041c | Shell | 1,063 | 31 | for setup in $subjectDataDir/all/eeg-fMRI/setups/*; do
setupfile=$(basename ${setup%.mat})
tmpScriptName="tmpRegAnalysis$setupfile"
# create temporary script forwarding part number and number of parts
echo "setup_sel='$setup';">$DIR/scriptTemplates/$tmpScriptName.m
# wait for script to be created
while [ ! -f... |
0e22342dcc39395aee4d96416b725739a5ecd2a753e30ca8cf35b5349f54809b | Shell | 1,067 | 30 | #!/bin/bash
# Define your configurations
MODELS=("NeuroStream" "NeuroStream-SST")
DATASETS=("data/processed/semantic_eeg_raw.pth" "data/processed/semantic_eeg_5_95_std.pth" "data/processed/semantic_eeg_14_70_std.pth")
SEEDS=(1 2 3 4 5)
# Ensure the script stops if any individual run crashes critically
set -e
for MOD... |
55d37c9b00f05235997c00e618f751db7404ead9ca8b35f1b01d224792e0b339 | Shell | 1,072 | 31 | for setup in $subjectDataDir/all/eeg-fMRI/setups/*; do
setupfile=$(basename ${setup%.mat})
tmpScriptName="tmpRegAnalysis$setupfile"
# create temporary script forwarding part number and number of parts
echo "setup_sel='$setup';">$DIR/scriptTemplates/$tmpScriptName.m
# wait for script to be created
while [ ! -f... |
37d6fb63c629d40e21c7a7414182494878d23cc798cf2b1d0893c9d543fc9f94 | Shell | 1,083 | 14 | #!/bin/bash
for graphtype in dag rulegraph
do
hippunfold ../../test_data/bids_T1w /tmp/out participant -np --modality T1w --${graphtype} --keep-work | ./proc_subgraph.py out_${graphtype}/T1w
hippunfold ../../test_data/bids_T1w /tmp/out participant -np --modality T1w --${graphtype} --keep-work --config autoto... |
5f92c0e8438fe42c7c2b844057fa28bccd401da464146bfcfc7b0528249737cf | Shell | 1,086 | 36 |
# binary masks
GRAY="$workingDir/graymattermask.nii"
WHITE="$workingDir/whitemattermask.nii.gz"
BRAIN="$workingDir/mask.nii"
RIM_OUT="$workingDir/rim.nii.gz"
LAYNII_DIR="$workingDir/../5_laminar/laynii"
mkdir $LAYNII_DIR
LAYNII_OUT="$LAYNII_DIR/layers.nii.gz"
# Create rim volume: outside brain=0; pial/CSF boundary=1... |
72de7682aa73b90e75d330c90dd2fed2fa7e7b020c331aa874ae8a5af98416f9 | Shell | 1,091 | 45 |
rm -r $workingDir/*
ls $functionalsDir/*.nii* > $workingDir/volumes.txt
rets=($(cat $workingDir/volumes.txt | grep Retinotopy))
tasks=($(cat $workingDir/volumes.txt | grep silent))
# motion correct using mcflirt
motionCorr () {
newName=tmp-$RANDOM-fmriRealignANTs2-single
newFile=$DIR/scriptTemplates/$newName.sh
... |
cdbe534c18e83cfaf14e7d6032f468190573904a0ecf3c2293505b023a485af9 | Shell | 1,091 | 22 |
counter=0
for f in $subjectsDir/2_distcorrection/task-mcf*.nii; do
firstVols=`seq 0 3 $(($(fslnvols $f) - 1))`
fslsplit $f $subjectsDir/2_distcorrection/
for firstVoltmp in $firstVols;do
firstVol=$(echo $firstVoltmp | awk '{ printf "%04i", $0 }')
thirdVol=$(echo $(($firstVoltmp + 2)) | awk '{ printf "%04i", $0 }')
... |
37cb4e4cff852f50b0e54a7c2c8eec141bf12cbdf0c477b1064ba86a3a5b35d5 | Shell | 1,125 | 43 |
#$Project$
#$Log$
#Revision 1.1 2003/02/11 18:36:09 hines
#Initial revision
#
#Revision 1.1.1.1 2003/01/01 17:46:35 hines
#NEURON -- Version 5.4 2002/12/23 from prospero as of 1-1-2003
#
#Revision 1.1.1.1 2002/06/26 16:23:07 hines
#NEURON 5.3 2002/06/04
#
# Revision 1.1.1.1 2001/01/01 20:30:36 hines
# prepar... |
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