sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cb5628cad29ff293978ea329a9d8918e264838f3cace6fb4f145c4fa952777c3 | Shell | 663 | 12 | #!/usr/bin/env bash
cd models
# The VGG-19 network is obtained by:
# 1. converting vgg_normalised.caffemodel to .t7 using loadcaffe
# 2. inserting a convolutional module at the beginning to preprocess the image
# 3. replacing zero-padding with reflection-padding
# The original vgg_normalised.caffemodel can be obtained ... |
0515886a2dd8081309054fab90fc4fd9190f0572053ea0fc464162678f51535f | Shell | 666 | 15 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J bw_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o bw_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e bw_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam.err
# convert to... |
c6bc5380f738a108efe2b6c00a718879ee64d9466fb5c13770d371c969e53869 | Shell | 667 | 18 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J bw_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o bw_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e bw_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam.err
# convert... |
1834502754dc94bddb63919f53467402a7b899e66ef12c9907b51911a9530815 | Shell | 670 | 28 | # Copyright John Maddock 2008.
# Use, modification and distribution are subject to the
# Boost Software License, Version 1.0. (See accompanying file
# LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
#
# Generates PNG files from the SVG masters.
#
# Paths to tools come first, change these to match y... |
8df7c5214e46235971337afa864231a644280e2fc828329221db7d1cf2212f32 | Shell | 675 | 18 | #!/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... |
561ace07133a05bb99a1b568edfb8910f9111bcca6e2924eec5a376fff621640 | Shell | 676 | 15 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J bw_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o bw_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e bw_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam.err
# conv... |
a139464b74709a6cda69850d6ea908c40df4cad4d82bae017e41306621edb1e2 | Shell | 679 | 9 |
fslmaths $subjectsDir/3_coregistration/fctRBrgraymattermask.nii.gz -thr $threshold -uthr 1 -bin $subjectsDir/3_coregistration/tmp1
fslmaths $subjectsDir/3_coregistration/fctRBrwhitemattermask.nii.gz -thr $threshold -uthr 1 -bin $subjectsDir/3_coregistration/tmp2
fslmaths $subjectsDir/3_coregistration/fctRBrt1brain.n... |
9e892fb1a38ea8e9fc991ac5d9b500731d69bdb271f6828d66257bf2214674fd | Shell | 684 | 23 | #!/bin/bash
## brainageR script for collating brain predicted age results within a single directory
## James Cole, King's College London james.cole@kcl.ac.uk
## software version 1.0 09 Aug 2018
directory=$1
output_name=$2
if [ "$#" -ne 2 ]; then
echo "You must specify two arguments, collate_brain_ages.sh <director... |
97a42063f034360ac9ea466758bb243cf38c705cda7da5e6fbc195b47c215551 | Shell | 703 | 12 | #!/bin/bash
fmriRealigned=$(ls $subjectDataDir/CURRENTSUBJECT/1_realignment/ | grep mcf[0-9].nii | grep -v inverted | cut -d"_" -f1)
fmriCorrectedDist=$(ls $subjectDataDir/CURRENTSUBJECT/2_distcorrection/ | grep corrected | cut -d"_" -f2)
if [[ $(echo "$fmriRealigned" | grep $retString | wc -l) -eq $(echo "$fmriCorre... |
346b2a7ec7edf6132f72698ce86afbe33841cd42d8d1e1b19e6aef94366289cb | Shell | 712 | 24 | module load ANTs
for f in $workingDir/task*-between.nii.gz;do
condname=$(basename $f | cut -d'-' -f1)
mkdir $workingDir/$condname-params
if [[ $condname == "task0" ]];then
addtrans = ""
else
addtrans="-t $workingDir/$condname-mcf-between_0GenericAffine.mat"
fi
for vol in `seq 0 $(( $(fslnvols $f) - 1 ))`;do
antsAppl... |
2dd0e188c0ff798424fbaeda18ed9c745ad589c3bc5e1a776a040e2a21962d97 | Shell | 722 | 14 | pip install torch==2.1.0+cu118 --index-url https://download.pytorch.org/whl/cu118
pip install torchvision==0.16.0+cu118 --index-url https://download.pytorch.org/whl/cu118
pip install torchaudio==2.1.0+cu118 --index-url https://download.pytorch.org/whl/cu118
pip install torch-scatter==2.1.2 -f https://data.pyg.org/whl/t... |
55ba664ef2452bee8e7278179af0928912c3b526884f6eee8544f45576a96da3 | Shell | 737 | 17 | # make sure to remove space in provided dir by creating a symlink?
# ln -s PD/Elite/LARS/2019/august/190820\ Camilla\ wolo 190820_Camilla_wolo
# export KEYMINIO=<get the key from minioserver server-drive.promec.sigma2.no user promecshare>
CURRENTEPOCTIME=`date +%s`
DATAPATH=$1
WRITEDIR=$HOME/Data
DIRNAME=$(basename $DA... |
6838b5ba5a947db43fa9b4f4c374659283be164a3e31a1ad5777dbd9f98423bc | Shell | 748 | 15 | #!/bin/bash
#SBATCH -n 10
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J EX_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o EX_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e EX_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
cb69b1ca6f6e9e2df6d0407d5549ef8f6a9e2d13fe95b11f3731604635bcc7ed | Shell | 748 | 23 | # inter task realignment
mkdir $workingDir/interTask
ref_vol_raw="$workingDir/../A_miscResults/task-ref.nii.gz"
ref_vol="$workingDir/../A_miscResults/realign-ref.nii.gz"
fslmaths $ref_vol_raw -mas "$workingDir/../A_miscResults/m_task-ref.nii.gz" $ref_vol
for f in $workingDir/intraTask/*.nii*; do
case "$f" in
... |
401f4a8476ab771a39961b7069f0d8462b051175d75b55d8db11a00b75b6b9eb | Shell | 750 | 38 | #!/bin/bash
#SBATCH --time=1:30:00
#SBATCH --mem=80GB
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
##SBATCH --constraint=gpu80
##SBATCH --cpus-per-task=4
#SBATCH -o 'logs/%A.log'
if [[ "$HOSTNAME" == *"tiger"* ]]
then
echo "It's tiger"
module load anaconda
source activate 247-main
elif [[ "$HOSTNAME" == *"della... |
2dfd91457dfe06f83db7b530d4989a1c38ef0847a01a8238889192963e4d4bc8 | Shell | 757 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP210_PD_NP19-91_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP210_PD_NP19-91_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP210_PD_NP19-91_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for bam ... |
c0e14221230f9b5636b1a7d509932a9e4c3764225be10bf8a51e2bcc1d2d2ac8 | Shell | 757 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP212_PD_NP21-04_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP212_PD_NP21-04_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP212_PD_NP21-04_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for bam ... |
c1d51782d972dd936946c095ba9f8044cb9fbdfe1bf8f355ea9fa424c1b605d9 | Shell | 757 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP177_PD_NP21-57_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP177_PD_NP21-57_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP177_PD_NP21-57_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for bam ... |
f560491e75714409c864535787141cec1e391b7d9cb7fd6690bd9093543c55ac | Shell | 757 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP194_PD_NP22-55_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP194_PD_NP22-55_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP194_PD_NP22-55_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for bam ... |
34945af63ee9aa1f0b5bb10a6acf9e73f99559d2c1ca001e4984305732ce4ad9 | Shell | 760 | 25 |
mkdir dataset
# JND Dataset
wget https://perceptual-similarity.s3.us-west-2.amazonaws.com/dataset/jnd.tar.gz -O ./dataset/jnd.tar.gz
mkdir dataset/jnd
tar -xf ./dataset/jnd.tar.gz -C ./dataset
rm ./dataset/jnd.tar.gz
# 2AFC Val set
mkdir dataset/2afc/
wget https://perceptual-similarity.s3.us-west-2.amazonaws.com/da... |
6e5d10a7ee0dd0c0bc52497f729cfae572055beeb054777c7453f19707c88748 | Shell | 760 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 90:00:00
#SBATCH -J FC_ASAP173_PD_NP21-57_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP173_PD_NP21-57_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP173_PD_NP21-57_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
8457f17a7026416d5d951496b1b87c4662e8307b24211ff188a897458f52b5c9 | Shell | 760 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP222_PD_NP21-04_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP222_PD_NP21-04_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP222_PD_NP21-04_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
a638216b5b22e34be6790f5c14720c208d24bc64402f95795b560ce970699a70 | Shell | 760 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP178_PD_NP21-208_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP178_PD_NP21-208_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP178_PD_NP21-208_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
218cde960f8606b86d7d53debfbe53cdbbf7cc94c9f2a441478c68f1989daa16 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP193_PD_NP22-55_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP193_PD_NP22-55_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP193_PD_NP22-55_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
348ec96ee41baf78c48b3c48692c81bfde88ba6a1ca5298fff4419533b3dac8c | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP228_PD_NP19-91_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP228_PD_NP19-91_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP228_PD_NP19-91_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
48dc89ae6afd3b75fa8a580a1e1e990f1c30d0d3094f426cb26c79fcacbe3124 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP204_PD_NP21-04_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP204_PD_NP21-04_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP204_PD_NP21-04_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
4bf56dc8d7ee5a955a588d6a155f787d55a7dc28b32426d46617191686cd7999 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP195_PD_NP22-55_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP195_PD_NP22-55_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP195_PD_NP22-55_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
6c85ca8fd218ceb807798077804deca4adcd53800d2a110fca93802069cb6ff4 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP225_PD_NP23-21_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP225_PD_NP23-21_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP225_PD_NP23-21_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
6f1bfd9ae65cfa0a8ee713c4a0c7d23d4c15c9326f63f083d3561a22bb368122 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP179_PD_NP21-217_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP179_PD_NP21-217_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP179_PD_NP21-217_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
6fe9ef61cc68831836a0310f327c0ae323da037a9ec8667852e08d9c4f8e1ab4 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP208_PD_NP16-285_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP208_PD_NP16-285_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP208_PD_NP16-285_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
79bb89915df991258a59e992b8d2f49cece2d050288f9018c8f4b33dcb9acc69 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP209_PD_NP17-232_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP209_PD_NP17-232_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP209_PD_NP17-232_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
a7e63f9d371f2da95a40eafc74d2ad182505e43c1c4dc6ea06689be9cd367c4e | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP211_PD_NP19-137_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP211_PD_NP19-137_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP211_PD_NP19-137_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
c388e0ce2af71cccd74edacb46fa7de66bfc813465611d280752fd2e6afde6fe | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP207_PD_NP23-21_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP207_PD_NP23-21_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP207_PD_NP23-21_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
e2fab989ab20c3337eb8dbf7b9ce1be69017debdd27ff19055d8e6c4a72ecc5e | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP216_PD_NP19-91_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP216_PD_NP19-91_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP216_PD_NP19-91_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
f193d7eac83b007ae25df61abf2d34183575fd61f9fec9206fecc1b571cfa28b | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP156_PD_NP21-57_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP156_PD_NP21-57_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP156_PD_NP21-57_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
f99689c33637c0691b0ec81fcc4000b60b2068e232e0126235aa867ce154402e | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP190_PD_NP21-57_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP190_PD_NP21-57_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP190_PD_NP21-57_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
fa0c26e4388da522e026ac303668a34622452ce4223029c147a945733f1876f6 | Shell | 762 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP192_PD_NP22-55_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP192_PD_NP22-55_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP192_PD_NP22-55_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for b... |
0a5976be62948ff6f88727bf2e10cd31a26a5670ba2b728d2a03cad93ee9fc04 | Shell | 765 | 29 | #!/bin/bash
immv_wrapper_code=$(cat <<'EOF'
# replace the first line with your fslpython path
# -*- coding: utf-8 -*-
import re
import sys
from fsl.scripts.immv import main
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
sys.exit(main())
EOF
)
# Create the immv ... |
45e3fc8b6eedc8305c12e7b7754193e049fbfe17175e70fccb6cf75d77ac53ee | Shell | 765 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP220_PD_NP19-137_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP220_PD_NP19-137_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP220_PD_NP19-137_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
6763d219bfcd0ac02111ffa4ad527d9a6e204c08b110e17dc928f2a40fc6a1dc | Shell | 765 | 27 | #!/usr/bin/env bash
set -euo pipefail
IN_DIR="trimmed-reads" # where SRR*_1/2*.fastq(.gz) live
OUT_DIR="qc-fastqc" # FastQC output directory
THREADS=16 # per-FastQC threads
mkdir -p "${OUT_DIR}"
for i in $(seq 1747192 1747211); do
SAMPLE="SRR${i}"
# Match either .fastq or .fastq.gz
... |
0a20c7d075780d4dcc617833ed562bf1f8262f1bcec06309fc3740696cb44f2b | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP163_PD_NP21-208_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP163_PD_NP21-208_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP163_PD_NP21-208_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
1253cd13f8b0207ebe9756062d51babf0ba3ded4c5a4d28686bdd0de9c6f9032 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP185_PD_NP21-217_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP185_PD_NP21-217_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP185_PD_NP21-217_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
29fdaa15dbae4e4cabe1a2e114ebf11226328f4371219008d21aeaa4aabe3e9d | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP206_ctrl_NP22-75_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP206_ctrl_NP22-75_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP206_ctrl_NP22-75_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
4884eee86a61258a38bafcd2896cb19a853c6a434b4903f1b4f42461907388a7 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP164_PD_NP21-217_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP164_PD_NP21-217_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP164_PD_NP21-217_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
499b4347b2591b941df8390d93d9cb311db83cb167d363bab291f41d11fc765d | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP214_PD_NP16-285_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP214_PD_NP16-285_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP214_PD_NP16-285_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
4a3afe9f5d0852eccf97dfe05a39c502f3ecee098abc3f58a3c6239b9043cc4a | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP227_PD_NP17-232_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP227_PD_NP17-232_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP227_PD_NP17-232_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
51849c8f72550cb6a1a69597413971fcc206c14958212290042ab937293f21ed | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP196_PD_NP16-285_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP196_PD_NP16-285_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP196_PD_NP16-285_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
8e32365dce469dafbd9bf37c36779b1f87be85622d1f35a94cd6868329612b52 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP226_PD_NP16-285_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP226_PD_NP16-285_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP226_PD_NP16-285_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
aeeb0e92e0aba0ad04b7ba6de8be67010c9224de203a8c5f697958a2d5182f40 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP191_PD_NP21-208_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP191_PD_NP21-208_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP191_PD_NP21-208_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
c259bb23b40c4a4072b7897d4db18df7d7e3835f7e7164a8bc59b99ae438dcaa | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 90:00:00
#SBATCH -J FC_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP158_PD_NP21-217_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
d5fb29484096f350fe66e90343bee2a3ba51c9604114b1486351de7dcff43bb3 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP157_PD_NP21-208_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP157_PD_NP21-208_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP157_PD_NP21-208_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
d8dd129b7f0a017011ab7aa2ad5279abb4171bc4f838f0397111c95bfdbccb59 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 90:00:00
#SBATCH -J FC_ASAP159_ctrl_16-119_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP159_ctrl_16-119_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP159_ctrl_16-119_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
fa6cc7c52b96d9ed7fba9c1fabd847778978a045d1a4f3035f2f5fb9ff679d50 | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP202_PD_NP19-137_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP202_PD_NP19-137_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP202_PD_NP19-137_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
fa84d2454aeeb47b36fa6699b6351cc5900ef6ff3c59080363f3fba4651946cc | Shell | 767 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP215_PD_NP17-232_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP215_PD_NP17-232_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP215_PD_NP17-232_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc for... |
a7e8aaba7a283aae337e81d0b19723a186e6eb26d01d2be26a48dbd795627863 | Shell | 770 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP175_ctrl_NP16-284_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP175_ctrl_NP16-284_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP175_ctrl_NP16-284_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
a933f8c72f174b797d8eae21683f42f3cf18f3ee67fb373a750b71f82a0941b0 | Shell | 770 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP180_ctrl_NP16-119_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
0609aefb41d81a31d2f56adc75cc7bd2e3cc756cd8b33f18b9ac6b16ae2f7fda | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP224_ctrl_NP22-75_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP224_ctrl_NP22-75_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP224_ctrl_NP22-75_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
0c19adef4a341c961bef02950ac9aa20d01b2852b3bc30dafb3ee92cb3e2646a | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP170_ctrl_NP17-20_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP170_ctrl_NP17-20_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP170_ctrl_NP17-20_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
116c891d972f0a0a8db90a25b809f9a83c5ee74749f6b222de896886e95d63c4 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP181_ctrl_NP16-293_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP181_ctrl_NP16-293_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP181_ctrl_NP16-293_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
201b76bba8573ce272f6e0386b770cb3c8e83184c7f7f85741ad0c464eace665 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP223_ctrl_NP22-37_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
2a3a200ade8aa75ddf71d37fbcca083f017d8a5acd34ad267be3f3a57feb427f | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP230_ctrl_NP21-04_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP230_ctrl_NP21-04_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP230_ctrl_NP21-04_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
2d3c46fc94a8767a9ba519623d164ebc3176d61dd477d4e130bb0f42d26e7493 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP201_ctrl_NP22-75_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP201_ctrl_NP22-75_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP201_ctrl_NP22-75_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
4f76ebbe0900234fa1decb7d250e3dc3519403fc57e72989f45c7813d4bfc3d4 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP219_ctrl_NP22-75_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP219_ctrl_NP22-75_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP219_ctrl_NP22-75_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
56b9dffb784550185d8a745055bbff9ecd6125a091d6d1668b35a2695d3532f9 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP184_ctrl_NP18-148_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP184_ctrl_NP18-148_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP184_ctrl_NP18-148_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
7696dec995ef22dac31244663e9b7ec7b979b2f34cbe1920e9cf10c28b83a21f | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP231_ctrl_NP23-21_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP231_ctrl_NP23-21_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP231_ctrl_NP23-21_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
8750c1ad7dd556f6f6eeb605db4371c022305ea0142f47a5f73c90b36d82dc5f | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP218_ctrl_NP22-37_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP218_ctrl_NP22-37_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP218_ctrl_NP22-37_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
89a266370f602e61b0dfa20c152feb634c101d1049306b103177b1ec21694095 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP203_ctrl_NP19-218_SN_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP203_ctrl_NP19-218_SN_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP203_ctrl_NP19-218_SN_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
bebecb302f8b49a37f0da52c7acfa11d66fd70f96548fa55fb8705bf2bda368e | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP167_ctrl_NP17-20_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP167_ctrl_NP17-20_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP167_ctrl_NP17-20_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
cc617fbc1dba4dd224402521feee97a93bcf8a1113d0f3fe8d31b2994acd5503 | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP172_ctrl_NP18-46_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP172_ctrl_NP18-46_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP172_ctrl_NP18-46_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
d25fb498bd8765bf6857a19f8d32ef33c85050645c8cd5cd9a1d1a12d3c97e8d | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP200_ctrl_NP22-37_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP200_ctrl_NP22-37_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP200_ctrl_NP22-37_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
f22cef37c186149e2e76ed5f5d301c277c599038327d58e548505530ba255cbc | Shell | 772 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP161_ctrl_NP18-46_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP161_ctrl_NP18-46_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP161_ctrl_NP18-46_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run Fc ... |
b59e7d9e5285042ae8bef6feece65aadff9b1830eb22c440d6ce2c7f9664d95c | Shell | 775 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP176_ctrl_NP18-148_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP176_ctrl_NP18-148_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP176_ctrl_NP18-148_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
c65e42dad7d18bd8729eb0689f4d179c40d75eea4b2ec1e02963627c7363cfc6 | Shell | 775 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP221_ctrl_NP19-218_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP221_ctrl_NP19-218_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP221_ctrl_NP19-218_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
029179a78071a14064b6e638b23fdc4686b2640b56c5cd755bb37d87e6c49029 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP168_ctrl_NP16-284_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP168_ctrl_NP16-284_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP168_ctrl_NP16-284_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
17e0c731791d86c0b10f957be18f9909e2b26b2a8b0b26a5ef8950a88d64e31e | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 30
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 90:00:00
#SBATCH -J FC_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP160_ctrl_NP17-216_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
272f426d76cde89b451c465a633c7f35cf7f1eaaaf8a46d016d31710861112a5 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP189_ctrl_NP18-148_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP189_ctrl_NP18-148_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP189_ctrl_NP18-148_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
302cde51e41ab82dcb86b2f94eda2bbe902d2fb8423ada20000b74b59a44bceb | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP199_ctrl_NP19-218_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP199_ctrl_NP19-218_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP199_ctrl_NP19-218_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
5e338cfc24c9e2210e3d2806130d6a7cf3913c2c86160ef891be1abc4a8453ad | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP166_ctrl_NP16-293_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP166_ctrl_NP16-293_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP166_ctrl_NP16-293_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
700f9339380e1e6d88a1a2ea771c7e3b78a5fd7e550e61cc589c3f3f5d2eb4ee | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP174_ctrl_NP16-119_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP174_ctrl_NP16-119_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP174_ctrl_NP16-119_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
8b8a366704fcd332662dc29be17046e2412b29f9df390aca3c712c049d05fa23 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP162_ctrl_NP18-148_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP162_ctrl_NP18-148_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP162_ctrl_NP18-148_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
8d94b6f897f6d2db936d4938308ec2f54518c3be92ffc4cdcb5bf6125920d4d1 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP186_ctrl_NP16-119_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP186_ctrl_NP16-119_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP186_ctrl_NP16-119_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
c5b0c39411c816a2b13256f1fd2ac4647ada2417aa6d106620f872a0ea2bb9d2 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 30:00:00
#SBATCH -J FC_ASAP188_ctrl_NP16-293_AMY_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP188_ctrl_NP16-293_AMY_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP188_ctrl_NP16-293_AMY_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
c886a4b3d07347dada35aa7a0b99b03f5a167c7bc9d1eb6707567f4da61d2bf3 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP217_ctrl_NP19-218_PUT_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP217_ctrl_NP19-218_PUT_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP217_ctrl_NP19-218_PUT_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
d9f4d7678fbcbc2665433b7191a57c7923616b15ac7251ab00c1b1d10ce89a29 | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP165_ctrl_NP16-284_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP165_ctrl_NP16-284_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP165_ctrl_NP16-284_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
fe2809aea13ce2ac92f438c25eba7e37f6c5a5224fb5d9446c66c5082c038b7d | Shell | 777 | 16 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 98:00:00
#SBATCH -J FC_ASAP229_ctrl_NP19-137_PFC_bulkAligned.sortedByCoord.out.bam
#SBATCH -o FC_ASAP229_ctrl_NP19-137_PFC_bulkAligned.sortedByCoord.out.bam.out
#SBATCH -e FC_ASAP229_ctrl_NP19-137_PFC_bulkAligned.sortedByCoord.out.bam.err
# Run ... |
d9ac456b129bba571fbe7c005b068e1d6f15f88497ac927c91afe6264e4234aa | Shell | 781 | 19 | #!/bin/bash
WORKDIR="/home/zamor/Documents/TRISTAN/dataset_recaroline/dataset-9"
singularity run --cleanenv \
--bind /home/team/freesurfer/7.4.1/license.txt:/freesurfer-license.txt:ro \
--bind /home/zamor/Documents/TRISTAN/dataset_recaroline/dataset-9/rawdata:/rawdata:ro \
--bind /home/zamor/Documents/TRISTAN/d... |
6c438133e4e13a65473063197c38aa9be503f0cac35fb44a94e0fd7c9275b41e | Shell | 783 | 29 | #!/usr/bin/env bash
# safe-pr-review.sh — PR review wrapper that hardcodes --comment.
#
# Usage: safe-pr-review.sh <pr-number> <body-file>
#
# Forces --comment so the agent cannot approve or request changes on
# a PR. Reads the review body from a file to avoid shell-quoting pitfalls
# with attacker-influenced content.
... |
e157629bece3cd623af2117797b67ce6391730f19aee57c4274a8a3724976bc4 | Shell | 805 | 21 | #git checkout 5600b6d208fba90345e1ce52284626a976d9f63c scratch.slurm slurmFastQC.sh
#dos2unix scratch.slurm slurmFastQC.sh
#bash slurmFastQC.sh $PWD/TK
RUNCMD=fastqc
DATADIR=$1
PARAMFILE=scratch.slurm
CPU=40
CURRENTEPOCTIME=`date +%s`
WRITEDIR=$RUNCMD.$CURRENTEPOCTIME.results
FILES=$(ls $DATADIR/*.f*q.gz|tr "\n" " ")
e... |
3bed29bf8bcf77108256cded86ded4241a911efd3bd7bbb2924b9723bb5fe4d3 | Shell | 810 | 15 | mkdir tes
tar cvf t.tar *.txt *.log
tar -xf $PWD/t.tar -C $PWD/tes/ --wildcards --ignore-case "*.txt"
cd tes
ssh-copy-id 'ash022@login0.nird-lmd.sigma2.no'
sftp 'ash022@login0.nird-lmd.sigma2.no'
#Connected to login0.nird-lmd.sigma2.no.
#sftp> get -a *.txt
find PD/Qexactive/Mirta/ -iname "*20210309_CVID_1180*"
ls -1 PD... |
af7f8ed5266a7e8e544976f5809851c764eec1eb5a2f121ca251d37caf23df68 | Shell | 823 | 31 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
# Download the mini dataset (coco val2017_100, with only 100 images)
# to be used in unittests & integration tests.
cd "${0%/*}"
BASE=https://dl.fbaipublicfiles.com/detectron2
ROOT=${DETECTRON2_DATASETS:-./}
ROOT=${ROOT/#\~/$HOME} # expand ~ to HOME... |
292afbf6c43f8a06eb195785090cd42dcb059275cf8dff50d21af7095267e1fd | Shell | 850 | 27 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
BIN="python tools/train_net.py"
OUTPUT="instant_test_output"
NUM_GPUS=2
CFG_LIST=( "${@:1}" )
if [ ${#CFG_LIST[@]} -eq 0 ]; then
CFG_LIST=( ./configs/quick_schedules/*instant_test.yaml )
fi
echo "=====================================================... |
b68e6757791e512be47fbaa6b711c4461ad3ed5a94122e213bcc9d5bf5229982 | Shell | 850 | 21 | #!/bin/sh
# this is a quick demo on how to use miraEST for EST assembly and
# SNP analysis
#
# For the time being, the input files MUST have the prefix 'step1_in' to
# be processed correctly by miraeST, I'm sorry.
echo "This demo must be reworked wor 2.9.x and is currently not available, sorry."
exit
echo "Cleani... |
646e3a71dab9610c07c4dd80fafff6373e4ce1051a60f78ce8c5c53a0f4b40e3 | Shell | 853 | 20 | # bash backUpTTP.sh $HOME/TIMSTOF/LARS/2023/Data
# module load git/2.42.0-GCCcore-13.2.0
# module load Python/3.11.5-GCCcore-13.2.0
# make sure to remove space in provided dir by creating a symlink?
# ln -s $HOME/TIMSTOF/LARS/2022/june/220613\ Kristine/ 220613_Kristine
# export KEYMINIO=<get the key from minioserver s... |
c4ff9bd57eed4065fd1c0a72cdfcefba9bb7ad908ce686a03be24ffe29c22c71 | Shell | 869 | 36 | #!/bin/sh
major=7
minor=1
a=$1
if test "$a" = "" ; then
a=.
fi
echo "#define NRN_MAJOR_VERSION \"$major\""
echo "#define NRN_MINOR_VERSION \"$minor\""
cd $a
if hg identify > /dev/null && test -d .hg ; then
gcs=`hg identify -i`
lcs=`hg identify -n`
branch="`hg identify -b`"
tags="`hg identify -t`"
sha=`echo $gc... |
2e1245bf2123a8863a2e054749932eac2db0816aa6fe9fd62d85836c63d3c00c | Shell | 875 | 37 | #!/usr/bin/env bash
SCRIPT=run_network_simulations.py
cpus1="21-28"
counter=1
while [ $counter -le 10 ]
do
numactl --physcpubind=$cpus1 \
--localalloc \
python $SCRIPT \
-t "deg_vs_del" \
-m "minimal_SLSTDP_synapse" \
-s $counter \
... |
58b87b0933cafbe1e3e75edb551020f1fdf9187661fe897ffef7ec12a68f0d14 | Shell | 875 | 22 | #!/bin/bash
workingDir="/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/subjectData/S1/1_realignment"
vol='/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/subjectData/S1/A_miscResults/ret-ref.nii.gz'
mask='/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/subjectData/S1/A_miscResults/m_ret-ref.nii.gz'
re... |
fa557617526c80e76954268aab34f59c045df0f9a4b9323f5738cc0f9532a163 | Shell | 883 | 39 | #!/bin/sh
TOPDIR="/Home/siv11/ash022/bin/modeller9v3"
EXETYPE=i386-intel8
LLP=${TOPDIR}/lib/${EXETYPE}
if test -z "${LD_LIBRARY_PATH}"; then
LD_LIBRARY_PATH=${LLP}
else
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${LLP}
fi
if test -z "${DYLD_LIBRARY_PATH}"; then
DYLD_LIBRARY_PATH=${LLP}
else
DYLD_LIBRARY... |
a0a7f16143ff4870b95d8e6fdc1d69ae30b278a944a77cc96773052d4dd0b171 | Shell | 886 | 28 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
BIN="python train_net.py"
OUTPUT="instant_test_output"
NUM_GPUS=2
SOLVER_IMS_PER_BATCH=$((NUM_GPUS * 2))
CFG_LIST=( "${@:1}" )
if [ ${#CFG_LIST[@]} -eq 0 ]; then
CFG_LIST=( ./configs/quick_schedules/*instant_test.yaml )
fi
echo "====================... |
d85943e7ebc835230a6ee463b8157aab6da22c2420022cb3cab869f4fdb0d0cd | Shell | 888 | 42 | #!/bin/bash
set -euo pipefail
DEFAULT_URL="https://zenodo.org/records/19100654/files/data_root.zip?download=1"
DEFAULT_DEST_DIR="~/Downloads"
if [ "${1:-}" = "-h" ] || [ "${1:-}" = "--help" ]; then
echo "Usage: $0 [destination_dir] [zip_url]"
echo
echo "Example:"
echo " $0 /path/to/data_root"
e... |
92e712fe4b641448f5b15511ff2a7b29b2daffa4070b2cc4460cba09626e0c0e | Shell | 908 | 42 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
# cd to detectron2 project root
cd "$(dirname "${BASH_SOURCE[0]}")/.."
{
black --version | grep -E "25\." > /dev/null
} || {
echo "Linter requires 'black==25.*' !"
exit 1
}
ISORT_VERSION=$(isort --version-number)
if [[ "$ISORT_VERSION" != 4.3* ]... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.