sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6c83b5c6c6998497df85f16f29f59d219554064b71218553eaf6997b66a998eb | Shell | 1,163 | 37 | #!/bin/bash
# moves data from subfolder within ../subjectData/SXX/<analysis step> according to regexp into
# ../subjectData/SXX/<analysis step>/<year>-<month>-<day>-<hour>-<minute>-<second>
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/.."
# locate raw and processed data directories
while IFS='' read -r lin... |
a462772b345165b3bc2f6f590fee67a7e96797f1f7c9b51f9f3696826edd2cbf | Shell | 1,164 | 30 | #!/bin/bash
## By Anoushka Joglekar 04/2020
f_name=$1;
outFolder=$2;
cat $outFolder/tmp* | tr -d "[ ']" > $outFolder/"DeconvBC_"$f_name".csv"
rm $outFolder/tmp*
cat $outFolder/"DeconvBC_"$f_name".csv" | awk '{tot++1;polyA[$2]++;totLen+=$11;\
if($5!~/no_bc|,/){bc++1;len+=$11;};if(!(see[$5])) {see[$5]++1;count++1;}; t... |
c02650f5f51a8ea848f770db9fecdfe0909e041b5cd94b4498cb3ddb8b9708ee | Shell | 1,178 | 33 | #!/bin/bash -e
echo "Installing dependencies"
python -m pip install --upgrade pip build wheel
python -m pip install --upgrade -r requirements.txt
if [ -n "${OPTIONAL_DEPENDS}" ]; then
for DEP in ${OPTIONAL_DEPENDS}; do
if [ ${DEP} == "mayavi" ]; then
python -m pip install numpy vtk
... |
0f19f20bf3bf3aa7172c2cbfc5a69e0d589fddf9911ee7c2066cf5f31628cb5b | Shell | 1,199 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.5_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=168:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=60G
#SBATCH --output=slurms/output_f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.5_3dlpips_AEv5_%j.out
#SBATC... |
88417ff382d61c3473a051760002b7959c4515624935e83affa153aeadb74401 | Shell | 1,200 | 43 | #!/usr/bin/env bash
set -euo pipefail
# Optional: activate conda env if needed
# source "$(conda info --base)/etc/profile.d/conda.sh"
# conda activate gatk_env # or env where featureCounts is installed
# Paths / parameters
BAM_DIR="../STAR-WASP-output" # where *_WASP_RG.bam live
GTF="filtered_chr1-22_X.gtf... |
7b04ff879f385c50d8d210751f99b3916411056947d051059274f687e05ca32e | Shell | 1,203 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=168:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=60G
#SBATCH --output=slurms/output_f2_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5_%j.out
#SBA... |
b3d62452ea2b6ca7f82cad7b787fb8d437e3111d04d35f6cc2fc59025b0640b8 | Shell | 1,204 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nfg32_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=140:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=150G
#SBATCH --output=slurms/output_f2_nfg32_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5_%j.out
#SB... |
bc85e676fadf0313d220cf7cf44e309fdac454056e0c4fa6b112637bec294515 | Shell | 1,204 | 22 | #!/bin/bash
#SBATCH --job-name=f4_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=140:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=150G
#SBATCH --output=slurms/output_f4_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5_%j.out
#SB... |
fca64d7b812026cb24be88e8dd157ae529dcb9ccbf7bc90ad90a1527d5573d96 | Shell | 1,230 | 42 | #!/bin/bash
#SBATCH --partition=standard ##highmem ##serial
#SBATCH -J "AscB3LYP"
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128 #Maybe change to 128
#SBATCH --cpus-per-task=1 # Set to match NProcs %Pal keyword?
##SBATCH --mem=4800
#SBATCH --time=24:00:00
#SBATCH --account=e89-sur
#SBATCH --qos=standard #short #lowpr... |
d1f31db83e95d924a4943e9a95e86c13c538ddd7164798fdc53b8bf9d407d2a9 | Shell | 1,233 | 46 |
############################################################################
# Copyright (c) 2022-2024 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
VERSION="$(cat ./VERSION)"
TARGET_DIR=Spl-IsoQuant-$VERSION
r... |
271600b4754f0d7bc3f79bc42e9aa5b2ef44b3da76701229abe9a050c271f42e | Shell | 1,234 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nfg64_nfd64_dw1e-1_lpw2.0_l1w0.0_lrgtod0.5_3dlpips_AEv5_gan_finetune.sh
#SBATCH --account=def-mdadar
#SBATCH --time=168:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=60G
#SBATCH --output=slurms/output_f2_nfg64_nfd64_dw1e-1_lpw2.0_l1w0.0_lrgtod0.5_3dlpips_AEv5_... |
cbfd063eadd803fdbcf1e9356b743b7bdc7b6a7a02f5a65687797a189ec3bd74 | Shell | 1,234 | 41 | #!/usr/bin/env bash
set -euo pipefail
# Optional: activate conda env if needed
# source "$(conda info --base)/etc/profile.d/conda.sh"
# conda activate gatk_env
IN_DIR="../STAR-WASP-output" # directory with *_WASP_Aligned.sortedByCoord.out.bam
OUT_DIR="../STAR-WASP-output" # write RG BAMs in same dir
THREADS=16 ... |
87da53982d54df44b16488961b7b1862d11a01f15557b8132fb2a4669f9e8e66 | Shell | 1,235 | 25 | # 1. Create the base environment
conda create -n espl python=3.11 numpy=1.26.4 -y
conda activate espl
# 2. Install ALL conda-forge dependencies first.
# We explicitly include libstdcxx-ng to ensure DGL and PyG have the correct C++ backend.
conda install -c conda-forge ase openmm openff-toolkit openmmforcefields openff... |
1f38db0cb3f0bfdc52824b7edcdacb74ca91a0f367c47762d915480941397fd7 | Shell | 1,250 | 15 | # read raw file, that is the outcome of "fail save" edf to asc converion after renaming the file extension to .txt (sould be called SXX-raw.txt)
rawFile=$workingDir/$subject-raw.txt
# each onset of a new block has a header line, that is found. The line after the next line is analyses and the sample value is extracted,... |
e0526068cf4b4c93b38468d5377b6638751a6bb52d4cfeb08f78d405a904912c | Shell | 1,251 | 38 | #!/bin/sh
#
#
#
JEMBOSS_HOME=.
export JEMBOSS_HOME
LIB=$JEMBOSS_HOME/lib
export LIB
CLASSPATH=${JEMBOSS_HOME}:$LIB/JembossPrintAlignment.jar
CLASSPATH=${CLASSPATH}:$LIB/jakarta-regexp-1.2.jar
CLASSPATH=${CLASSPATH}:$LIB/jalview.jar
CLASSPATH=${CLASSPATH}:$LIB/mail.jar
CLASSPATH=${CLASSPATH}:$LIB/activation.jar
CLASS... |
90a62a43b9f09901c970f1548c8ca447c9d5226ef78a86b6d475b86cfe17873b | Shell | 1,254 | 22 | #!/bin/bash
#SBATCH --job-name=f2_nodegrade_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dlpips_AEv5.sh
#SBATCH --account=def-zeighami
#SBATCH --time=140:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=1
#SBATCH --mem=150G
#SBATCH --output=slurms/output_f2_nodegrade_nfg64_nfd64_dw5e0_lpw2.0_l1w0.0_lrgtod0.05_3dl... |
f444737519eab23969ccb78683d732bd258bfa9bc84b4f0d0784f4f3596dd1c3 | Shell | 1,254 | 42 | #!/bin/bash
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 $i
done
done < "$DIR/configs/.dataPathConfig.c... |
963534d75f132302c9977862b8ef9c11a5c6917a17533dbda2680182712d8ed1 | Shell | 1,255 | 42 | #!/bin/bash
## By Anoushka Joglekar. Edited 04/2020
outDir=$1;
tabFile=$2;
isIso=$3;
isTSS=$4;
isPolyA=$5;
if [[ $isIso = "TRUE" ]]
then
cat $outDir/$tabFile | awk 'BEGIN{OFS="\t"} NR>1 {a[$2"_"$4"_"$5]+=1;}END \
{for(i in a) {split(i,c,"_"); print c[1]"::"c[3],c[2],a[i]}}' \
| grep -v "none" > $outDir/"NumIsoPerCe... |
c123f3f125ac2922466aca1477b26077a00a52cceb36ef0ce9b0d285e6a462d7 | Shell | 1,259 | 11 | #git checkout 119d313328587684637b161d95a06c140bebe3e0 slurmTM.sh scratch.slurm
#dos2unix scratch.slurm slurmTM.sh
#bash slurmTM.sh $PWD/TK9
DATADIR=$1
RUNCMD=trimmomatic
PARAMFILE=scratch.slurm
CURRENTEPOCTIME=`date +%s`
WRITEDIR=$RUNCMD.$CURRENTEPOCTIME.results
mkdir $DATADIR/$WRITEDIR
for i in $DATADIR/*1.fastq.gz ;... |
01db7eb67e7bae5e0b8a087c3c49be58e9702cb246d42d629efb32e49084afdf | Shell | 1,271 | 45 | #!/usr/bin/env bash
set -euo pipefail
# source "$(conda info --base)/etc/profile.d/conda.sh"
# conda activate gatk_env
REF="Homo_sapiens.GRCh37.chr1-22_X.fa"
IN_DIR="../STAR-output-last-try"
OUT_DIR="genotype_per_sample_files"
THREADS=4 # threads per HC process
MAX_JOBS=4 # number of samples run in... |
99a97ddcd981a60e99365d43f1d73d39c83406139522d6c3ec9fefc36dc44f2d | Shell | 1,278 | 16 | #bash idxGen.sh
#git checkout 069e21a60b8255c8e0c493413565ace1b92e84e3 scratch.slurm slurmSTAR.sh
#dos2unix scratch.slurm slurmSTAR.sh
#bash slurmSTAR.sh $PWD/TK $PWD/CHM13v2-T2T/index_len150
DATADIR=$1
MAPFILE=$2
RUNCMD=star
PARAMFILE=scratch.slurm
CPU=40
CURRENTEPOCTIME=`date +%s`
WRITEDIR=$RUNCMD.$CURRENTEPOCTIME.re... |
c702cbae7f49c2e8e58b15d2a1d36d927ca1978b052f4bbe69f7b4fc39355c7c | Shell | 1,281 | 35 | # make pre-label
# 01 - V1v
# 02 - V1d
# 03 - V2v
# 04 - V2d
# 05 - V3v
# 06 - V3d
# 07 - hV4
export SUBJECTS_DIR=$subjectsDir
transmat=$DIR/supportFiles/mni1522fsaverage.txt
transmattail=$subjectsDir/0_freesurfer/mri/transforms/talairach.xfm
for hemi in lh rh;do
for roi in `seq 1 7`;do
roi... |
52929cebfe8b6cc129bae40f44a71694a817c101f9a7bea4a5ccca5250fe3e37 | Shell | 1,294 | 44 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
BIN="python tools/train_net.py"
OUTPUT="inference_test_output"
NUM_GPUS=2
CFG_LIST=( "${@:1}" )
if [ ${#CFG_LIST[@]} -eq 0 ]; then
CFG_LIST=( ./configs/quick_schedules/*inference_acc_test.yaml )
fi
echo "============================================... |
7bdbdee7518792c7f9b08eb1d16423efa44d5033862db6c8407b0688444c46a8 | Shell | 1,299 | 44 | subjectsDataDir=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/subjectData
ROI=$1
#for s in `seq 1 52`;do
#for p in 25;do # 5 25;do
#for cond in L R;do
#for cond in Lc Rc Mc;do # Pc nPc Pc_nPc;do #LL RR LR RL
for cond in "L_B" "R_B" "L_R" "L+_R+" "L+_R-" "L-_R+" "L-_R-";do # Pc nPc Pc_nPc;do #LL RR LR RL
#for ... |
4d884fcf72cc20ff00160682124462c00970c030a4093aed45b60bf26c38c90e | Shell | 1,307 | 46 | #!/usr/bin/env bash
# safe-label.sh — label wrapper with a denylist.
#
# Usage: safe-label.sh <number> <add|remove> <label>
#
# Blocks the "ready-for-fix" label so agent workflows cannot apply it and
# thereby trigger the bug-fix PR workflow. All other labels pass through.
# The denylist is intentionally small; this is... |
2648912e6c5f6b9b06dba7aaee97a6cdc963f321d7e91a9420f5f452b94796f9 | Shell | 1,313 | 46 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
root=$(readlink -f $1)
if [[ -z "$root" ]]; then
echo "Usage: ./gen_wheel_index.sh /absolute/path/to/wheels"
exit
fi
export LC_ALL=C # reproducible sort
# NOTE: all sort in this script might not work when xx.10 is released
index=$root/index.html... |
372291faf5ab33817afef3513a31eff19ade26bd0f1d9a6a6f991dc7d4793203 | Shell | 1,330 | 40 | #!/usr/bin/env bash
set -euo pipefail
ROOT=${1:?usage: bootstrap_pisa2022_revision_env.sh REPOSITORY_ROOT}
ENV_NAME=${ENV_NAME:-pisa2022-revision}
ENV_FILE="$ROOT/environment.yml"
[[ -f "$ENV_FILE" ]] || { echo "Missing environment file: $ENV_FILE" >&2; exit 2; }
if command -v mamba >/dev/null 2>&1; then
SOLVER=(m... |
9da9f253b3d3915fa388dd58c59aa7eb6d7785b0fb0b229b0fff0f82e355f210 | Shell | 1,342 | 65 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
[[ -d "dev/packaging" ]] || {
echo "Please run this script at detectron2 root!"
exit 1
}
build_one() {
cu=$1
pytorch_ver=$2
case "$cu" in
cu*)
container_name=manylinux-cuda${cu/cu/}
;;
cpu)
container_name=manylinux-... |
6f593d6f1d102e499e22cdd3a057245a2eb299d4230f5410fabc2614c6323782 | Shell | 1,345 | 54 | #!/bin/bash
# method: TransE, RotatE, DistMult, QuatE...
GPU=$1
DATASET=$2
MODEL=$3
ARGS="$4 $5 $6 $7"
LR=(0.01)
TRAIN_CSV_PATH="./csv_data/merged_test_clinvar_data.csv"
A=(0.5)
MODE="missense"
SEED=(12345)
if [ ${DATASET} == "train_clinvar_2022_all_test_clinvar_20230326" ]
then
DIM=(128)
ALPHA=(0.23)
... |
a665f77b52d998062395ab14c9f6693e1b5a5b518ecc1210626a315b6ff5c205 | Shell | 1,349 | 66 | # copyright John Maddock 2003
# Distributed under 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.
#
# locate all the header dependencies:
for file in ../../../boost/regex/*.hpp ; do
if [ -f $file ]; then
if [ $file != ../../../boo... |
778b9fb65049c20745921996bd11195ed58b2f26d67d95aff32413d1f7b88453 | Shell | 1,352 | 27 |
nnUNetv2_train $1 3d_fullres 0 -tr nnUNetTrainer_5epochs --npz
nnUNetv2_train $1 3d_fullres 1 -tr nnUNetTrainer_5epochs --npz
nnUNetv2_train $1 3d_fullres 2 -tr nnUNetTrainer_5epochs --npz
nnUNetv2_train $1 3d_fullres 3 -tr nnUNetTrainer_5epochs --npz
nnUNetv2_train $1 3d_fullres 4 -tr nnUNetTrainer_5epochs --npz
nn... |
515d30710d30d52aa7dd0746abaf6d6dba0282eabd6618d906e1640da37bf17d | Shell | 1,358 | 17 | #!/bin/bash
set -euxo pipefail
HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --h... |
ddc93a6c8b8e12d9eda3b7cd27a6a30f74fdf3d21808c1c59d0e7f9ffc4140cd | Shell | 1,373 | 35 | #!/bin/sh
echo "Running the assembly."
echo "Main characteristics:"
echo "- Sanger & 454 hybrid assembly"
echo "- loading everything from CAFs (previously made in this pipeline),"
echo " except the backbone"
echo "- a backbone is loaded from a GBF file (but used only starting with pass 3)"
echo "- 7 passes with a max... |
7cae11b37722f54df16c563a958f41eb4cf470ce93f1d3af49feea84a6137a0d | Shell | 1,382 | 75 | #!/bin/bash
declare -a BuildConfigs
declare -a ObjDirs
BuildConfigs=(
Release
Debug
FastDebug
Profile
QualityScores
ThreadedDebug
ThreadedFastDebug
ThreadedProfile
ThreadedRelease
)
ObjDirs=(
"bin"
)
BASE_DIR="`pwd`"
function makeDirectories()
{
echo
echo "Creating directories... |
e9806d1a99887e62a43df15e698efe818440253b89116a1d151eca19f7476571 | Shell | 1,390 | 19 | mkdir -p $HOME/promec/promec/TIMSTOF/LARS/2026/260211_Steven/
#winZipDir.bat L:\promec\TIMSTOF\LARS\2026\260211_Steven
rclone ls --include "**.zip" NS9036K:PD/TIMSTOF/LARS/2026/260211_Steven/
rclone copy -Pv --include "**.zip" NS9036K:PD/TIMSTOF/LARS/2026/260211_Steven/ $HOME/promec/promec/TIMSTOF/LARS/2026/260211_Ste... |
c97d39160685e97e8197492936aa8efc7e832ac823a49bdbe3f4e34193263820 | Shell | 1,393 | 16 | #git checkout d0c2421846c29bbb3facddd46b16511f4537649b scratch.slurm
#dos2unix slurmHISAT2.sh scratch.slurm
#rename '__.1P.fq.gz' '_1.fastq.gz' /cluster/home/ash022/scripts/TK9/trimmomatic.1701618021.results/*
#rename '__.2P.fq.gz' '_2.fastq.gz' /cluster/home/ash022/scripts/TK9/trimmomatic.1701618021.results/*
#bash sl... |
89488e12237146e2346c8e6de5bef3704e9b93bf23f0ecdae6b43a126c03fd0f | Shell | 1,394 | 28 | t1File=$(ls ${rawT1Dir}/*t1mprage*nii.gz)
mideface --i $t1File --o $t1File --odir $rawT1Dir/qa --pics --code rawT1
mideface --check $t1File $rawT1Dir/rawT1.txt
t1File=$subjectsDir/0_freesurfer/mri/orig/001.mgz
mideface --i $t1File --o $t1File --odir $subjectsDir/0_freesurfer/mri/orig/qa --pics --code 001
mideface --ch... |
20bf688f1f3b5c1800cce21932f2428402f764333c8c58e259b8392d4cc09910 | Shell | 1,414 | 14 | #git checkout 53b672d5f9da4ac8bef8076cd54f91a1b8916fe0 scratch.slurm slurmST.sh
#dos2unix scratch.slurm slurmST.sh
#bash slurmST.sh $PWD/TK9/trimmomatic.1701618021.results/hisat2.1701897177.results
#bash slurmST.sh $PWD/TK9/trimmomatic.1701608001.results/hisat2.1701618338.results
#bash slurmST.sh $PWD/TK9/trimmomatic.1... |
da4f3a444d1d31fd29ff361db6b47015ec02c1c753e3a829b8e1584158324a98 | Shell | 1,445 | 54 | #!/usr/bin/env bash
set -euo pipefail
# Optional: activate conda env if needed
# source "$(conda info --base)/etc/profile.d/conda.sh"
# conda activate gatk_env
REF="Homo_sapiens.GRCh37.chr1-22_X.fa"
BAM_DIR="../STAR-WASP-output"
VCF_DIR="genotype_sample_files" # per-sample VCFs from HaplotypeCaller
OUT_DIR="ASE_res... |
448bd6b5908a5ea7e365d11a1c1b4314c89f1145784642db24558aa4b17fd7c8 | Shell | 1,451 | 56 | #!/usr/bin/env bash
set -euo pipefail
# Config
IN_DIR="../fastq_files" # where SRR*_1.fastq / SRR*_2.fastq live
OUT_DIR="trimmed-reads" # output folder
THREADS=16
mkdir -p "${OUT_DIR}"
# Loop SRR1747192 .. SRR1747211 (inclusive)
for i in $(seq 1747192 1747211); do
SAMPLE="SRR${i}"
R1="${IN_DIR}... |
433c4b53ed021a846c74904cac4781a75cfbf86abad6f689881c81c36e8b08c9 | Shell | 1,453 | 31 | # performs surface reconstruction using FreeSurfer
# if specified in the config, the FreeSurfer environment is set up.
if [[ $setupFreesurfer -eq 1 ]]; then
export FREESURFER_HOME=$freesurferHome
source $FREESURFER_HOME/SetUpFreeSurfer.sh
fi
# SUBJECTS_DIR is the folder were all files of a particular subject are st... |
5bab9c424e2c20b1b92a91eb64d56a98fd01061e0c110b56a7f995f97e805dff | Shell | 1,462 | 40 | #!/usr/bin/env bash
# Create the tested local Python environment for the CW-Net toy demo.
set -euo pipefail
SCRIPT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd -- "$SCRIPT_DIR/../.." && pwd)"
ENV_PREFIX="${CWNET_ENV_PREFIX:-$REPO_ROOT/.venv-codeocean}"
CONDA_COMMAND="${CONDA_EXE:-conda}"
... |
3b5743a7f1e34249934eaea553753e23aca007abcdd4a84d30d0d40c8dc703f0 | Shell | 1,526 | 10 | #!/bin/sh
tex $5 '\def\Link#1.a.b.c.{\expandafter\def\csname tex4ht\endcsname{\expandafter\def\csname tex4ht\endcsname{#1,html}\input tex4ht.sty }}\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\let\svrm=\rm\def\rm{\svrm\ifx\c\commen... |
6b28e1f6cf0d4fe431154bf439c0aa8c8b35cb30c745b4a81180440ec5c0509e | Shell | 1,550 | 79 | #!/bin/bash
#
# Takes input on STDIN. Each line specifies the name of a vertex
# (first word on the line) and the set of vertices it has edges to (remaining
# words on the line.)
#
function echoerr { echo "$@" 1>&2; }
function debug {
# echoerr $@
true
}
function ham
{
read VERTEX EDGES
REST=$(cat)
... |
ff1b40b9bd1b57836a0b89deb7949bce69bc025b2eb939299b0fce5c700c1b96 | Shell | 1,570 | 26 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 50:00:00
#SBATCH -J computeMatrixHERVs
#SBATCH -o computeMatrixHERVs.out
#SBATCH -e computeMatrixHERVs.err
# In order to know what LTRs to plot, I've intersected LTRs in repeatmasker with the retrotector annotations and only kept the longest ... |
0a0c8deb56f32769fdf05be54cd95746f7a8a45d187c274685f12e9a52ee6859 | Shell | 1,579 | 9 | #!/bin/sh
latex $5 '\makeatletter\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\def\Link#1.a.b.c.{\g@addto@macro\@documentclasshook{\RequirePackage[#1,html]{tex4ht}}\let\HCode\documentstyle\def\documentstyle{\let\documentstyle\HCode\... |
aa73d30de49a0a1efd4c5b2d58fa8eaffbb83ec57bb92af800c0c5d3cf89335b | Shell | 1,612 | 59 |
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
... |
b42fd7048cfd6ddc54d12029b044e577d65ef6b6a55c645b3a550088b83bf9e5 | Shell | 1,620 | 78 | #!/bin/sh
# Build ideal unitigs given a fasta or frg file.
# Align ideal unitigs back to the reference with nucmer.
# Generate a mummerplot.
#
# ASSUMES all programs are in your path.
# mummer: nucmer, mummerplot
# kmer: snapper2, convertToExtent
# wgs-assembler: bogus
FAS="../FRAGS/porph... |
8d058b1bd9301dc903acf0f5a51201583368c65b0138508499fd60ca98c14651 | Shell | 1,621 | 9 | #!/bin/sh
xelatex -no-pdf $5 '\makeatletter\def\HCode{\futurelet\HCode\HChar}\def\HChar{\ifx"\HCode\def\HCode"##1"{\Link##1}\expandafter\HCode\else\expandafter\Link\fi}\def\Link#1.a.b.c.{\g@addto@macro\@documentclasshook{\RequirePackage[#1,html]{tex4ht}}\let\HCode\documentstyle\def\documentstyle{\let\documentst... |
4c34f2cd27b4abfd488d3349aa63c5230cc0f38b667c5b50684be556b9e1a6c0 | Shell | 1,629 | 29 | /bin/bash
#change the following paths according to the AriocP Installation, directory containing experiment fasta/q files, ref fasta file and representative configuration file './AriocP.cfg' for that version respectively
cd
wget https://github.com/RWilton/Arioc/releases/download/v1.42/Arioc.x.142.zip
unzip Arioc.x.142.... |
7e2928f4078e5208f817a7d0ecdb5efdeef9b435c6fd14692029968273b5b71c | Shell | 1,649 | 44 | #!/bin/bash
workingDir=$1
inv_counter=0
non_inv_counter=0
for f in $workingDir/stage1/*.par; do
find_this=$(basename $f)
touch $workingDir/$find_this
corresponding_line_number=$(grep -Fn "${find_this%.*}.nii.gz" $workingDir/stage2/names.txt | cut -f1 -d:)
corresponding_line_stage2=$(sed "${corresponding_line_numb... |
a7a0f7104c6c31e33a2652456d951bf55a2dc0cfa098bc6f29f7ece7d065fe96 | Shell | 1,660 | 44 | #bash slurmFP.sh /nird/projects/NS9036K/NORSTORE_OSL_DISK/NS9036K/promec/promec/Elite/LARS/2018/mai/Vibeke\ V
#wget https://rest.uniprot.org/uniprotkb/stream?download=true&format=fasta&query=%28%28taxonomy_id%3A2%29+AND+%28reviewed%3Atrue%29%29
#cat /mnt/z/Download/uniprotkb_proteome_UP000005640_2025_09_09.fasta /mnt/z... |
9c43ae664bfdec92e4206c96b78aa0863ae1280c6d60e3348d1529d1826e7f87 | Shell | 1,680 | 41 | #!/bin/bash
# ------------------------------------------------------------------------------
# Title: Running Cytospace Alignment on Spatial Transcriptomics and scRNA-seq Data
# Author: Yiran Song
# Date: March 18, 2025
# Description:
# This script automates the execution of Cytospace using single-cell RNA-seq
# and s... |
7e9f9d712ba523af90852966a75f660cf8e955511970d56765dddd1eefe2bb60 | Shell | 1,709 | 47 | #!/bin/bash
## IJ BAR: https://github.com/tferr/Scripts#scripts
## Places scripts (symlinks) and latest jars in a local Fiji installation
## so that the ImageJ updater can upload all files to the BAR Update site
## Source and destination paths
PROJECT_DIR=`dirname $(pwd -P)`
FIJI_DIR="/Applications/IJ/FijiUploadToBAR.... |
e538c07dc0f741ce6e5d7bb5bf8ea08f372f2e6ec6e24a7d36bf67085457af87 | Shell | 1,716 | 16 | #git checkout 765cd0b3e385a4c0e4aa0656f9db4249ec47cbaf fp.workflow.txt
#cd /mnt/promec-ns9036k/raw
#perl -p -i -e 's/\r\n/\n/g' $HOME/scripts/fprunHF.sh $HOME/scripts/fp.workflow.txt OR try
#perl -e"BEGIN{ binmode STDOUT }" -pe1 $HOME/scripts/fp.workflow.txt > fp.workflow.txt
#perl -e"BEGIN{ binmode STDOUT }" -pe1 $H... |
6eaa7822192afd247f938faceefa792a0cd0e8b53c60f4ae985844832c3f0d0d | Shell | 1,727 | 46 | #!/bin/bash
## By Anoushka Joglekar 03/2020
## Edited 07/2020
rawOutput=$1;
filteredOutput=$2;
concat=$3;
filterReads=$4;
fqFolder=$5
if [[ $concat = "TRUE" ]]
then
cat $rawOutput/DeconvBC*.csv | grep -v "no_clust" | grep -v "no_bc" | grep -v "," \
>> $filteredOutput/"FilteredDeconvBC_AllFiles.csv"
sed -i $'1i\\\nNam... |
c803cac6ad9f651bf1cec1e0d8e0e9a7083aca042f91feb09e9d151e7852c913 | Shell | 1,818 | 34 | # creates a difference volume between the last and the first volume of a consecutive block of scans before scans were interrupted by a pause to obtain the EEG data. This difference exposes a T1-like contrast that can be coregistered to the T1 more easily. This is particularily important since we deal with partial brain... |
7ef6e0192b445e4c6b6cc87d7cd7188fc5e618ffd538c14566124edc5c8090b6 | Shell | 1,841 | 69 | #!/usr/bin/env bash
set -euo pipefail
GENOME_DIR="GrCh37_STAR"
READ_DIR="trimmed-reads"
VCF_DIR="genotype_sample_files"
OUT_DIR="../STAR-WASP-output"
THREADS=20 # threads per STAR run (increased to 16)
MAX_JOBS=1 # run samples sequentially (no parallel execution)
mkdir -p "${OUT_DIR}"
align_sample() {
l... |
cdd36a023f4ea30f32d35d23ea22b55b02b027cf050b310823fa0c7e5f98e563 | Shell | 1,844 | 76 | #!/bin/bash
# Get the directory of the current script
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Set the parent directory of the script directory
PARENT_DIR="$(dirname "$SCRIPT_DIR")"
# Set the PATH for sratoolkit using an environment variable or default path
SRATOOLKIT_PATH="${SRATOOLKIT_PATH:-$PA... |
134826fe4466fa4fc4a6d915caf6ad6432ab0eb124ca8fb903497eb655530674 | Shell | 1,846 | 125 | #!/bin/bash
mkdir toolboxes
cd toolboxes
whichOne=analyzePRF
GHuser=kendrickkay
if [ -d "$whichOne" ]
then
cd $whichOne
git pull
cd ..
else
git clone https://github.com/$GHuser/$whichOne
fi
whichOne=knkutils
if [ -d "$whichOne" ]
then
cd $whichOne
git pull
cd ..
else
git clone https://github.com/$GHuser/$whichOne
f... |
41c9a85492c185e058dfc748d7c44797839a5a078f658127b37054d4569bf3fe | Shell | 1,861 | 64 | #!/bin/bash
# Extract_areas.sh
#
# Description:
# This script extracts the surface area (or other scalar values) of each
# cortical region from a CIFTI dlabel file using the corresponding scalar file.
#
# Inputs:
# - LABEL_FILE: CIFTI label file with parcellated cortical regions
# (.dlabel.nii)
# - AREA_FILE: CIFT... |
40751063db5bce5f5696ac9b415e747f2183c709af0beb393bcae0441d06ef7c | Shell | 1,870 | 48 | #!/bin/bash
# Anoushka Joglekar
# April 2020
fastqDir=$1;
starOut=$2;
progPath=$3;
refGenome=$4;
numThreads=$5;
## Create a fastq guide
for i in $(ls $fastqDir/*.fastq.gz) ; do echo $i | awk -v path=$(realpath $i) \
'{n=split($1,a,/\/|.fastq/); print a[n-1]"\t"path}' ; done > Misc/fastqGuide
## Running STAR program... |
51ac2b48f2083e34082b1beb360d3311e3de7da7893e6e2d1814abfe5f14181d | Shell | 1,884 | 48 | #!/bin/bash
# create environment
# create alignment files from input csv & compute distances with RAxML
python src/0_create_raw_input/main.py --input-dir data/tiny_data --output-dir data
# format non-interpolated input
python src/2_dataset_formatting/no_interpolation/main.py \
--data-dir data/no_interpolation \
... |
7500affcf4eee40b7eb33ab21e607c1bfd198802a478ef8bd6b52a5c9029b07a | Shell | 1,889 | 78 | #!/usr/bin/env bash
set -euo pipefail
# init conda
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate gatk_env
REF="Homo_sapiens.GRCh37.chr1-22_X.fa"
DICT="Homo_sapiens.GRCh37.chr1-22_X.dict"
OUT_DIR="../STAR-output-last-try"
mkdir -p "${OUT_DIR}"
##############################
# 0) PREPARE REFEREN... |
3d3fc6bc0a93cb2982511ff93f9a56a696996b837c791af17dd38cc698adbfdc | Shell | 1,915 | 36 | # if specified in the config, the FreeSurfer environment is set up.
if [[ $setupFreesurfer -eq 1 ]]; then
export FREESURFER_HOME=$freesurferHome
source $FREESURFER_HOME/SetUpFreeSurfer.sh
fi
# SUBJECTS_DIR is the folder were all files of a particular subject are stored. Hence the subject itself is called 0_freesurfe... |
981fe781e3e19cc7912b0d0040086484be71c78c52b71418abbac13c3bba0eb6 | Shell | 1,948 | 59 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="${SCRIPT_DIR:-./}"
PYTHON_BIN="${PYTHON_BIN:-python3}"
TRAIN_SCRIPT="${TRAIN_SCRIPT:-RINAMI_train_and_test.py}"
BASELINE_ROOT="${BASELINE_ROOT:-../pth/baseline_models}"
LOG_ROOT="${LOG_ROOT:-${BASELINE_ROOT}/logs}"
SPLITS="${SPLITS:-1 2 3}"
RUN_MEGA_TEST="${RUN_MEGA_... |
07e7b6155f8720583e4730f1149704259a79d5e8785e2c45f524d7b3b26b9128 | Shell | 1,965 | 41 | #!/bin/sh
# By Anoushka Joglekar 06.2022
# File to convert from IsoQuant corrected BED file to
# a corrected all-info file
# Column 6: Corrected Intron Chain
# Column 9: Corrected Exon Chain
# Column 10: Old intron chain
# Column 11: Old exon chain
corrBed=$1;
allInfo=$2;
allInfoCorrected=$3;
cat $corrBed | awk 'NR>1... |
b859502873a9c724d93ba33bdf6b0bd4a954516a7ce254ed04e1ca950d939379 | Shell | 1,980 | 52 | #!/bin/bash
#===============================================================
# '--raw_file' : Input PLINK .raw file, default=None.
# '--phen_file' : Input phenotype file, default=None.
# '--mask' : Input grouping file (biological prior), default=None.
# '--gebv_files' : Dynamic list of GEBV files, default=[].
# '--ou... |
6a0c2f9a4339f525d55b722f0fd598b4d1f5f0baf694b55b8e8aacc3f6322df1 | Shell | 2,071 | 39 | #!/bin/bash
#SBATCH -n 20
#SBATCH -N 1
#SBATCH -A csens2024-3-2
#SBATCH -t 50:00:00
#SBATCH -J computeMatrixL1
#SBATCH -o computeMatrixL1.out
#SBATCH -e computeMatrixL1.err
regions="/scale/gr01/shared/jjakobsson/backup/raquelgg_fs3_jakobssonlab/annotations/hg38/rmsk/hg38_rmsk_TEtranscripts_FL_L1_marked.bed"
expressed... |
2a9fe1e68ea8ed0f51c6b2e74c9d1c7bb1e8d8906e1f7b95edc2e19a29a428cc | Shell | 2,086 | 51 | #!/bin/bash
# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR setting for your setup
export FSLDIR=/opt/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh > /dev/null 2>&1
# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses ... |
9b23242ed31e56c2b50b589be48c08008f2292f5863f8e78802d6bb637e16d37 | Shell | 2,102 | 10 | bsub -q gpu.legacy -gpu num=1:j_exclusive=yes:gmem=1G -L /bin/bash ". /home/isensee/load_env_cluster4.sh && cd /home/isensee/git_repos/nnunet_remake && export nnUNet_keep_files_open=True && . nnunetv2/tests/integration_tests/run_integration_test.sh 996"
bsub -q gpu.legacy -gpu num=1:j_exclusive=yes:gmem=1G -L /bin/bash... |
cc7d60c24de302ab19da435ac84e6e79b1e6c87a6280230217a20d6f7cd23f6a | Shell | 2,115 | 44 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal... |
a54a21dbed6c56ad0070e609a61c0e96b91bd0e09062d2852cdc028d98050fae | Shell | 2,155 | 45 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# A shell script that parses metrics from the log file.
# Make it easier for developers to track performance of models.
LOG="$1"
if [[ -z "$LOG" ]]; then
echo "Usage: $0 /path/to/log/file"
exit 1
fi
# [12/15 11:47:32] trainer INFO: Total training time... |
194fce5c201ff7f6418bb49600b4c4f92a458271462e85370776115c131fd14b | Shell | 2,163 | 56 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
6d33de73f32ea54471ca3ea82989015689886874224daf548bafca70e7bb4569 | Shell | 2,183 | 71 | #!/bin/bash
DIR="$( 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 $i
done
done < "$DIR/configs/.dataPathConfig.csv"... |
e8c7e16f7e2dcaaee08214409af8676a80e4e544bf05df81f1a63a5fd4d70385 | Shell | 2,197 | 16 | #cd /mnt/promec-ns9036k/raw
#ash022@deep-learn-1746533977-deep-learning-tools:/mnt/promec-ns9036k/raw$ bash $HOME/scripts/fprunTTP.dl.sh /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/promec/TIMSTOF/LARS/2025/251103_STEVEN $HOME/scripts
#git checkout fa54e2fa0a932cbdb29be54f2bdf242d66d939ab fprunTTP.sh
#perl -p -... |
eb134be2aeb44496326499bf61312cef3d50e84d6cdd7f646dca280141c3c5cb | Shell | 2,211 | 33 | #bash mqrun.sh $HOME/MaxQuant_v.2.0.2.0/bin/MaxQuantCmd.exe $HOME/Animesh/OrbitrapElite_PeptideDDA/OrbitrapElite_PeptideDDA/20200909_MKA_H12C_PeptidesDHB_DDA/ $HOME/FastaDB/uniprot-human-iso-june21.fasta mqpar.xml 1 0.10
#USAGE: bash mqrun.sh <full path to MaxQuantCmd.exe> <full path to directory containing raw files/>... |
b000e886cca4d583e8b93f863a2e5db66c120f1b63e7d8b79dfc396f73e335f7 | Shell | 2,212 | 50 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
ee47af53d422b8f8a6aeae928a089abafe2f6f82e3aa6713dc6a7ad650a67a27 | Shell | 2,222 | 69 | #!/usr/bin/env bash
set -euo pipefail
############# user settings ############
SCRIPT_DIR="${SCRIPT_DIR:-./}"
PYTHON_BIN="${PYTHON_BIN:-python3}"
TRAIN_SCRIPT="${TRAIN_SCRIPT:-RINAMI_train_and_test.py}"
OUT_ROOT="${OUT_ROOT:-../pth/pth_RINAMI_trained}"
LOG_ROOT="${LOG_ROOT:-${OUT_ROOT}/logs}"
SPLITS="${SPLITS:-1 2 3... |
ef0b6e9d682b5b1ab79f3d6f52d2e3a4c00c676a1353b3f35df645749f980fdb | Shell | 2,243 | 75 | #!/bin/bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# Check if the first argument is provided; if not, read from pipe (stdin)
if [ -f "$1" ]; then
# Case: sh qsub2slurm.sh script.sh 1
INPUT_FILE="$1"
RUN_NOW="${2:-0}"
else
# Case: echo "script.sh" | sh qsub2slurm.sh 1
RUN_NOW="${1:... |
8db18a33162e8f510dfe5669c3f96d361123b8ec0615126a71c97b0087c87ce4 | Shell | 2,245 | 63 | #!/bin/bash
DIR="$( 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 $i
done
done < "$DIR/configs/.dataPathConfig.c... |
72a3b95371cfaaf29bcf3db3145bb2dc4d0581184a904c7f229737ed1bfbdc46 | Shell | 2,249 | 53 | #!/bin/bash
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 $i
done
done < "$DIR/configs/.dataPathConfig.c... |
58d56932a2b1a8c75a24ece7084d0fb7353a7f66dca6bb032de7d2da28f7f1d4 | Shell | 2,308 | 75 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
# Function to retry functions that sometimes timeout or have flaky failures
retry () {
$* || (sleep 1 && $*) || (sleep 2 && $*) || (sleep 4 && $*) || (sleep 8 && $*)
}
# Install with pip a bit more robustly than the default
pip_install() {
retry ... |
40b3fafc92994ef778fa095c08259f95167964031fec0691ef09e9d0d13130cc | Shell | 2,345 | 35 | #USAGE: bash mqrunTTPdia.sh $HOME/MaxQuant_2.0.3.0/bin/MaxQuantCmd.exe $HOME/PD/TIMSTOF/LARS/2021/Oktober/211013_Shengdong/DIA/DIA/DIA $PWD/human.fasta $HOME/PROMEC/promec/libMQ/homo_sapiens/missed_cleavages_1/peptides/peptides.txt $HOME/PROMEC/promec/libMQ/homo_sapiens/missed_cleavages_1/evidence/evidence.txt $HOME/PR... |
51160f7273b23d4df317119e8edeeab3a0383d999a0296425d62797baae746eb | Shell | 2,347 | 70 | #!/bin/bash
#WORKDIR="/home/zamor/Documents/TRISTAN/ismrm_dataset/sub-02/data_ONAVoffPEERSoff"
#WORKDIR="/home/zamor/Documents/TRISTAN/data_Caro"
#subjects=("sub-02")
#for sub in "${subjects[@]}"
#do
# for ses in 1
# do
# SUBID="${sub}"
# SESID="ses-${ses%}"
# WORKSUBDIR="${WORKDIR%}/${SUBID%}/${SESID%}"
# mkdir... |
445a1ccbbf712b68e8a7e58f0726d6776b86ba89edb53564b2e699ed7e57dca8 | Shell | 2,360 | 54 | # if specified in the config, the FreeSurfer environment is set up.
if [[ $setupFreesurfer -eq 1 ]]; then
export FREESURFER_HOME=$freesurferHome
source $FREESURFER_HOME/SetUpFreeSurfer.sh
fi
# SUBJECTS_DIR is the folder were all files of a particular subject are stored. Hence the subject itself is called 0_freesurfe... |
9681af07a4fb90f2833ac611b8c689a6f8e453e1b3ab550ffbae4e147ab8ef07 | Shell | 2,366 | 72 | T1mask=$freesurferDir/mri/brainmask.mgz
T1maskref=$workingDir/T1mask.nii.gz
if [[ -f $freesurferDir/mri/brainmask.orig.mgz ]];then
cp $freesurferDir/mri/brainmask.orig.mgz $freesurferDir/mri/brainmask.mgz
else
cp $freesurferDir/mri/brainmask.mgz $freesurferDir/mri/brainmask.orig.mgz
fi
cp $T1mask $workingDir/fctmaskT... |
5d311ad9ff7e3dad249cb929e924e31d497b05ed539b2a060189b902fb6e2bfe | Shell | 2,399 | 63 | #!/bin/bash
DIR="$( 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 $i
done
done < "$DIR/configs/.dataPathConfig.c... |
2e42c42c885abb73f4cf91ce3350b8c0ba2e749c824eaa709ee24530446a3c73 | Shell | 2,401 | 62 | #!/bin/bash
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 $i
done
done < "$DIR/configs/.dataPathConfig.c... |
c0f52efe029e93bb81cc8b18df42a7a49d14bf178e4a6841f92bcdbc2b19c5f3 | Shell | 2,411 | 56 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal... |
3b765981ad15852d516a217470b8a8867414e3254ac37a7afb7e580195541fce | Shell | 2,491 | 31 | #git checkout d0c2421846c29bbb3facddd46b16511f4537649b scratch.slurm
#wget https://github.com/lh3/minimap2/releases/download/v2.29/minimap2-2.29_x64-linux.tar.bz2
#tar xvjf minimap2-2.29_x64-linux.tar.bz2
#cp minimap2-2.29_x64-linux /cluster/projects/nn9036k/
#dos2unix slurmMinMap2.sh scratch.slurm
#bash slurmMinMap2.... |
d250b4c1148fed12b7a1fb35b96fb705a334d9cfe996338f21bfc499a4e11759 | Shell | 2,498 | 71 | #!/bin/bash
#rsync -Parv /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/promec/TIMSTOF/LARS/2026/260408_Steven/260408_Steven_*.d /mnt/promec-ns9036k/steven/
#rsync -Parv /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/promec/TIMSTOF/LARS/2026/260211_Steven/260211_Steven_*.d /mnt/promec-ns9036k/steven/
#rsy... |
7e88aaf69e8f9b0101fa57eb57316a27c91c2896bccf0f6ae4836c788845a0bd | Shell | 2,518 | 56 | # performs surface reconstruction using FreeSurfer
# if specified in the config, the FreeSurfer environment is set up.
if [[ $setupFreesurfer -eq 1 ]]; then
export FREESURFER_HOME=$freesurferHome
source $FREESURFER_HOME/SetUpFreeSurfer.sh
fi
# SUBJECTS_DIR is the folder were all files of a particular subject are st... |
5fc7e9719f89df2355d0fd31696b4a28eed5a4c62dfaed1c43a9cda07afa4230 | Shell | 2,521 | 34 | ## hhblits
git clone https://github.com/animesh/hh-suite
mkdir -p hh-suite/build
cd hh-suite/build
cmake -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
wget https://www.uniprot.org/uniprot/P13051.fasta
cat P13051.fasta >> P13051.msa.fasta
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08... |
3a8dd80d0c6100f907d692d556d830c3a534a48733324468b7514aa8014e8451 | Shell | 2,535 | 100 | #!/usr/bin/env bash
set -e
ENV_NAME="pHoptNN"
echo ">>> Checking for conda..."
if ! command -v conda >/dev/null 2>&1; then
echo "ERROR: conda not found. Install Miniconda or Anaconda first."
exit 1
fi
# Enable 'conda activate' inside this script
eval "$(conda shell.bash hook)"
echo ">>> Creating conda env '$ENV... |
a5b00232c18fc33388d3192c596ff73cc3d6b23988316a93b2a66ceaffcdd456 | Shell | 2,539 | 44 |
mkdir $workingDir/anatomy
#optional --out_orientation PSL or RAS or you name it
mri_convert $freesurferDir/mri/orig.mgz $workingDir/anatomy/t1.nii.gz
mri_convert $freesurferDir/mri/ribbon.mgz $workingDir/anatomy/t1ribbon.nii.gz
mri_convert $freesurferDir/mri/brain.mgz $workingDir/anatomy/t1brain.nii.gz
mri_convert $f... |
a915f970100c65d5cdc97bc473c903e0806e891904c7eba45bc6e736ba1fcb8d | Shell | 2,547 | 28 | #bash download_fasta.sh
# 5192 74865 670432
# 4416 55550 513224
# 4042 8084 117218
#EcolHIsTagsSyn.fasta:>sp|A5A627|TISB_ECOLI Small toxic protein TisB OS=Escherichia coli (strain K12) OX=83333 GN=tisB PE=1 SV=1
#EcolHIsTagsSyn.fasta:>sp|sufA5A627|TISB_ECOLI Small toxic protein TisB OS=Escherichia coli ... |
5932d37113659301d3a2e5c8620cb06f0a3974cc10e9af936d4774fd1eb86f9c | Shell | 2,588 | 55 | #!/bin/bash
export SUBJECTS_DIR=/path/to/FS_out
export SAVE_DIR=/path/to/FS_out_fsaverage_remapped
ID_FILE=/path/to/ids.txt
N=10
resample(){
sub=${1}
echo $sub
mkdir -p $SAVE_DIR/$sub
mkdir $SAVE_DIR/$sub/mri
mkdir $SAVE_DIR/$sub/surf
mkdir $SAVE_DIR/$sub/label
cp $SUBJECTS_DIR/$sub/mri/orig.m... |
ef260732c03f7da21dc455527aa589dcd7494d97645b81b17ce0c182ab7e224f | Shell | 2,620 | 63 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
fe4745728bcaeeecf801a3f5911135091a3c14b5bcb28faaa94726c003d9cd30 | Shell | 2,672 | 87 | #!/bin/bash
# This script iterates through all Chemprop Docker image versions, runs pip freeze in each,
# and saves the output to a file named after the version.
# Check for required tools
command -v docker >/dev/null 2>&1 || { echo "Error: Docker is not installed."; exit 1; }
command -v curl >/dev/null 2>&1 || { ech... |
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