sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
b1176151c174b91f871b4a14b08e41d56cd78dfe818a4443918539cbde244e07 | Shell | 282 | 8 | #!/usr/bin/env bash
DUMP2CRAWL=$1
aws s3 cp "s3://commoncrawl/crawl-data/${DUMP2CRAWL}/warc.paths.gz" ~/temp/
rm -f ~/temp/warc.paths
gunzip ~/temp/warc.paths.gz
parallel -j $(nproc --all) --will-cite python process_ccrawl.py -path "{1}" ">" "~/logs/{%}.txt" < ~/temp/warc.paths
|
82ae56f54c124a64975f32296b05cd803a87463ca516bc5f6619dcc4a1a7f17e | Shell | 283 | 13 | #!/bin/bash
working_dir=$(realpath `dirname $0`)
echo "working_dir: $working_dir"
## prepare input files
# wget -o $working_dir/data/hg19.fa.gz -c https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.fa.gz
cd $working_dir/scripts
python3 ./setup.py build_ext --inplace
|
6958b20960d679090d6aa42b24f7d3a08a488de87bcb290aad50deaa4fb7d0d7 | Shell | 291 | 9 | #!/usr/bin/env bash
# Create and provision the Python virtual environment (Linux / macOS)
set -e
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
pip install -r requirements.txt
echo
echo "Environment ready. Activate later with: source .venv/bin/activate"
|
795cbdfc2107a0d5152ed5db992fd3ac9849857f5d32b272c9504f20c0643529 | Shell | 293 | 5 | /Users/xunuo/projects/SFARI/bin/rename_cds_to_exon.py \
--sample_gtf /Users/xunuo/projects/SFARI/nextflow_results/transcripts_filtered.fasta.transdecoder.genome.gff3.gtf \
--sample_name SFARI \
--reference_gtf /Users/xunuo/Genomic_references/GENCODE/ \
--reference_name gencode |
356b312af0e585f87f6596f3771f70e3fdd707024d96feeccaffc72d08522086 | Shell | 295 | 10 | # usage:
# extractSJfromGTF.sh in.gtf > out.sj
#
# assumes transcript_id in the 12th field of GTF
#
awk '$3=="exon" {print $12,$1,$4,$5,$7}' $1 |\
sort -k1,1V -k2,2V -k3,3n |\
awk 'BEGIN {OFS="\t"} {if (t==$1) {print $2,e1+1,$3-1,$5}; e1=$4;t=$1 }' |\
sort -k1,1V -k2,2n -k3,3n -k4,4 | uniq
|
46ed4b05e10f0b9690d928d9dad627b32d682848628333e8ce2fbbd9bad58063 | Shell | 301 | 18 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
d=$2
exp=$name
python -u tools/main.py \
--load_best \
--eval \
--data_dir data/$d \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:5}| tee $work_path/out/log.txt
|
ea0b1c93fad4bc2ad26685aa17389f4825c72ce9a298d49d1201bd7d63ac13dc | Shell | 301 | 9 | xargs rm < .gitignore
git checkout -- data/g1000_eur_hm3_chr21.ld
git checkout -- data/g1000_eur_hm3_chr22.ld
git checkout -- data/g1000_eur_hm3_chr@.snps
git checkout -- data/trait1.fit1.json
git checkout -- data/trait2.fit1.json
git checkout -- data/fit2.json
git checkout -- tiny/chr21qc.mixer.ld
|
724b8eb4faeeb41fabc89d7f0ccf74da081a4b91c5a191e44f3df0c35f6217e6 | Shell | 302 | 11 | #!/usr/bin/env bash
# Create the spatialGE conda environment named spatialGE_env
# conda env create -f spatialGE.yml -n spatialGE_env
# Activate the environment
# conda activate spatialGE_env
# Install the required R packages
Rscript -e "remotes::install_github('FridleyLab/spatialGE@1.2.0.0000')"
|
c1fed2158a2d7cb71be1b80e9d6cd42422fe3cb80e453bcb6f52a1d3eb304b6c | Shell | 305 | 12 | #!/usr/bin/env bash
set -euo pipefail
version=20260914
archive="plink2_linux_x86_64_${version}.zip"
# Pinned Linux 64-bit build from https://www.cog-genomics.org/plink/2.0/
wget "https://s3.amazonaws.com/plink2-assets/alpha7/${archive}"
unzip -j "$archive"
rm "$archive"
cp plink2 /bin
plink2 --version
|
0651959dbee0d438dd3b9e9d94e5c14563378dd7ce9317b38fe91405ab02cd8c | Shell | 307 | 10 | #!/usr/bin/env bash
# Create the DR.SC conda environment named drsc_env
# conda env create -f DRSC.yml
# Activate the environment
# conda activate drsc_env
# Install the required R packages
Rscript -e "remotes::install_version(package = 'DR.SC', version = '3.3', repos = 'https://cran.uni-muenster.de/')" |
4ff12e087ed7b92f2d20e1389cee351b0143a77ca75b5012c3569a7580b25bef | Shell | 308 | 12 | #!/bin/bash -xve
# cibuildwheel runs docker containers as root, and when running as uid 0, pip refuses to use a cache
# directory that is not owned by uid 0.
UV_CACHE_DIR="$1"
if [ ! -z "${UV_CACHE_DIR}" ]; then
mkdir -p "${UV_CACHE_DIR}"
chown $UID "${UV_CACHE_DIR}"
chmod 777 "${UV_CACHE_DIR}"
fi
|
505bf20f3b321d819c060c8ade820b952e76d3d34f0172b20e11ca3e4b3eb554 | Shell | 309 | 9 | #!/bin/bash
#SBATCH --job-name=iupred
#SBATCH --output=slurm_logs/iupred.out
#SBATCH --time=0-2:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
python /home/s/shreejoy/nxu/tools/iupred2a/iupred2a.py -a nextflow_results/V47/orfanage/orfanage_peptide.fasta long > export/iupred2a_result.txt |
914a8de8db42f96c76e885cb6d55338d5c9cfa85bc67d27cb79636b82fb0ed9e | Shell | 311 | 5 | export KALDI_ROOT=`pwd`/../../..
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$PWD:$PATH
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/config/common_path.sh is not present -> Exit!" && exit 1
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
|
39b8df7031e650480178c8695cd59865e7023e72a281484d73ba4bb1ec4853bc | Shell | 313 | 13 | #!/bin/bash
#SBATCH --job-name=c4_wvf_vaes
#SBATCH --output=output_c4_wvf_vaes.txt
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu
#SBATCH --time=12:00:00
#SBATCH --mem=10G
module load cuda/12.3.2
source /mnt/home/hyu10/.bashrc
conda activate celltype_ibl
python celltype_ibl/scripts/wvf_VAE_training_seed_sweep.py |
1441e3c432be0a973609e1a8a95de868b3d4372b1ed546de63876cc4cabe550c | Shell | 314 | 9 | #!/bin/bash
cd ${MONQ}/config && \
hostnamevar=$(hostname) && \
sed -i "s/<host>.*</<host>$hostnamevar</" *.svr && \
cd ${MONQ}/bin && \
echo y | ./startServer xmlElem && \
echo y | ./startServer plainText && \
echo cancer | DistFilter svr=plainText | head && \
/usr/local/tomcat/bin/catalina.sh run
|
a4af068707b24792f986bfbd7b78443e45abe5027e6d92a1b6cf4a48b52b35d5 | Shell | 315 | 18 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
infer_file=$2
exp=$name
python -u tools/main.py \
--load_best \
--har \
--infer_file $infer_file \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:6}| tee $work_path/out/log.txt
|
c37c0e335f3c9f044e987e5871941184a3268bbdbdecfabe76c92eaec23cc7e2 | Shell | 316 | 10 | #!/usr/bin/env bash
# Create the stardust conda environment named stardust_env
# conda env create -f stardust.yml
# Activate the environment
# source activate stardust_env
# Install the required R packages
Rscript -e "remotes::install_github('InfOmics/stardust', ref = 'f1b541704d4b4189b4daf4132289a084253349d9')" |
1fcd2a94f4ded4320c50d796100242f59fe7db68e1753c4f9e11e3086320d1c3 | Shell | 317 | 18 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
infer_file=$2
exp=$name
python -u tools/main.py \
--load_best \
--infer \
--infer_file $infer_file \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:6}| tee $work_path/out/log.txt
|
8238bd500cf12ce456a32b1527b199854ba29b5ba1563eda26a3311894399d0b | Shell | 318 | 9 | #!/bin/sh
#PBS -l walltime=01:00:0
# Useful only when this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Example BET procedure/parameters (to be optimized based on your data)
bet ${img} ${outDir}${name}_brain.nii.gz -f 0.4 -B
|
d563a2ee3c2f718e1791b4f1acde4224083892c4c109190c410996ee26c28066 | Shell | 319 | 10 | #!/usr/bin/env bash
# Create the precast conda environment named drsc_env
# conda env create -f precast.yml
# Activate the environment
# conda activate precast_env
# Install the required R packages
Rscript -e "remotes::install_version(package = 'PRECAST', version = '1.6.3', repos = 'https://cran.uni-muenster.de/')" |
1f53e56fc40797435152c755442d63776d13bed0f612dd50e520a0c63d88f808 | Shell | 320 | 18 | #!/bin/bash
cd ..
source ./venv1/bin/activate
rclone copy -P onedrive:'**fulldirectory/finalfolder**' /home/**rest_of_directory_to**/TargetLists
cd /home/**rest_of_directory_to**/StereoPylot
git pull
# Pick one and uncomment it
# cd RightHand
# cd LeftHand
python StereotaxicUI.py
read -p "press enter to exit..." |
3c02b1e6c56042d77ed8370a1500f252598cd41cd18f29f426957edcee80e630 | Shell | 320 | 18 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
infer_file=$2
exp=$name
python -u tools/main.py \
--load_best \
--saliency \
--infer_file $infer_file \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:5}| tee $work_path/out/log.txt
|
c9c899d2b7b99eeaf6cfb4f714513c0fe26551cfbe8269edaba5c4938a2696f8 | Shell | 320 | 17 | #!/bin/bash
if [ $# -lt 1 ]; then
echo "usage: $0 [ acc | cons ]"
exit 1
fi
step="$1"
if [ "$step" == "acc" ]; then
../scripts/evaluate_mlm_per_region.py
elif [ "$step" == "cons" ]; then
../scripts/fetch_embed_cons.py
else
echo "unknown step: $step, must be one of 'acc' and 'cons'"
exit 1
fi
|
c69eca6c1e389d1dfe72732de49f22c15a740fa35c3959cd99c814ddace31ff5 | Shell | 322 | 20 | #!/bin/bash
black='\E[30m'
red='\E[31m'
green='\E[32m'
yellow='\E[33m'
blue='\E[34m'
magenta='\E[35m'
cyan='\E[36m'
white='\E[37m'
if ! ./$1 > /dev/null 2> .runtest.log ; then
echo -e $red Test $1 failed: $black
echo -e $blue
cat .runtest.log
echo -e $black
exit 1
else
echo -e $green Test $1 passed$black
f... |
6bb6d07a2d0fcdba05a4b7795f549525adb74c639b70de000a5645ac014a71df | Shell | 323 | 12 | #!/bin/bash
set -e
for wdl in test_*.wdl
do
json=${wdl%.*}.json
result=${wdl%.*}.result.json
echo "./test.sh ${wdl} ${json} ${1}"
#./test.sh ${wdl} ${json} ${1}
#python -c "import sys; import json; data=json.loads(sys.stdin.read()); sys.exit(int(not data[u'match_overall']))" < ${result}
#rm -f ${result}
do... |
b3691fd7f9396b002c2444444c110f3ba2ca64f0100dcb6b07a25a1a7322ea3d | Shell | 324 | 18 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
infer_file=$2
exp=$name
python -u tools/main.py \
--load_best \
--saliency_img \
--infer_file $infer_file \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:5}| tee $work_path/out/log.... |
daa2844f38d977a5286f59feb9bbc8d884b80eb33e12f8275dcaeebc017dfecb | Shell | 324 | 14 | #!/bin/bash
i_hsq=2
for i_coding in $(seq 0 2); do
for i_noncoding in $(seq 0 2); do
for i_s2coding in $(seq 0 2); do
for i_repeat in $(seq 10); do
sbatch run_optimize.e1.sh ${i_hsq} ${i_coding} ${i_noncoding} ${i_s2coding} ${i_repeat}
done
done
done
don... |
6c8f7d71ce92563131f5e3ad4556cab0167ff9f1db670048a6bc827b2a00539a | Shell | 325 | 21 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
d=$2
exp=$name
python -u tools/main.py \
--train \
--eval \
--lr 0.001 \
--data_dir data/$d \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
${@:5}
#| tee $work_path/out/log... |
89e46a5905842f37c0a0a363a6222d4caff162fba1b238118cc23b83a89a8a96 | Shell | 325 | 13 | PWD=`realpath "$0"`
PWD=`dirname $PWD`
# train NPE models
#for CONFIG in $PWD/npe-config/*.yaml; do
# snakemake --configfile $CONFIG \
# --snakefile $PWD/../../workflow/training_workflow.smk
#done
# coverage experiment and figures
snakemake --configfile $PWD/experiment-config.yaml \
--snakefile $PWD/experiment.... |
12dac7502232ffb944c8e6ccf91094cdba95e381217435b48efca08fb40e034f | Shell | 327 | 13 | for fil in $(ls Code/TWAS_data/*/*_exc_BHsig.txt | head -n 1)
do
head $fil -n 1 > Code/TWAS_data/all_exc_BHsig_assocs_PGCancestryTWAS.txt
done
for fil in $(ls Code/TWAS_data/*/*_exc_BHsig.txt)
do
echo $fil
tail $fil -n +2 >> Code/TWAS_data/all_exc_BHsig_assocs_PGCancestryTWAS.txt
done
... |
97a1e2779c02bcc9aa33fdf428c1807d29fed1587faef371c59cf700260a9495 | Shell | 329 | 10 | #!/bin/sh
set -euo pipefail
version=25.3.1-0
curl -sSL https://github.com/conda-forge/miniforge/releases/download/$version/Miniforge3-$version-$(uname)-$(uname -m).sh -o /tmp/mambaforge.sh \
&& mkdir /root/.conda \
&& bash /tmp/mambaforge.sh -bfp /usr/local \
&& rm -rf /tmp/mambaforge.sh
export PATH=$PATH:/opt/... |
b005f86c16e36f0ade30b6bd95b16a70ab2788ca5f57efdd60b14406c47e42f4 | Shell | 329 | 11 | #!/usr/bin/env bash
# Create the SpatialARI conda environment named SpatialARI_env
# conda env create -f SpatialARI.yml -n SpatialARI_env
# Activate the environment
# conda activate SpatialARI_env
# Install the required R packages
Rscript -e "remotes::install_github('RoseYuan/ClusteringMetrics@5691a9e', dependencies... |
c862a606e3ba84ad61fc3978110b1dd275da3bfdd499700000fa91f772066a80 | Shell | 332 | 13 | #!/bin/usr/env sh
# Copyright (c) 2018-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
set -e
LG=$(basename --suffix=".txt" "${1}")
./filter_utf8 < "shard/${LG}.txt" \
| ./dedup > "shard/$... |
480d827205950a2f6ae120d9885d400a007f100683f4278afdccff7d0ecfc11d | Shell | 333 | 11 | #!/usr/bin/env bash
# Create the BANKSY conda environment named banksy_env
# conda env create -f banksy.yml
# Activate the environment
# conda activate banksy_env
# Install the required R packages
Rscript -e "remotes::install_github('prabhakarlab/Banksy', dependencies = FALSE, ref = 'dbda6fde952e65f45409d9bca8e1f821... |
65c34aab8ab9daf5dde189ec1ca37b84005f5d22c95102aafaa9f7013f8895f5 | Shell | 337 | 9 | #!/usr/bin/env bash
#SBATCH --job-name=TransDecoder_LongOrfs
#SBATCH --output=slurm_logs/TransDecoder_LongOrfs.out
#SBATCH --time=0-1:0
#SBATCH -n 1
#SBATCH -N 1
module apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg TransDecoder.LongOrfs -S -t proc/merge_collaps... |
0c4de44aa78266e36030ea83b8a91675dc4dff4caa221ffe9bda17fe7b5108c8 | Shell | 339 | 15 | #!/bin/sh
echo "namespace Eigen {"
echo "/** \page ExampleList"
echo "<h1>Selected list of examples</h1>"
grep \\addexample $1/Eigen/src/*/*.h -R | cut -d \\ -f 2- | \
while read example;
do
anchor=`echo "$example" | cut -d " " -f 2`
text=`echo "$example" | cut -d " " -f 4-`
echo "\\\li \\\ref $anchor \"$text\""
done... |
618cd5855b720636ba3a9031e87a4836f2be32ab9b340b226d577fce016c4528 | Shell | 345 | 13 | PWD=`realpath "$0"`
PWD=`dirname $PWD`
# train NPE models
#for CONFIG in $PWD/npe-config/*.yaml; do
# snakemake --jobs 30 --configfile $CONFIG \
# --snakefile $PWD/../../workflow/training_workflow.smk
#done
# coverage experiment and figures
snakemake --jobs 10 --configfile $PWD/experiment-config.yaml \
--snakef... |
b6132c0aaf6426ef67a070f69821619378cf15151b901d9c2be3186ecbf376ad | Shell | 345 | 12 | #!/usr/bin/env bash
# Create the MERINGUE conda environment named scmeb_env
# conda env create -f meringue.yml
# Activate the environment
# source activate meringue_env
# Install the required R packages
Rscript -e "remotes::install_github('JEFworks-Lab/MERINGUE', ref = 'ca9e2ccabd95680d9ca0b323a8a507c038f2ea13', bui... |
86155966379dbc8d8cc41f064bb63c1ffb8c3f9a7789996aab0b845cc4b47a41 | Shell | 346 | 9 | #!/bin/bash
echo "Starting surface projection: $(date)"
# Run the MGH to SamSrf .mat conversion script
matlab -nodisplay -nosplash -nodesktop -r "try; run('retinotopy/FS_SurfaceProjection_MGHtoMAT'); catch e; disp(getReport(e)); exit(1); end; exit" \
> logs/FS_SurfaceProjection_MGHtoMAT.log 2>&1
echo "Finished sur... |
ea5267b7d5d914112ce12796c5f99b84b6dd30eae4c5389688dd1f6daf294337 | Shell | 347 | 17 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=10:00:00
#SBATCH --partition=cpu_long
#SBATCH --mem=20G
#SBATCH --cpus-per-task=8
module purge
module load anaconda3/2023.09-0/none-none
source activate novae
cd /gpfs/workdir/blampeyq/novae/scripts/experime... |
e3383ed76dbfc74b740542dfca97ef22148f6500ad892e69b73012abb81f4ddc | Shell | 350 | 17 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --time=10:00:00
#SBATCH --partition=cpu_long
#SBATCH --mem=20G
#SBATCH --cpus-per-task=8
module purge
module load anaconda3/2023.09-0/none-none
source activate novae
cd /gpfs/workdir/blampeyq/novae/scripts/experime... |
84386714fd76618cf2304884b564b7687cd0ce33bf2672513a60d226df1a2bc4 | Shell | 352 | 9 | #!/bin/bash
# this function runs replication of all results in our paper
#
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
root_dir=`dirname "$(readlink -f "$0")"`
bash root_dir/CBIG_pMFM_replication_part1_pMFM_main.sh
bash root_dir/CBIG_pMFM_replicatio... |
1e988785ce7f19613adfabaa6ffd516d623f23af3084841865b62d1af4574c2c | Shell | 356 | 15 | #!/bin/bash
set -e
PROJECT_DIR=$(pwd)/..
python update_from_repo.py
# Add post-cookiecutter commands that you always want run here:
git checkout -- $PROJECT_DIR/README.md
git checkout -- $PROJECT_DIR/AUTHORS.rst
git checkout -- $PROJECT_DIR/Pipfile
git checkout -- $PROJECT_DIR/.cookiecutter/update.sh
# Enter patch ... |
3b7390468c41eadf6e0dc091845bf048b152f2806f9ed24abc95d112a353da12 | Shell | 356 | 22 | #!/bin/bash -e
BOOST_DIR=${HOME}/dev/lib/boost_1_36_0/
YASMIC_DIR=.
source ccfiles.sh
OFILES=`echo ${CCFILES} | sed -e 's/\.cc/\.o/g'`
CFLAGS="-O2 -c -I${BOOST_DIR} -I${YASMIC_DIR}"
function echocmd {
echo $@
$@
}
for file in ${CCFILES}; do
echocmd g++ $CFLAGS $file
done
echocmd ar rc libmbgl-macosx-intel-32.a... |
e98e655fd03f54f4188220265364bbebc38bcd3ff17dabe86e7b6fba9b7f843b | Shell | 357 | 12 | #!/bin/sh
#
# Copyright (C) 2000 Stephen Cleary
#
# Distributed under the Boost Software License, Version 1.0. (See accompany-
# ing file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
#
# See http://www.boost.org for updates, documentation, and revision history.
#
m4 -P -E -DNumberOfArguments=$1 poo... |
1e42f044651659d1237406bac011e98fdfc3a8eaa7d4cdd7d084f2aeae7b1988 | Shell | 358 | 21 | #!/bin/bash
work_path=$(dirname $0)
name=$(basename $work_path)
# echo `date +%Y%m%d%H%M%S`
p=$1
d=$2
infer=$3
exp=$name
python -u tools/main.py \
--load_best \
--saliency_img \
--infer \
--infer_file $infer \
--data_dir data/$d \
--p_name $p\
--out_dir $work_path \
--exp_name $exp\
... |
a69893f97748a6b2ec0c311bbdd18dee15e816fd7a6ea40ed7496a73f2e61f18 | Shell | 358 | 10 | #!/bin/bash
# Run from analysis/ folder
echo "Starting map_to_fsaverage projection: $(date)"
# Run the SamSrf map-to-fsaverage script
matlab -nodisplay -nosplash -nodesktop -r "try; run('retinotopy/generate_avgmap'); catch e; disp(getReport(e)); exit(1); end; exit" \
> logs/generate_avgmap.log 2>&1
echo "Finished ... |
3bfcf92ce868964041e0e3caae21063b2cc11001e09e1f71534c2ffcd3b09819 | Shell | 360 | 20 | #!/usr/bin/env bash
##
# @file train_pc.bash
# @author Simon Yu
# @date 02/13/2024
# @brief Script for training PC models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
./train_pc.py -e 50 -s 42
./train_pc.py -e 50 -s 52
./train_pc.py -e 50 -s 62
./train_pc.p... |
b2b79c990aac005ff0083b6994367fb7c85312208a7545dcac23e841d19f6d8f | Shell | 360 | 10 | #!/bin/bash
# Run from analysis/ folder
echo "Starting map_to_fsaverage projection: $(date)"
# Run the SamSrf map-to-fsaverage script
matlab -nodisplay -nosplash -nodesktop -r "try; run('retinotopy/map_to_fsaverage'); catch e; disp(getReport(e)); exit(1); end; exit" \
> logs/map_to_fsaverage.log 2>&1
echo "Finishe... |
51e63a61be2d5cecc3dfaa5ed4ec6ecc4a037a273eca77fb545a777f8ed196ea | Shell | 366 | 19 | #!/bin/bash
# download all MERSCOPE datasets
sh merscope_download.sh
# convert all datasets to h5ad files
python merscope_convert.py
# download all Xenium datasets
sh xenium_download.sh
# convert all datasets to h5ad files
python xenium_convert.py
# download all CosMX datasets
sh cosmx_download.sh
# convert all d... |
73144834b66a1e60b1ec2125c7d6eb045b91584aa0799bba83b588bfc853131f | Shell | 367 | 14 | #!/bin/bash
#SBATCH --job-name=deeploc
#SBATCH --output=slurm_logs/deeploc.out
#SBATCH --time=1-0:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba deactivate
module load NiaEnv/2019b python/3.11.5
source .virtualenvs/deeploc/bin/activate
.virtualenvs/deeploc/bin/deeploc2 \
-f /scratch/nxu/SFARI/nextflow_results/V47/o... |
20cbef2bdb9e99d2e789e823c44fd579c59ec5ca5f7d2909b6fe25e3dfbc6aee | Shell | 368 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_main.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
source activate pMFM
python CBIG_pMFM_step3_test_main.py
mv ../output/step3_test_res... |
06af98d8595a65181f8769cc98fb0dbf20240f3dedfc09b43b18cf99da60b802 | Shell | 369 | 9 | #!/usr/bin/env bash
#SBATCH --job-name=hmmsearch
#SBATCH --output=slurm_logs/hmmsearch.out
#SBATCH --time=0-12:0
#SBATCH -n 1
#SBATCH -N 1
module load apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg hmmsearch --cpu 40 -E 1e-10 --domtblout pfam.domtblout Pfam-A.hm... |
914bcad2e849e0c45ccb5023626ff830425bbb4fcb5b439614d0ee233cc80748 | Shell | 371 | 14 | #!/bin/bash
export OMP_NUM_THREADS=1
export TOKENIZERS_PARALLELISM=false
# If no GPU available, set `--device cpu`
python train.py --train-file data/Muris_gene_rankings.txt.gz --val-file data/val.txt \
-j 1 --max-len 64 -b 8 --epochs 10 --device cuda \
--lr 0.003 --lr_scheduler_type cosine \
--output-dir checkpoint ... |
ef79cfc191d4a7f9d922ddc8815517b0c15d3520043065f7de426af322353159 | Shell | 371 | 12 | #!/bin/sh
#
# Copyright (C) 2001 Stephen Cleary
#
# Distributed under the Boost Software License, Version 1.0. (See accompany-
# ing file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
#
# See http://www.boost.org for updates, documentation, and revision history.
#
m4 -P -E -DNumberOfArguments=$1 poo... |
593957ddff6d2aa8f166264753ab352440182be6081c6a41efb34e36abee4110 | Shell | 375 | 15 | #!/bin/bash
#SBATCH --job-name=novae
#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
#SBATCH --mem=32G
#SBATCH --time=01:00:00
#SBATCH --cpus-per-task=1
#SBATCH --partition=cpu_med
module purge
module load anaconda3/2023.09-0/none-none && source activate novae
cd /gpfs/workdir/blampeyq/novae/data
sh _script... |
89ce87bbc06a2e0f40e65eae8598a02104ac8ccbb79db2a97c9ec37fad49dd00 | Shell | 375 | 12 | #!/usr/bin/env bash
# Create the SC.MEB conda environment named scmeb_env
# conda env create -f SC.MEB.yml
# Activate the environment
# source activate scmeb_env
# Install the required R packages
# conda run -n scmeb_env R -e "install.packages('SC.MEB')"
Rscript -e "remotes::install_version(package = 'SC.MEB', versi... |
eade93dfebcee9074fa20fd6da867f5abdb75fc4c0d9daa41587eba0cc7969e3 | Shell | 375 | 8 | #!/bin/bash
# Smoothes fMRIPrep results with 10mm gaussian kernel
# Cyrus Eierud, TReNDS 050522
fslmaths /out/fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-*1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
-kernel gauss 4.2466452 \
-fmean /out/fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_... |
5da4b2bd9982ee8d883b756fed63530c87a10c5d792563ab91b582d3a3a270de | Shell | 378 | 17 | PWD=`realpath "$0"`
PWD=`dirname $PWD`
# train NPE models
#for CONFIG in $PWD/npe-config/*.yaml; do
for CONFIG in $PWD/npe-config/*_100000.yaml; do
snakemake --configfile $CONFIG \
--jobs 30 \
--snakefile $PWD/../../workflow/training_workflow.smk
done
## get coverage on a "true" model
#python3 predict_on_tr... |
18cf807933f1c93a66bdb8c14ff9909805e6eaaf9ac2ec8bf2510b5ec26974b6 | Shell | 380 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step1_training_main.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
source activate pMFM
python CBIG_pMFM_step1_training_main.py
mv ../output/step1_... |
0896481a888c5881bd5f29e3bff52613d2feca98c2a181affc4b00d9d978f2f7 | Shell | 386 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step2_validation_main.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
source activate pMFM
python CBIG_pMFM_step2_validation_main.py
mv ../output/st... |
9ee425ce908bdc7e5e92240e54b6ab9028e6a4600aa4a78efc09783f068bcb0d | Shell | 389 | 12 | #!/usr/bin/env bash
#SBATCH -J getSingleCellObject
#SBATCH -o slurm_logs/getSingleCellObject.out
#SBATCH -t 0-1:0
#SBATCH -n 1
#SBATCH -N 1
bin/get_SingleCell_object.py \
--id_to_sample proc/id_to_sample.txt \
--classification proc/merged_collapsed_classification.filtered_lite_classification.txt \
--read_s... |
43e75b8e781beb4a1e38572facce44f390373220eace5dfc360ce07198cbc144 | Shell | 393 | 10 | #!/bin/sh
#PBS -l walltime=01:00:0
# Useful only when this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Example BET procedure/parameters (to be optimized based on your data)
standard_space_roi ${img} ${outDir}${name}_roi.nii.gz... |
fa86480a168a8b86ccd917a76512cc907a4a5b268f210fd073fe9e36cb8061ee | Shell | 395 | 24 | #!/bin/bash -e
BOOST_DIR=${HOME}/dev/lib/boost_1_36_0/
YASMIC_DIR=.
source ccfiles.sh
OFILES=`echo ${CCFILES} | sed -e 's/\.cc/\.o/g'`
CFLAGS="-O2 -c -I${BOOST_DIR} -I${YASMIC_DIR}"
function echocmd {
echo $@
$@
}
for file in ${CCFILES}; do
echocmd g++ $CFLAGS $file
done
echocmd ar rc libmbgl-macosx-ppc-32.a $... |
37b026b2d16b6d7fb9d635dad14ce95ef004dc18b151145eda14c326f126e739 | Shell | 396 | 14 | #!/usr/bin/env bash
# Run Simulation + UNet + dynamic_segmentation_CID self-training.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$ROOT"
DATA_DIR="${1:-./data}"
SUB_PATH="${2:-basic}"
MAX_EPOCHS="${3:-100}"
shift 3 2>/dev/null || true
python3 main.py \
--sub_path "$SUB_PATH... |
5f63510159a7d59e66edce4a4217276d6c334d8bc6f5aec28997d6331a257f3c | Shell | 397 | 12 | #!/usr/bin/env bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
SCRIPT=`realpath $0`
MECAB=`dirname $SCRIPT`/thirdparty/mecab-0.996-ko-0.9.2
export PATH=$PATH:"$MECAB/bin":"$MECAB/lib"
e... |
63b76d5266888e1277bca6194dc30b35cc10b64abfe99f8a191068874146a97b | Shell | 397 | 21 | #!/bin/bash
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=4
#SBATCH --array=1-9
#SBATCH --mem=48G
#SBATCH --qos=nopreemption
#SBATCH -p cpu
INDEX_PATH="path/to/index"
QUERY_PATH="path/to/query"
DATA_PATH="path/to/data"
cd $DATA_PATH
query_name=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $QUERY_PATH)
echo "downloading ${q... |
55deccdef2b5945eb2faeaf32837d66c6a9e9a1ccccf2e7a61a30a5d583ccd23 | Shell | 399 | 13 | #!/bin/sh
#shell script to update the R interface files
#note: this requires that a current version of PEER is build and ready to run using cmake
cp ./../build/R/peer.R ./peer/R
cp ./../build/R/peerR_wrap.cxx ./peer/src/peerR_wrap.cpp
#clean
rm -f ./peer/src/*.o
rm -f ./peer/src/*.so
rm -f ./peer/src-i386/*.o
rm -f... |
561ff6a7d2bf6acaf8269abb18b046634196e47f61f9207b31985caa04187bd9 | Shell | 399 | 11 | #!/usr/bin/env bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
SCRIPT=`realpath $0`
KYTEA=`dirname $SCRIPT`/thirdparty/kytea
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$KYTEA/lib:/usr/local... |
aff62abc5cc0e7252609a9ffa6b02310de80f73de9381df00063ae29b34ec896 | Shell | 399 | 22 | #!/bin/bash -e
BOOST_DIR=${HOME}/dev/lib/boost_1_36_0/
YASMIC_DIR=.
source ccfiles.sh
OFILES=`echo ${CCFILES} | sed -e 's/\.cc/\.o/g'`
CFLAGS="-O2 -c -I${BOOST_DIR} -I${YASMIC_DIR}"
#CFLAGS="-g -c -I${BOOST_DIR} -I${YASMIC_DIR}"
function echocmd {
echo $@
$@
}
for file in ${CCFILES}; do
echocmd g++-3.3 $CFLAGS $... |
42dd3d8e26e55c578a9870f1b6f06aa06b87371fb61f9bf77a681254e06a5a7e | Shell | 400 | 13 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
input=$1
ext=${input#*.}
filename=${input%%.*}
output=${filename}_MNI2mm.${ext}
MNI_ref_id=FSL_MNI152_FS4.5.0
MNI_temp_2mm=${FSL_DIR}/data/standard/MNI152_T1_2mm_brain.nii.gz
mri_vol2vol --mov $i... |
abe4100e58dd93a494635598650f5bec758691996fca7dde1e91f6252e8344b0 | Shell | 401 | 17 | PWD=`realpath "$0"`
PWD=`dirname $PWD`
# train NPE models
for CONFIG in $PWD/npe-config/*.yaml; do
snakemake --configfile $CONFIG \
--jobs 50 \
--snakefile $PWD/../../workflow/training_workflow.smk
done
# predict on DroMel data
for CONFIG in $PWD/npe-config/*rnn.yaml; do
snakemake --configfile $CONFIG \
... |
7cb17cc8e01b120f799c0e504a3e5a3fc5e366c132a3f14f26c4790952ac48c5 | Shell | 403 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step7_perturbation_analysis.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
source activate pMFM
python CBIG_pMFM_step7_perturbation_analysis.py
mv ... |
b30c11c7393f7cd87fcd6d79527efa18f5c1b3a9922f5801d85801da4e4c0e96 | Shell | 404 | 17 | #!/bin/bash
export OMP_NUM_THREADS=1
export TOKENIZERS_PARALLELISM=false
export CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7
# An example of training on NVIDIA A100
torchrun --nproc_per_node=8 train.py
--train-file data/Muris_gene_rankings.txt.gz --val-file data/val.txt \
-j 1 --max-len 64 \
--lr 0.003 --lr_scheduler_type c... |
1b8f37e24536934f86d50090edb78f733ed300081ef0160d4ba46c1c0a909a23 | Shell | 405 | 8 | #!/bin/bash
#SBATCH --job-name=iPSC_2_S5_L001
#SBATCH --output=slurm_logs/iPSC_2_S5_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/iPSC_2_S5_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/iPSC_2_S5_L001... |
25ec8db22ee2f20d717dc1017ab30375f6c822f670300a21663ef3ba564f0b98 | Shell | 405 | 10 | #!/bin/bash
# Source this to fix all environment paths for running outside Docker
BASE="/home/mnt/liut/K-attention/K-attention/Kattn-sim-dev"
export KATTN_BASE_DIR="$BASE"
export KATTN_SRC_DIR="$BASE/src"
export KATTN_RESOURCES_DIR="$BASE/resources"
export KATTN_RESULTS_DIR="$BASE/results"
export PYTHONPATH="$BASE/src:... |
6a09dbe4cbe0a2c733db23e9482922e9d0fde02817da2d4d925a1f5c4532ea86 | Shell | 405 | 8 | #!/bin/bash
#SBATCH --job-name=CN_2_2_S9_L001
#SBATCH --output=slurm_logs/CN_2_2_S9_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_2_2_S9_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/CN_2_2_S9_L001... |
e0f4784ba363842c15550f2a98949f5dc26914ab91b405c4889a846112527d5f | Shell | 405 | 8 | #!/bin/bash
#SBATCH --job-name=CN_2_1_S8_L001
#SBATCH --output=slurm_logs/CN_2_1_S8_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_2_1_S8_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/CN_2_1_S8_L001... |
fa04947be70fefaf7f022e6e400acf9590fa55f9c78ac8a149a8aa894727691a | Shell | 405 | 8 | #!/bin/bash
#SBATCH --job-name=iPSC_1_S1_L001
#SBATCH --output=slurm_logs/iPSC_1_S1_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/iPSC_1_S1_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/iPSC_1_S1_L001... |
0c5b8f76f716ad1f611caa09a3eeca8908d55838c2565b2b94f0a97cbd9d9a73 | Shell | 406 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step4_generate_simulated_fc_fcd.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../part1_pMFM_main/scripts
source activate pMFM
python CBIG_pMFM_step4_generate_simulated_fc_fcd... |
f1c638ea77aab446a010fe578954d6264412b97b22c7b20086c5b75f2819d313 | Shell | 407 | 7 | # Baron
# res=1
# while [ $(echo "$res < 5.5"|bc) = 1 ]; do
# echo "Fold = $res"
# CUDA_VISIBLE_DEVICES=2 python run_embedding_sc.py --ckpt_path ../0.1B-trans-pGAU-shuffle5-autobin100-mask0.3-bts1024-0226-bin100-k8s-lr1e-4-resume/models/model_step\=36999.ckpt --ckpt_name 50M-0.1B-res --tgthighres $res --data_path .... |
248c232ae1098b0b434cbd288ebb2540aca6b3dc27e4551d2344f01615674c1b | Shell | 409 | 9 | #!/bin/bash
#$ -l mem_free=50G
#$ -l h_vmem=50G
#$ -l h_rt=24:00:00
#$ -cwd
#$ -j y
#$ -R y
#$ -t 1-12
matlab -nodisplay -nodesktop -r "addpath(genpath('/users/jcatalli/code_pipeline')); tic; try countSpots('/dcl01/lieber/ajaffe/Maddy/RNAscope/Histology/10Ximages', '/dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/... |
743b3b6c0d2db2bfb8324e9877a2f2bc84c8245689e5838e2be6552101dc43d4 | Shell | 409 | 12 | #!/usr/bin/env bash
# Preprocess Simulation raw data into NPZ patches (train/val/test).
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$ROOT"
DATA_DIR="${1:-./data}"
FORCE="${2:-}"
if [[ "$FORCE" == "--force" ]]; then
python3 scripts/preprocess_simulation.py --data_dir "$DATA_DI... |
c849faa11ec6f6e44d589beff1af4e16755de7fe974c732759121f9d199057dc | Shell | 409 | 10 | #!/usr/bin/env bash
NUM_FOLDS=1024
MAX_SEQ_LENGTH=1024
FN=${1}
OUT_BUCKET=${2}
rm -rf logs_${MAX_SEQ_LENGTH}
mkdir logs_${MAX_SEQ_LENGTH}
parallel -j $(nproc --all) --will-cite "python prepare_data.py -fold {1} -num_folds ${NUM_FOLDS} -base_fn gs://${OUT_BUCKET}/data_${MAX_SEQ_LENGTH}/ -input_fn ${FN} -max_seq_length... |
d8ee944087837028027bd97d3bca9aab88c55ac8917d7fcfb723bc9ef1ada086 | Shell | 409 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_SOMA_training.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/SOMA_algorithm/scripts
source activate pMFM
python CBIG_pMFM_SOMA_training.py
m... |
129782613daf3dd2c3f8bd7c7d7e80c3912e3c37746d8a4d56336bfde8b31f54 | Shell | 410 | 8 | #!/bin/bash
#SBATCH --job-name=iPSC_3_S10_L001
#SBATCH --output=slurm_logs/iPSC_3_S10_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/iPSC_3_S10_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/iPSC_3_S10_... |
450c0594458d956f122c747f031dcabee65e7f0e3c1902640c176a1a73cf4d6d | Shell | 410 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_2_1_S6_L001
#SBATCH --output=slurm_logs/NPC_2_1_S6_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_2_1_S6_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/NPC_2_1_S6_... |
845f5b2eb915ee1720f6c34b1568d5891b3e460e1ae8738f6de2a62e91bf6ac2 | Shell | 410 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_2_2_S7_L001
#SBATCH --output=slurm_logs/NPC_2_2_S7_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_2_2_S7_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/NPC_2_2_S7_... |
8e7e5c6a01f1f8c4d00c1ec10d108308fb5588a37215356f4975b19310314758 | Shell | 410 | 8 | #!/bin/bash
#SBATCH --job-name=CN_3_1_S13_L001
#SBATCH --output=slurm_logs/CN_3_1_S13_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_3_1_S13_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/CN_3_1_S13_... |
b72c670ec4170c4543bae01992cc5042b2ea7b68f8aff8b7f68a8620b6ea2a4f | Shell | 410 | 8 | #!/bin/bash
#SBATCH --job-name=CN_3_2_S14_L001
#SBATCH --output=slurm_logs/CN_3_2_S14_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/CN_3_2_S14_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/CN_3_2_S14_... |
615fd111acc5fe2b1795832b0f7b0cc6cf89862cb486e9767ac537cba206619c | Shell | 411 | 21 | #!/bin/bash
dir=/Volumes/public/Backup/horiDir/qst/TauLNM//PET_SUVR/PSP_tau/
cd ${dir}
for subj in `ls `;do
cd ${dir}/${subj}/
mkdir -p ./roi/
echo ${subj}
for i in 3.27;do
fslmaths spmT_0001.nii -thr ${i} -bin ./roi/roi_thr${i}.nii.gz
flirt -in ./roi/roi_thr${i}.nii.gz -ref /Applications/NHPPipelines-master/gl... |
ce219f23b5c74c9fcefc40fa238aa7f513a9af018bc5b4617b1f0e8c208ed1aa | Shell | 411 | 23 | #!/bin/bash -e
BOOST_DIR=${HOME}/dev/lib/boost_1_36_0/
YASMIC_DIR=.
source ccfiles.sh
OFILES=`echo ${CCFILES} | sed -e 's/\.cc/\.o/g'`
CFLAGS="-O2 -fPIC -c -I${BOOST_DIR} -I${YASMIC_DIR}"
CFLAGS="-g -fPIC -c -I${BOOST_DIR} -I${YASMIC_DIR}"
function echocmd {
echo $@
$@
}
for file in ${CCFILES}; do
echocmd g++-3... |
f3077f5aa808e126ec5c0d158a66229dc82ba7353f4d1a0a3a2810b043716038 | Shell | 413 | 9 | #!/bin/bash
#$ -l mem_free=50G
#$ -l h_vmem=50G
#$ -l h_rt=24:00:00
#$ -cwd
#$ -j y
#$ -R y
#$ -t 1-12
matlab -nodisplay -nodesktop -r "addpath(genpath('/users/jcatalli/code_pipeline')); tic; try countSpots_old('/dcl01/lieber/ajaffe/Maddy/RNAscope/Histology/10Ximages', '/dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPi... |
14134699f2626b17e55b1c50dce0cdd4412f3d52d8a37975efc74887f2196105 | Shell | 415 | 11 | #!/usr/bin/env bash
# Create the maple conda environment named maple_env
# conda env create -f maple.yml
# Activate the environment
# source activate maple_env
# Install the required R packages
Rscript -e "remotes::install_github('carter-allen/spruce', ref = '47b02300cc9a1d83213682bd78464115867d1763')"
Rscript -e "r... |
7bdfa9dc82e6f7ef4167043b93935cdec116e884c58e1c2ca24efc96a0f046d5 | Shell | 415 | 21 | #!/bin/bash
dir=/Volumes/public/Backup/horiDir/qst/TauLNM//PET_SUVR/PSP_GMandWM/
cd ${dir}
for subj in `ls `;do
cd ${dir}/${subj}/
mkdir -p ./roi/
echo ${subj}
for i in 3.27;do
fslmaths spmT_0001.nii -thr ${i} -bin ./roi/roi_thr${i}.nii.gz
flirt -in ./roi/roi_thr${i}.nii.gz -ref /Applications/NHPPipelines-maste... |
863a42e8ceee108273564fe662b6b6a64a4bda5d4d507559ba907a232ce4d884 | Shell | 415 | 8 | #!/bin/bash
#SBATCH --job-name=NPC_3_1_S11_L001
#SBATCH --output=slurm_logs/NPC_3_1_S11_L001.out
#SBATCH --time=0-5:0
#SBATCH --nodes=1
#SBATCH --ntasks=1
mamba activate patch_seq_spl
salmon quant -i proc/salmon_index -l A -1 data/illumina/SFARI_data/NPC_3_1_S11_L001_R1_001.fastq.gz -2 data/illumina/SFARI_data/NPC_3_1_... |
5fa202f53eb8ad164d8a93d3010bb65deb9f4e4533a3b8134fe2a57cd0264bbe | Shell | 417 | 10 | #!/usr/bin/env bash
#SBATCH --job-name=gtf_to_alignment_gff3
#SBATCH --output=slurm_logs/gtf_to_alignment_gff3.out
#SBATCH --time=0-2:0
#SBATCH -n 1
#SBATCH -N 1
module apptainer
apptainer exec -e -B="/scratch/nxu/SFARI:/scratch/nxu/SFARI" ~/tools/transdecoder.v5.7.1.simg /usr/local/bin/util/gtf_to_alignment_gff3.pl p... |
9aa80709a2e4999fdddee6bef7adb2d54a059eba36d9ee060c14f318b0c4d7a2 | Shell | 417 | 15 | #!/bin/bash
set -eu
dir="$1"
echo "dir: $dir"
mkdir -p "$dir/log"
sbatch_args="-p wav2vec --nodes=1 --ntasks-per-node=1"
sbatch_args="$sbatch_args --gpus-per-node=1 --cpus-per-task=8 --mem=0 --time=24:00:00"
sbatch_args="$sbatch_args -o $dir/log/decode_sweep_%A.out"
sbatch_args="$sbatch_args -e $dir/log/decode_swee... |
13d3609d6d1f01058ac543bf379549f0b0d8e0b9a4a287b30779d1c823656323 | Shell | 418 | 13 | #!/usr/bin/env bash
# Customise the terminal command prompt
echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
export PROMPT_DIRTRIM=2
export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
# Update Nextflow
nextflow self-update
# Update welcome message
echo "Welcome... |
4494b59d415fa27dca9230e543f7d3084164d9b793d522f81662760735e2dcd4 | Shell | 418 | 9 | #!/bin/bash
# this function is the wrapper to run the `CBIG_pMFM_step3_test_fccost.py`
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ../../../../part2_pMFM_control_analysis/FC_cost/scripts
source activate pMFM
python CBIG_pMFM_step3_test_fccost.py
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.