sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bc49cef81bfa474af04d589d77deb6941a193bc2ae593a51a56fb5d5f9c85cbb | Shell | 639 | 11 | tag_assembly="soff250801"
path_project="/gpfs/scic/data/projects/CuttlefishOmics"
path_assembly="${path_project}/genome/assembly/${tag_assembly}"
path_pbhifi_mpibr="${path_project}/data/dna/mpibr_pbhifi"
path_pbhifi_sanger="${path_project}/data/dna/sanger_pbhifi"
path_hic_mpibr="${path_project}/data/dna/mpibr_hic"
path... |
cef99267c3c1a7d0d50ae9050124875d13015b77413afbc464080a116a215049 | Shell | 639 | 23 | #!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
# set -o xtrace
# Tar up the archive build:
(
cmake -DCMAKE_INSTALL_PREFIX="archive" -DBUILD_TYPE="Release" -DCOMPONENT="archive" -P "cmake_install.cmake"
if [ "$#" -ge 1 ] && [ "$1" == "STATIC_BUILD" ]; then
if [[ "$OSTYPE" == "linux-gnu"* ]] ... |
02dd0bed27a2e5a7eed44854ad46e771986f2f48847043c879b4fa1c4ebb0376 | Shell | 641 | 20 | #!/bin/bash -x
#Fetch plDDT from predicted structures and analyze results
dir=/proj/berzelius-2021-29/users/x_arnel/Hu.Map-2.0/
#########New dimers###########
DIR=$dir/pdb/$1-$2/
MODEL=$DIR/unrelaxed_model_1.pdb
METRIC=$DIR/result_model_1.pkl
META=../data/new_dimers/newset.csv
IT=10 #Interface threshold Å
FETCH_ATOMS=... |
20330797fe5db3709c9aae50cf65e75e47a141123bd15f4a7077184e0091e64a | Shell | 641 | 32 | #!/bin/bash
## check if any files are provided
if [ "$#" -eq 0 ]; then
echo "No JUnit *.xml files are provided"
exit 1
fi
## check each JUnit xml file
while [ "$#" -gt 0 ]; do
# check if file exists
if [ ! -f "$1" ]; then
echo "JUnit file not found: $1"
exit 2
fi
echo "Verif... |
fe4c6ed176998d083bb40b903c35968dbfbd24d3f39359739a9166051e8322ac | Shell | 642 | 23 | #!/bin/bash -e
RUNS=$1
if [[ ! -f $RUNS ]]
then
>&2 echo "ERROR: file $RUNS not found!"
exit 1
fi
KK=`cat $RUNS`
for i in $KK
do
>&2 echo "Processing run ID $i.."
wget --quiet --output-document="$i.xml" "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=${i}&usehistory=y"
WebEnv=$(gre... |
2b1379388d09fb604ff3fb64e1dc9250b1d71382b7802e598a5d94458d0459c8 | Shell | 643 | 18 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download COCO128 dataset https://www.kaggle.com/ultralytics/coco128 (first 128 images from COCO train2017)
# Example usage: bash data/scripts/get_coco128.sh
# parent
# ├── yolov5
# └── datasets
# └── coco128 ← downloads here
# Down... |
a567282230702d3ab58b80041bf05afecbbac605e9f5dcf67ad80d7885a74bde | Shell | 643 | 27 | #!/bin/bash
optseq2 --ntp 212 --tr 1.7 \
--psdwin 0 25.5 0.85 \
--ev evt1 5.1 11 \
--ev evt2 5.1 5 \
--ev evt3 5.1 11 \
--ev evt4 5.1 11 \
--ev evt5 5.1 5 \
--ev evt6 5.1 11 \
--evc -1 0 1 -1 0 1 \
--evc 1 0 -1 -1 0 1 \
--evc -1 -1 -1 1 1 ... |
745194446e85995658d5930be17ead4f06bca88ae8bc85d33bd79bbefcd74476 | Shell | 644 | 23 | #!/bin/bash
set -e
bam=../test.enclosing.single.bam
ref=/storage/resources/dbase/human/hg19/Homo_sapiens_assembly19.fasta
/storage/nmmsv/GangSTR/src/GangSTR \
--stutterup 0.001 --stutterdown 0.001 --stutterprob 0.99 \
--frrweight 0.5 --enclweight 1.0 --spanweight 1.0 --flankweight 1.0 \
--bam $bam \
... |
3c090dad676f9cd12de8cb876228b382fd1bfba361e0fddbee27a637674a446f | Shell | 647 | 20 | #!/bin/bash
#SBATCH --job-name=adni_preprocess
#SBATCH --ntasks=24
#SBATCH --mem-per-cpu=16G
#SBATCH --time=12-24:00:00
#SBATCH --output=slurm_%j.out
module load anaconda3
module load matlab
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export MATLAB_HOME=HOME/TO/MATLAB
export PATH=${MATLAB_HOME}:${PATH}
export M... |
e2e5add231256465a00fafa1ff70fb7bcb947605c8dc7ad38cc4baa49950132a | Shell | 647 | 14 | #!/bin/bash
# Merge advntr calls
VCFS=$(ls /gymreklab-tscc/mousavi/analysis/callset_merge_project/data/advntr/*.vcf.gz | awk '{print $0 ","}' | tr -d '\n' | sed 's/,$//')
mergeSTR --vcfs $VCFS --out advntr.chr21
cat advntr.chr21.vcf | vcf-sort | bgzip -c > advntr.chr21.sorted.vcf.gz
tabix -p vcf advntr.chr21.sorted.v... |
103739bf6a49abfe6bc67b388c9fde4aea696212098bc53b4031f20a46f5286b | Shell | 648 | 36 | #!/bin/sh
#
# retry_cmd.sh [-n NLOOPS] [-s SLEEP] CMD
#
# Retry command until success or pre-specified number of failures
#
# 2018 Chris Markiewicz
# Released into public domain
NLOOPS=3
TOSLEEP=5
while true; do
case "$1" in
-n ) NLOOPS="$2"; shift 2 ;;
-s ) TOSLEEP="$2"; shift 2 ;;
-- ) s... |
b7b20d89f1a37c57abe457c70643432632c4bb496bce22da791d58d946306614 | Shell | 648 | 36 | #!/bin/sh
apt-get update && apt-get install -y ca-certificates && update-ca-certificates
# (!) Keep the list below sorted (!)
apt-get update && apt-get install -y --no-install-recommends apt-utils \
autoconf \
build-essential \
bzip2 \
cmake \
curl \
dos2unix \
gfortran \
git \
less \
li... |
3f29e3b5a02f05949e9b2f3a89fcba5889575a12b88f94fe6149c3dafdd0316c | Shell | 649 | 20 | #!/bin/bash
#SBATCH --job-name=adni_preprocess
#SBATCH --ntasks=24
#SBATCH --mem-per-cpu=16G
#SBATCH --time=12-24:00:00
#SBATCH --output=slurm_%j.out
module load anaconda3
module load matlab
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export MATLAB_HOME=HOME/TO/MATLAB
export PATH=${MATLAB_HOME}:${PATH}
export M... |
9e1be8cba7a4f636199cd674553890420bb789bd5270ecf264099a1b70b4469e | Shell | 652 | 26 | #!/bin/sh
# This is assumed to be running from the root of the repo
echo "[before] running in: $PWD"
# For debugging
echo "CI_COMMIT_BRANCH: "$CI_COMMIT_BRANCH
echo "CI_DEFAULT_BRANCH: "$CI_DEFAULT_BRANCH
python --version
git branch
# Needed for Sphinx (make in build-base) and pysam (build-base + others)
apk add build... |
b589a2ba370f4fe68ff3dbf8d344a04abfebfd7ed73ebf92baafc1be2d5fd8a8 | Shell | 652 | 11 | #!/bin/bash
# Run the CI/CD build via Docker
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)"
# The published MeRIT continuous-integration image (spec 002), pinned by the
# same immutable digest as .gitlab-ci.yml so the local gate and the runner
# cannot drift apart. It runs as... |
066bb3c0f6965ab785fcbabce367b364739cc376403051f2c20cc176ef8a325e | Shell | 654 | 29 | #!/bin/bash
# change to the dir of the script
cd $( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# change to the dir to the project
cd ../..
title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
upload_config=AI/upload.yaml
output_dir=${O... |
24c12405eeab6483f3833d2cf8046aa45e5cda5022c6e2a65fbd25099485d66a | Shell | 654 | 20 | #!/bin/bash
#SBATCH --job-name=oligodendroglioma_infercnv-%a
#SBATCH --chdir=/vast/palmer/pi/verhaak/kcj28/care_mut/
#SBATCH --output=/vast/palmer/pi/verhaak/kcj28/care_mut/logs/infercnv/oligodendrogliomas/infercnv_oligodendrogliomas-%a.log
#SBATCH --mail-type=FAIL,END
#SBATCH --mail-user=kevin.c.johnson@yale.edu
#SBA... |
0e322acee17974349bc47e0cce9d00c7dc3a3feafa52e1870f0c811d6bb81892 | Shell | 656 | 22 | #!/bin/bash
echo 'Getting BioPerl'
if [ ! -d bioperl-live ]; then
git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
fi
echo 'Getting HTSlib'
if [ ! -d htslib ]; then
git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
fi
echo 'Getting Bio::DB::HTS'
if [ ... |
263fd3ea8cb8a2186baf6459360bf077dad3bafc3041a96f9d5e5417520d6742 | Shell | 656 | 17 | #!/bin/bash
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id=$1
sub_dir=$2
bold=$3
FD_th=$4
DV_th=$5
output_dir=$6
${CBIG_CODE_DIR}/stable_projects/predict_phenotypes/Xie2025_LBC/\
step4_FC_change_reliability/script/CBIG_LBC_FCmetrics_Nmin_wrapper.csh \... |
6d4e48e3ce388bb70ff075af3423f682e59f0672f6f0817c6f67179142c30540 | Shell | 656 | 11 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="${CBIG_CODE_DIR}/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
cmd="cd ${rep_... |
749d16a5295c9913f7b25a47887848888a4c25d49c1bc5c2567f376d7f0225b9 | Shell | 656 | 40 | #!sh
if test -f $1/bin/cygpath ; then
N="`$1/bin/cygpath -u $1`"
PATH=$N/bin
fname="`cygpath -u $2|sed 's/\.[mM][oO][dD]$/.mod/'`"
cyg=yes
else
N=$1
if test -d $N/mingw/mingw64 ; then
PATH=$N/mingw/mingw64/bin:$PATH
fi
if test -d $N/mingw ; then
PATH=$N/mingw/usr/bin:$PATH
fi
if test -d $N/... |
2487c1c21d3d9c67b3a89d413204358e777d6455d62e0cf8ca2493c05a3eabd5 | Shell | 657 | 21 | #!/bin/bash
#SBATCH --job-name antsApplyTransforms
#SBATCH --time 7-00:00:00
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --hint=nomultithread
#SBATCH --output warp_logs1/warp_%a.out
#SBATCH --error warp_logs1/warp_%a.err
#SBATCH --account dbic
# this script maps ... |
e43faf9052548f55de1f040dd4d9ffc77b7bb964f8bc1b9f0a24e46dbff006a3 | Shell | 661 | 11 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="$CBIG_CODE_DIR/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
cmd="cd ${rep_di... |
89d1c2a1875ec9d169a837e5d6d507b31a458c0da0a275cc2b2b9f24d473cf7f | Shell | 662 | 24 | #!/bin/bash
# Load required modules on Sherlock
module load python/3.11.0 # use a specific version, not just python/3.9.0
# Install poetry if not already installed
if ! command -v poetry &> /dev/null; then
pip install poetry
fi
# Tell poetry to create the venv inside the project directory
# This avoids home dir... |
59b7c0483e3f04d468c148244d791954cdae9c4130494e3970dbb18ce9498c6a | Shell | 663 | 12 | #!/bin/bash
cd /lustre/atlas/proj-shared/nro101/BigNeuron/data/taiwan16k/reconstructions_for_img_nopreproprcessing/
for foldername in `ls -d */`
do
echo $foldername
# mkdir /lustre/atlas/proj-shared/nro101/BigNeuron/data/taiwan16k/images/$foldername
# mv $foldername /lustre/atlas/proj-shared/nro101... |
43affe2235bb78419aab822689548dba577a4384a73b63d1bf06efde08c51dff | Shell | 664 | 23 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download latest models from https://github.com/ultralytics/yolov5/releases
# Example usage: bash data/scripts/download_weights.sh
# parent
# └── yolov5
# ├── yolov5s.pt ← downloads here
# ├── yolov5m.pt
# └── ...
python - <... |
098e97457a3af5d8f4fa2b5b719ce05d61f1e7da0e42bb18a92b13c652cdae3f | Shell | 665 | 10 | #!/bin/bash
set -eu -o pipefail
# Genome data
wget -c -O NA12878_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz
wget -c -O NA12878_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_2.fastq.gz
wget -c -O NA12891_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ER... |
8c5de315ecf276bbfc284fc11602cf6dca58dc1b8ad431b92c300a8571499977 | Shell | 668 | 20 | #!/bin/bash
gcta=tools/gcta-1.94.4-linux-kernel-3-x86_64/gcta64
while getopts ":i:g:o:p:h" opt; do
case $opt in
i) infile="$OPTARG" ;;
c) covars="$OPTARG" ;;
p) pheno="$OPTARG" ;;
o) outfile="$OPTARG" ;;
h) echo "Usage: $(basename "$0") [-i infile] [-g groupfile] [-p pheno]... |
b9285becfc2c46e1071e32865308cc77f3f9b4d17e3ddbdb7e38507579cc9305 | Shell | 669 | 7 | #!/bin/bash
mkdir -p tmp/
#testing for a single test file
#poetry run pytest tests/test_evaluation.py --k_fold_data_dir="data/pytest_data/k_fold_mode/" --test_data_dir="data/pytest_data/train_val_test_mode/" --meta_file="data/pytest_data/pytest_dataset_metadata.parquet" --out_root_dir="./tmp/" --model_file="./data/trai... |
db29431ad589178acfb4e898c00d3a9400a03390e3633cd264399b4a8fbdc890 | Shell | 670 | 36 | #!/bin/bash
info_message()
{
echo "remove_nones.sh - Remove any lines containing the string 'None' from a"
echo "text file."
echo ""
echo "This is particularly useful for RDF files, since the Java parser"
echo "included in NSMNTX raises an error when it encounters 'None'."
echo ""
}
INPUT_FNAM... |
314952cddc929039e616a66d8c4563bf68fca8adc02af3b70987913fc753dd81 | Shell | 671 | 26 | #!/bin/bash
set -euo pipefail
install_path="$(pwd)/build"
mkdir --parents "${install_path}"
cat <<EOF >./installer-input.txt
mode=silent
destinationFolder=${install_path}
agreeToLicense=yes
product.MATLAB Runtime - Core
product.MATLAB Runtime - Graphics
product.MATLAB Runtime - Numerics
product.MATLAB Runtime - Non ... |
c427d5c074c76e142606ab4153fa1ac8f981735be63ea709b5139ad9417689b3 | Shell | 672 | 23 | #! /bin/bash
input=$1
R --no-save --quiet << istop
data=read.table("$1", header=TRUE)
require(lattice)
pdf("$1.pdf")
print(wireframe(score ~ scale * rotate, data, drape = TRUE, aspect = c(3,1), colorkey = TRUE))
dev.off()
max_rotate=0
scales=c(12.5,25,50)
for (i in 1:length(scales)){ data2=data[data\$scale==scales[i],]... |
f04285b564d05ff8fa680b785233009eb73dc2d123cd986ccc7783b1a1c7f8c0 | Shell | 679 | 20 | #!/bin/bash
#SBATCH -c 8 # cores (region/neuropil classification)
#SBATCH -t 02-00:00 # 2 days
#SBATCH -p priority
#SBATCH --mem-per-cpu=16G # 8 * 16 = 128 GB total
#SBATCH -o jobs/banc_synapses_v3_%j.out
#SBATCH -e jobs/banc_synapses_v3_%j.err... |
9c731306c5afff0ed1568fb6075204817f2dc5e0ceaf01bd3e11a2784dbd6583 | Shell | 680 | 23 | #!/bin/bash
#conda activate ldsc
indir=outMarkerP_LDscore
path_ldsc=ldsc
path_data=ldsc/data
path_resource=ldsc_ph/resources
group=$1
chr=$2
echo ">$group.$chr"
bfile=$path_resource/1000G_EUR_Phase3_plink/1000G.EUR.QC.$chr
outname=$group.$chr
snpfile=hm.$chr.snp
py... |
fa4b42f48a03ed38695ad26d1871c648ac347407375aa9d27027bfea0a3f4feb | Shell | 681 | 21 | #!/bin/bash
PYTHON_SCRIPT="../src/image_generation.py"
DATA_DIR="../data/"
G_OPTION="all"
M_OPTION="mlp_sd"
B_OPTION=80
S_OPTION=4
P_OPTION="mlpsd_s${S_OPTION}_tmp.pth"
O_OPTION="../output/"
#python $PYTHON_SCRIPT -d $DATA_DIR -g $G_OPTION -m $M_OPTION -b $B_OPTION -p $P_OPTION -s $S_OPTION -o $O_OPTION
#python $PYT... |
2dd59042c43e981d9907c0c447a86ce8bbf9c24d4ff39886d1538fffa9dcf8c5 | Shell | 682 | 8 | surf_name=$1 ; surf_ext=$2 ; mkdir -p ${surf_name}
convert ${surf_name}.${surf_ext} -crop 1020x720+160+240 ${surf_name}/lateral.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 1020x720+160+1340 ${surf_name}/medial.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 400x720+2165+240 ${surf_name}/anterior.${surf_ext}
c... |
cc0618b2ff32813a67b4e258ffbcbac313191d8ccddb680c2ffe9fb39e3cbfda | Shell | 682 | 8 | surf_name=$1 ; surf_ext=$2 ; mkdir -p ${surf_name}
convert ${surf_name}.${surf_ext} -crop 1020x720+160+240 ${surf_name}/medial.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 1020x720+160+1340 ${surf_name}/lateral.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 400x720+2165+240 ${surf_name}/anterior.${surf_ext}
c... |
f6c74c914235d39bb26b5dac7adb53c2b807691028d27c831c05cc4162932f65 | Shell | 683 | 19 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
input_dir=$pd/data/brain_dataset/network_inference/input
output_dir=$pd/data/brain_dataset/network_inference/output
# infer networks for each subsampling of each replicate
for i in `ls $input_dir`
do
sleep 20
name=`cut -d . -f... |
1041280799fdb9a7a35a3e04b08bb72579c3279d7c88cdce1a3806426242c0e3 | Shell | 684 | 24 | #!/usr/bin/env bash
set -e
ver=$(fgrep '#define VERSION ' gffcompare.cpp)
ver=${ver#*\"}
ver=${ver%%\"*}
srcpack=gffcompare-$ver
source prep_source.sh
linpack=$pack.Linux_x86_64
echo "preparing $linpack.tar.gz"
echo "-------------------"
/bin/rm -rf $linpack
/bin/rm -f $linpack.tar.gz
mkdir $linpack
cd $srcpack
make cl... |
5adbbfe0985b4e5144e0403ef48e041c76c43e583ace2c7f62aa0163bf54fde3 | Shell | 684 | 21 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
wd=$pd/data/neural_differentiation_dataset/genomes
# create gorGor6 and macFas6 annotations using liftoff
for genome in gorGor6 macFas6
do
sbatch --cpus-per-task=8 \
--mem=10G \
--job-name=${genome}_liftoff \
... |
cbbedc89af29af1628e9a22a3d83bf4587ec7835b9f6476bb7d37218aa38c4ca | Shell | 684 | 21 | #!/bin/bash
PYTHON_SCRIPT="../src/gen_eval.py"
DATA_DIR="../data/"
G_OPTION="all"
M_OPTION="mlp_sd"
B_OPTION=10
S_OPTION=4
P_OPTION="mlpsd_s${S_OPTION}_tmp.pth"
O_OPTION="../output/"
python $PYTHON_SCRIPT -d $DATA_DIR -g $G_OPTION -m $M_OPTION -b $B_OPTION -p $P_OPTION -s $S_OPTION -o $O_OPTION
#python $PYTHON_SCRIP... |
2ca1eeb0b0996cd67432d942247c0b131af151d054a5d58cc30f343e8c009e65 | Shell | 685 | 20 | #!/bin/bash
mkdir -p subsampled_bam
for file in merged_bam/*.bam; do
base=$(basename "$file" .bam)
echo "Subsampling $base"
total=$(samtools view -c "$file")
for target in 2000000 5000000 10000000 20000000 50000000 100000000; do
frac=$(echo "scale=6; $target / $total" | bc)
f... |
d4e177eb0dcb1b50454540a352d83f6ea304fb93b3b0b32bbcf0a85bc74e5e70 | Shell | 685 | 20 | #ATAC correct Tobias - subsample and then perform tn5 shift
#conda activate tobias_env
OUTDIR=subc_specific_peaks
GENOME=GRCh38.primary_assembly.genome.fa
MOTIF=motif_databases/CIS-BP_2.00/Homo_sapiens.meme
groups=("ast.C1" "mg.C4")
for group in ${groups[@]}
do
prefix=${group//./} # astC1 mgC4
PEAK=/geschwindlabshar... |
828f57e6dede28dfa0ccd9884ed7b8541e630899188a4b52a585402538d410c9 | Shell | 686 | 21 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
input_dir=$1
feature_file=$2
sub_fold=$3
score_ind=$4
outdir=$5
mode... |
52e509a0ce8925290ceeb7f10b9c0644859f07c00929f1164b691acf49e50e98 | Shell | 688 | 21 | #!/bin/bash
PYTHON_SCRIPT="../src/object_classification.py"
DATA_DIR="../data/"
G_OPTION="all"
M_OPTION="eegnet"
B_OPTION=80
S_OPTION=0
P_OPTION="eegnet_s${S_OPTION}_1x_0.pth"
O_OPTION="../output/"
#python $PYTHON_SCRIPT -d $DATA_DIR -g $G_OPTION -m $M_OPTION -b $B_OPTION -p $P_OPTION -s $S_OPTION -o $O_OPTION
#pyth... |
455feb77a0579c1e6370dd00442a066f2bf2442dd4ce18538057f6890f516ba6 | Shell | 689 | 24 | #!/bin/bash
# Example script to test a saved model on custom data
#
# Usage: bash test_model.sh
# Set your paths here
MODEL_PATH="models_output/nt_mean_model_36302.keras"
SEQ1_PATH="../notebooks/download/embeddings/nt_test_seq1.csv"
SEQ2_PATH="../notebooks/download/embeddings/nt_test_seq2.csv"
TARGET_PATH="../noteboo... |
a5a4590924da262d4e4b53538982a4571fcd24893fcf3792df627dedfec1f473 | Shell | 689 | 20 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
wd=$pd/data/neural_differentiation_dataset/genomes
# create STAR indices for all genomes
for genome in hg38 gorGor6 macFas6
do
mkdir $wd/${genome}_STAR_index
sbatch --cpus-per-task=15 \
--mem=30G \
--job-nam... |
6a14d11a54caa94ed0033b598e41009c0328acd111b17f42fddc8a450de596e3 | Shell | 691 | 21 | #!/bin/bash
#SBATCH --partition=xnat
#SBATCH --nodelist=cn10
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --mem=80000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=simon.henin@nyumc.org
#SBATCH --time 4-24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/decoding_anal... |
d05800cb25fccfb8e854706f541d47cf645367f08115f59698bbdbffc74b4a7e | Shell | 691 | 39 | #!/bin/bash
echo Installing nipype
source tools/ci/activate.sh
source tools/ci/env.sh
set -eu
# Required variables
echo INSTALL_TYPE = $INSTALL_TYPE
echo CHECK_TYPE = $CHECK_TYPE
echo NIPYPE_EXTRAS = $NIPYPE_EXTRAS
echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
set -x
if [ -n "$EXTRA_PIP_FLAGS" ]; then
EXTRA_PIP_FLA... |
780e9edcae7855a9cbaf890adb0d5a5164db535da686dad9deabd467c1f29251 | Shell | 692 | 29 | #!/bin/sh
path_simplicialTS="./SimplicialTS/"
julia_path=`which julia`
###Install the Package Compiler for Julia if it is not present
${julia_path} <<EOF
import Pkg;
try
@eval import PackageCompiler
println("PackageCompiler is installed")
catch
println("PackageCompiler is not installed!\n Installing it ... |
94c89e6207d2cca822ee3e3d685e589c15d5ffc56bd4fe0d7629c09073bee1d3 | Shell | 693 | 34 | #!/bin/sh
IFS=$'\n'
set -e
files=$(find "$APPDATA/WaveMetrics" -type f -iname Log.jsonl)
echo "files: $files"
for i in $files
do
name=$(echo $i | sed -e "s/.*WaveMetrics\/Igor Pro /IP/g" -e "s/Packages\///g" -e "s/\//_/g")
cp "$i" "$name"
done
folders=$(find "$APPDATA/WaveMetrics" -type d -iname Diagnostics)
e... |
67cb7ba914443ef6de6cfcd72bf7e8d081311ef1dd8f466c06f063fa22662d81 | Shell | 694 | 19 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
# Set the directory path
combine_log_dir="/data/project/sleep_ENIGM... |
ebcc3ab1838e399b9dd3b612ff45d6e6aebd3ca2bac9850273e1636e3e271b69 | Shell | 694 | 18 | #!/bin/bash
cd /home/fs0/jdf650/scratch/DPhil-Human-fMRI-OptimalPolicy/
# Parse arguments -------------------------------------------------------------
# Source the parsing functions
source scr/submit/parse_args.sh
declare cost_stay
declare cost_switch
# Parse arguments
parse_cost_args cost_stay cost_switch "$@"
# ... |
f8be57492c8c2227567a12e8efd0d640ffc7a658ea587df0535a7288164117dd | Shell | 694 | 25 | #!/bin/bash
#SBATCH --job-name=ucb-model-%a
#SBATCH --output=logs/ucb-model/loo_%A_%a.out
#SBATCH --error=logs/ucb-model/loo_%A_%a.err
#SBATCH --array=1-45
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-HybridModellingRobust
# julia s... |
0e31665083c251a06b8c97522de797bb71ec05a84330e729cb0f1ed65602a15f | Shell | 696 | 27 | #!/bin/sh
# This is assumed to be running from the root of the repo
echo "[pages] running in: $PWD"
# Ensure the documentation build directory is present
mkdir -p ./docs/build
cp README.md docs/source/getting_started.md
cp CHANGELOG.md docs/source/
sed -i 's/\.\/docs\/source\///' docs/source/getting_started.md
sed -i... |
44eb6aa09546af4f9ac295a73d5113f61fa1d8fb2e74bf5609050ef7c96c06e7 | Shell | 696 | 18 | #!/usr/bin/env bash
################################################################################
#Setup variables for the script:
UNALIASED_SCRIPT_NAME=$( readlink "${BASH_SOURCE[0]}" || echo "${BASH_SOURCE[0]}" )
SCRIPTDIR="$( cd "$( dirname "${UNALIASED_SCRIPT_NAME}" )" && pwd )"
SCRIPTNAME=$( echo $0 | sed 's#... |
080065da37f02616c2b97ef1c3c5a45d0a2ce32ccc643b2e76577cfa7cf00ef4 | Shell | 698 | 20 | #!/bin/bash
# This script should be run inside the fmriprep singularity container by warp_to_MNI152NLin6Asym.sh
TEMPLATE_DIR=/dartfs-hpc/rc/lab/C/CANlab/modules/Neuroimaging_Pattern_Masks/templates
XFM_DIR=$TEMPLATE_DIR/transforms/ants
for INPUT in $(find probabilistic_maps_pmaps_157areas/ -type f -name "*nii.gz"); ... |
ba773cb98553ee616fd1820e61b59cdc959fee290bd7d255fa844d963107b488 | Shell | 698 | 23 | #!/bin/bash
set -e
# checks for correct installation
if [ ! $(docker -v | grep -c -w version) -eq 1 ]; then
echo "docker not found."
exit 1
fi
if [ ! $(groups | grep -c -w docker) -eq 1 ]; then
echo "add current user $(whoami) to docker group!"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
# build contai... |
d84e0c67656997f46b954902af0942971278d1b387eb04b936d2d08dd3f5232b | Shell | 698 | 38 | #!/bin/bash
# Usage message
usage() {
echo "Usage: $0 bamfile tag"
echo " bamfile : Path to the BAM file."
echo " tag : The tag to count values for (e.g., 'fn')."
exit 1
}
# Check for correct number of arguments
if [ "$#" -ne 2 ]; then
usage
fi
BAMFILE=$1
TAG=$2
# Check if the BAM file exists
if [ !... |
20292402f400b911cab9071749608d5971cd8758c1a5ea9b375c33c35403abbb | Shell | 699 | 28 | #!/bin/bash
# Author: Andrew Hamel
# Affiliation: Massachusetts Eye and Ear, Harvard Medical School
# Date: June 2022
#
#
# This script generates a mapping file between EntrezID, ensembl_gene_id (without decimal version),
# and gene symbol (HGNC) for all genes.
# Output file is tab-delimited
#
# Both input files c... |
623dec9b6261923e674b3a96b1760397f88445f12e11c6713e5073672321bf0d | Shell | 700 | 20 | #!/bin/bash
#SBATCH --job-name=downsample_nmf-%a
#SBATCH --chdir=/vast/palmer/pi/verhaak/kcj28/care_idh_mut/results/nmf_res_caremut/undifferentiated
#SBATCH --output=/vast/palmer/pi/verhaak/kcj28/care_idh_mut/logs/nmf/undifferentiated/downsample_undiff_nmf_%a.log
#SBATCH --mail-type=FAIL,END
#SBATCH --mail-user=kevin.... |
d25547eaf62df05046ae2367754fb53ec5948cc48569cbcba20b03aefeb01abe | Shell | 700 | 7 | #!/bin/bash
parallel -a $1 --pipepart --will-cite --block 1G --jobs 80% "awk '{if (\$6==\"CG\"){c++}else{h++}}\$4+\$5>0{if (\$6==\"CG\"){if (\$4<\$5){cunmeth++}else{cmeth++} }else { if (\$4<\$5){unmeth++}else{meth++}} }END{print cunmeth, cmeth, unmeth,meth,c,h}' >> $1.tmp"
awk 'BEGIN{cunmeth=0;cmeth=0;unmeth=0;meth=0... |
1a6697de6f0c5428bba889615d299d51f3132a9055673d3bb466532a574a0f55 | Shell | 701 | 22 | #!/usr/bin/env bash
ALLOWED_PATTERNS='Mlflow\(|"Mlflow"|import Mlflow$'
# add globs to this list to ignore them in grep
EXCLUDED_FILES=(
# ignore typos in i18n files, since they're not controlled by us
"mlflow/server/js/src/lang/*.json"
"mlflow/server/js/src/common/utils/StringUtils.ts"
"dev/clint/test... |
e0c7cb905cbe1e461a24428e4dd31a90403d10d0e9f0c7f961712cba822ddaab | Shell | 701 | 28 | #!/bin/sh
########################################
#TRINITY
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export trinity_work_dir=$3
export diginorm_work_dir=$4
cd $project_work_dir
echo "starting trinity assembly..."
if [ -d $trinity_work_dir ];
then
rm -r $trinity_work... |
5bf0d76776a70de37cf63c36210d63964020f1ee1269fb3c866ab95c1873a548 | Shell | 703 | 15 | #!/bin/bash
# this script exports labels from the glasser atlas in the same order they're in in the atlas. We will use this to
# confirm the nifti atlas parcels are ordered correctly. This should be run before
# create_CANLab2023_atlas_unrestricted.m or create_CANLab2023_atlas_cifti.sh scripts
export PATH=${PATH}:/ho... |
8a333674e6497a1412f8c218c4dcc693137ad2d9cd9e77b4c10e2950d91d3918 | Shell | 704 | 22 | #!/usr/bin/env bash
set -eu -o pipefail
cd "$(dirname "$0")/../.." # up to repo root
add_header() {
cat "$1" | ./hack/manifests/auto-gen-msg.sh >tmp
mv tmp "$1"
}
GOFLAGS=-mod=mod controller-gen crd:generateEmbeddedObjectMeta=true paths=./pkg/apis/... output:dir=manifests/base/crds/full
find manifests/base/crds... |
eb977bd37df40df103ebdfd6f315db4708ae2086b421a9aaf67c76a19feac873 | Shell | 704 | 22 | #!/bin/bash
export fasta_file=$1
export work_csv=$(basename $2)
awk -F',' '{print $3}' $2 | awk -F'"' '{if ($2 !="Queryid") print $2}' > id_file_tmp
cat $fasta_file | awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}' | awk -F"\t" '{gsub(">","",$1); print $1,$2}' | awk 'NR==FNR{a[$1];next} ($1 in a... |
4a8aec83a2f265c563343f529f40b98418add8d913ed584f6b39f2a3bd7af60a | Shell | 705 | 22 | #!/bin/bash
#SBATCH --job-name=rerun_NL26_infercnv
#SBATCH --chdir=/vast/palmer/pi/verhaak/kcj28/care_mut/
#SBATCH --output=/vast/palmer/pi/verhaak/kcj28/care_mut/logs/infercnv/astrocytomas/rerun_NL26_1_infercnv.log
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=kevin.c.johnson@yale.edu
#SBATCH --ntasks=1
#SBATCH --cpus... |
c5c06f5df104509343f77268b68f1a03d8dc024ec2261f8318584411d1694d23 | Shell | 711 | 33 | #source this file.
_BUCKET="testbcbio"
checkmounted(){ grep -s "$1" "/proc/mounts";}
if checkmounted "$_BUCKET"; then
echo "S3 bucket is mounted."
else
echo "Starting syslogd..."
service rsyslog start
echo "Mounting the bucket..."
cmd="goofys --sse $_BUCKET /mnt/$_BUCKET"
echo $cmd
$cmd
sleep 1
i... |
4b68d8fa0e697be3140f16da024a1e4ada7d9059b48489dbaa6d7b97f3d3df97 | Shell | 712 | 20 | #!/bin/bash
#SBATCH -p short
#SBATCH -t 0-0:45
#SBATCH -c 1
#SBATCH --mem=8G
#SBATCH -J banc_refresh_blacklist
#SBATCH -o data/scheduled_runs/refresh_blacklist_%j.out
#SBATCH -e data/scheduled_runs/refresh_blacklist_%j.err
###########################################################
### Pull fafb_alignment_decision == F... |
233d0457feed2edf5c2968a9b329cbb2717586fafc73e04a53921fadd2f9902e | Shell | 713 | 13 | #!/bin/sh
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_ChenTam2022_TRBPC
# remove useless stable projects
rm -r Standalone_ChenTam2022_TRBPC/stable_projects/brain_parcellation
rm -r Standalone_ChenTam2022_TRBPC/s... |
26b1c95b7b5f3b378e1c9a140d8615d53dd9d579f873a47166a543966cfc6234 | Shell | 713 | 35 | #!/bin/bash
input_dir=$1
output_dir=$2
echo "Unpacking builds from $input_dir to $output_dir"
file_regex=".*/lib_pod5-[0-9\.]*-(.*).tar.gz"
for i in "${input_dir}"/lib_pod5*.tar.gz; do
if [[ $i =~ $file_regex ]]
then
sku="${BASH_REMATCH[1]}"
echo "Extracting for SKU: $sku"
else
e... |
677460d51e2ba80921b720e9862dd89ffb8b242be79073dafe77513b7149af9a | Shell | 713 | 35 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 21 different methods.
#
function write_psb_script {
outputScript=$1;
inputfolder=$2;
exefilename=$3;
jobnumbers=$4;
echo "#PBS -l walltime=1:00:00" >> $outputScript;
echo "#PBS -l nodes=400" >> $outputScript;
echo "#PBS -q regular... |
fb364bbb5ba6f3576dbfd7db5103f67848a1b38fff3962d9e1854c9630af45fc | Shell | 715 | 22 | #!/bin/bash
###########################################################
### Publish per-version syn_id -> neuropil/region/side
### lookups to GCS.
###
### Builds slim parquets for v1, v2, v3 from on-disk sources
### and uploads to gs://lee-lab.../synapses/v{1.1,2.0,3.0}/.
###
### Usage: sbatch o2_banc_publish_lookups.s... |
fcdd931eb2566e429db52ec0641f366c38cd8ef49da3182e132d6e198813cb37 | Shell | 715 | 28 | #!/usr/bin/env bash
# Runs performance tests multiple times.
set -eu
if [ "$#" -lt 1 ]; then
echo "Usage: $0 [BENCHMARK_JSON_FILE_NAME_PREFIX] [OPTIONAL_PYTEST_ARGS]" >&2
exit 1
fi
benchmark_json_file_name_prefix=$1
for i in {1..3}
do
benchmark_json=tests/performance/results/${benchmark_json_file_name_prefix... |
6c319ccb70ca7d0502446860865f641e45e146da026159e3c8f319565db1ce71 | Shell | 717 | 27 | #!/bin/bash
#SBATCH --job-name=ddppo
#SBATCH --output=logs.ddppo.out
#SBATCH --error=logs.ddppo.err
#SBATCH --gpus 1
#SBATCH --nodes 1
#SBATCH --cpus-per-task 10
#SBATCH --ntasks-per-node 1
#SBATCH --mem=60GB
#SBATCH --time=72:00:00
#SBATCH --signal=USR1@90
#SBATCH --requeue
#SBATCH --partition=dev
# Copyright (c) Met... |
931ef4696bc42434cb145096c579542a947dfaef47ac028324d071cf11ca52e9 | Shell | 717 | 12 |
# scp -r guacamol tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/guacamol_tdc/
# scp -r guacamol_baselines/graph_ga tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/
scp -r guacamol_baselines/smiles_lstm_hc tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/
scp g... |
f1874172e258378625e207846b485e08e77f6302b1caec3e501977d5f59f0689 | Shell | 719 | 25 | #!/bin/bash
#SBATCH --job-name=symbolic-model-%a
#SBATCH --output=logs/symbolic-model/loo_%A_%a.out
#SBATCH --error=logs/symbolic-model/loo_%A_%a.err
#SBATCH --array=1-45
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
# Run the Julia script
cd /vols/Scratch/jdf650/DPhil-Human-fMRI-HybridModellingRo... |
7f9241ae01f93061517c782053df8f853c225e62f8fdab0db73fb103e2cb41d4 | Shell | 721 | 17 | #!/bin/bash
experiment=cosmx_eva
python -m cellcontrast --image_preprocess \
--preprocess_dir "data/raw/${experiment}/" \
--channel_names SKIP Keratin8/18 CD45 CD3e DAPI \
--cell_cutout 100 \
--foundation_model 'eva' \
... |
ff930868c84146396f47802def22aae40f1a153efe53f306f1b2d0b84b13510c | Shell | 722 | 20 | #!/bin/bash
#SBATCH --job-name=inferCNV-%a
#SBATCH --chdir=/vast/palmer/pi/verhaak/kcj28/care_mut/
#SBATCH --output=/vast/palmer/pi/verhaak/kcj28/care_mut/logs/infercnv/astrocytomas/infercnv_astrocytomas-%a.log
#SBATCH --error=/vast/palmer/pi/verhaak/kcj28/care_mut/logs/infercnv/astrocytomas/infercnv_astrocytomas-%a.e... |
80453b18d4403ee82d128f37f1f2753161fe665a254cd7968e18cd78acc486ce | Shell | 723 | 28 | parameters=(dti-FractionalAnisotropy-reg-NormMasked-T1w dti-Trace-reg-NormMasked-T1w dti-MidEigenvalue-reg-NormMasked-T1w dti-MinEigenvalue-reg-NormMasked-T1w)
views=(axial coronal sagittal)
mkdir -p backbones
for para in ${parameters[@]}
do
for view in ${views[@]}
do
pkl=/Users/fan/Downloads/model_slice_mixed_HC... |
810fc9e5fc0f07c0e34b757cad2e7fe2bcfe2bdee24a101493e50f42fc217868 | Shell | 724 | 23 | #!/bin/bash
# Source and destination directories
SRC_DIR="/vast/palmer/pi/verhaak/kcj28/care_mut/results/infercnv/astrocytoma_samples"
DEST_DIR="/vast/palmer/pi/verhaak/kcj28/care_mut/results/infercnv/astrocytoma_plots"
# Create destination directory if it doesn't exist
mkdir -p "$DEST_DIR"
# Loop over each sample s... |
83da10a90b0d04fada436602aafb15b8d56d5cdb2b9f81839391eca91eabc7a5 | Shell | 724 | 18 | #!/bin/bash
# 1. Allow Docker to draw on your screen (The "Magic" xhost command)
xhost +local:root
# 2. Run the container with all necessary flags for GUI support
docker run --name isaac-sim-experiment --entrypoint bash -it --gpus all --rm --network=host \
-e "ACCEPT_EULA=Y" \
-e "PRIVACY_CONSENT=Y" \
-e ... |
995269da5297bdaacc1e4db74356c3b5ce0ef8f601d3f14a7da70c24e334de4b | Shell | 724 | 18 | export path_dir=/media/StorageOne/zurbzh
export Project_name=$1
export project_work_dir=$path_dir/Projects/$1
if [ ! -d $project_work_dir ]; then
mkdir $project_work_dir
fi
/usr/local/bin/getorf -sequence $Project_name -outseq $project_work_dir/ORF_prot.pos -find 1 -minsize 120
hmmsearch --tblout $project_work_d... |
d33a1fa437786f07261a44e141f105392a1d9d41b3fe2d5f025cb5c8ab8382c1 | Shell | 725 | 19 | #!/bin/bash
#SBATCH --job-name=downloadGencode
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=150GB # Job memory request
#SBATCH --time=00-6:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=download... |
a7a1368bfafff82270c7735fc83903ccbafc60e161143315a3b9a0568502d579 | Shell | 726 | 29 | #!/bin/bash
#SBATCH --job-name=SPLiT_Seq_Demultiplexing
#SBATCH --time=72:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
python splitseqdemultiplex_0.2.3.py \
-n 10 \
-e 1 \
-m 2 \
-1 Round1_barcodes_new5.txt \
-2 Round2_barcodes_new4.txt \
-3 Round3_barcodes_new4.txt \
-f /mnt/isilon/dav... |
8ef934ef91b41ccc2f560bc0a68f0dd058a6407dcfbc7eee8c2d7f4e43292feb | Shell | 727 | 13 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="$CBIG_CODE_DIR/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
cmd="cd ${rep_d... |
45573f3c294136e7d1aa2f9effa83eff984bc54267967baac81f47a5883e4187 | Shell | 728 | 13 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Self-avoidance example
time PYTHONPATH=self_avoidance/:$PYTHONPATH python ../Admin.py 1 self_avoidance/selfavoidance.cfg
python ../scripts... |
67a7f736fbfefabfaefe2586aeac0e236573eb7644ef4d0ce12475f81847dc85 | Shell | 728 | 12 | # we provide a copy of ffhq-256 for convenience, downsampled using the same function as NVAE (https://github.com/NVlabs/NVAE) (personal communication with author)
# Resizing function is this one, with the default second argument and size=256
# https://pytorch.org/docs/stable/torchvision/transforms.html#torchvision.tra... |
6ac824f6e2ac1fb35ce91ecf01195be4528729f91bf7d289519c9cee5cf74ed4 | Shell | 728 | 25 | #!/bin/sh
# Script to do a local install of loky
set +x
export LC_ALL=C
INSTALL_FOLDER=tmp/loky_install
rm -rf loky $INSTALL_FOLDER 2> /dev/null
if [ -z "$1" ]
then
# Grab the latest stable release from PyPI
LOKY=loky
else
LOKY=$1
fi
pip install --no-cache $LOKY --target $INSTALL_FOLDER
cp -r $INSTALL_FOLDE... |
8cf87fd30a7be5b9732348312def00eaf091d5a533b31da8b71db16fd1a3a2ad | Shell | 729 | 15 | path_biotools="/gpfs/scic/software/biotools"
path_micromamba="${path_biotools}/micromamba/bin"
path_minimap2="${path_biotools}/minimap2-2.30"
path_seqtk="${path_biotools}/seqtk"
path_venv_blast="${path_biotools}/venv_blast"
path_venv_fastp="${path_biotools}/venv_fastp"
path_venv_seqkit="${path_biotools}/venv_seqkit"
pa... |
b771aceb3358ab1ea3adfb12eb1e1a0ac6b10aab059ced3e18904719023acf38 | Shell | 729 | 17 | #!/bin/bash
experiment=cosmx_kr
python -m cellcontrast --image_preprocess \
--preprocess_dir "data/raw/${experiment}/" \
--channel_names MEMBRANE CYTOKERATIN CD20 CD3 DAPI \
--cell_cutout 100 \
--foundation_model 'kronos'... |
339cb45d28e9cb289d4e968c9e5fcf75f081311559593d6c4037872408bd5df9 | Shell | 730 | 30 | #!/bin/bash
genes=(SPP1 SCGB3A2)
species=(human gorilla cynomolgus)
pd=/data/share/htp/hack_GRN/CroCoNet_scripts_and_data
input_dir=$pd/data/validations/POU5F1_LTR7_enrichment
output_dir=$pd/data/validations/POU5F1_LTR7_enrichment
for gene in "${genes[@]}"; do
for spec in "${species[@]}"; do
sbatch <<EOF
#!/b... |
5de22aa10b8f55fd59337637a10c8ece684aae09c859d60ccf87d7dd46f83a0d | Shell | 732 | 17 | #!/usr/bin/env bash
set -eux
# Make sure go path is owned by vscode
sudo chown vscode:vscode /home/vscode/go || true
sudo chown vscode:vscode /home/vscode/go/src || true
sudo chown vscode:vscode /home/vscode/go/src/github.com || true
# create cluster using the minimum tested Kubernetes version (k3d-up.sh also
# appli... |
67be55653f9b3b072a05d7e0413d4e6ff6b488195e2f849e4473df2e973e20ae | Shell | 735 | 11 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
# rep_dir="${CBIG_CODE_DIR}/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
rep_dir="$CBIG_CODE_DIR/stable_projects/predict_phenotypes... |
162479b6821a61f3d7551fc4b21d4032fc76dc30f94a2c331c3f48439680fe27 | Shell | 736 | 21 | #!/usr/bin/env bash
set -euo pipefail
DGX_USER="${USER:-$(id -un)}"
REPO_DIR="${REPO_DIR:-/nfs/home/${DGX_USER}/nnunet-tree-semantic-extension}"
NNUNET_ROOT="${NNUNET_ROOT:-/nfs/home/${DGX_USER}/nnunet}"
OUTPUT_DIR="${OUTPUT_DIR:-${REPO_DIR}/outputs}"
WBP_METRIC_WORKERS="${WBP_METRIC_WORKERS:-8}"
export NNUNET_ROOT
e... |
1b36969d96ffc648bde9fc87dfdbbaa036fde8f5273bb26a0ec363b9f4720e8a | Shell | 736 | 29 | #!/bin/bash
COMPRESS_METHODS="zlib gzip bz2 xz lzma lz4"
EXPECTED=0
for PRE in "PREV_" "" "NEXT_"; do
env="${PRE}oldest"
conda activate $env
# Generate non compressed pickles.
python create_numpy_pickle.py
EXPECTED=$((EXPECTED+1))
# Generate compressed pickles for each compression methods su... |
8bfc087646d3d381c8da10c8247de49963421c2d98a759d622f968e1b1af1487 | Shell | 736 | 22 | EVAL=../eval_docking.py
#Evaluate the Docking
##########new_dimers#######
##AF2
DOCKQFILES=./dockqstats_newdimers_af2 #Path to file location
OUTFILE=./dockqstats_newdimers_af.csv
#python3 $EVAL --dockqfiles $DOCKQFILES --outfile $OUTFILE
##########Marks###########
##AF2
DOCKQFILES=./dockqstats_marks_af2 #Path to... |
a797c5abe216c9c99cc8da811921c519daf313097582debeea51dfe814037f33 | Shell | 736 | 17 | #!/bin/bash
# This script downloads the reference transcripts from NCBI and creates a regions file that includes the locations of the CDS regions
# datasets version: 14.6.0
source Scripts/functions_bash.sh # To access custom functions defined in functions_bash.sh
file_ids="Data/04.Download_Ref_CDS_regions/in/acc_numb... |
38cc0434c3610584ef4f1361c7dda9bc77a3eaa8c410ed8ae9afd03fcf173641 | Shell | 737 | 25 | #!/bin/bash
rm -rf ../data/stage1/checkpoints
mkdir -p ../data/stage1/checkpoints
#python3 ./prepareTrainData.py
CUDA_VISIBLE_DEVICES=0
for cfg in redet_r50 rotated_retinanet_r50
do
for f in 0 1 2 3 4
do
for lr in 0.08 0.04 0.02 0.008 0.004
do
wd=../data/stage1/checkpoints/$cfg/${cfg}_${f}_${lr}
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.