sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7e51149abc785bb0517f520429faf121d00326977f5b6c812e1cf7976de3aea8 | Shell | 1,490 | 42 | #!/bin/bash
#SBATCH --account=hai_cellnet
#SBATCH --nodes=1
#SBATCH --output=slurm_out/out.%j
#SBATCH --error=slurm_out/err.%j
#SBATCH --time=24:00:00
#SBATCH --partition=booster
#SBATCH --gres=gpu:4
cd ~/"$USER" || exit
# load modules
ml purge
ml Stages/2023
ml GCC/11.3.0
ml OpenMPI/4.1.4
ml CUDA/11.7
ml cuDNN/8.6.0... |
181f93b5efdc855dda70c5433b7ea4f4e3075e0aa8dbd700e6402028675d9856 | Shell | 1,492 | 42 | #!/bin/bash
#
# merge_cutoffs.sh
#
set -e
batch=$1
lower_batch=$(echo $batch | awk '{print tolower($0)}')
workdir=/data/talkowski/Samples/SFARI/DeepSeq/HarrisonCompare/GT_Filtering/${lower_batch}_RF
fout=${batch}.cutoffs.txt
echo "svtype source metric cutoff direction" | sed -e 's/ /\t/g' > $fout
sed -e '1d' ${wo... |
1bed98032b51ef279670da728ce48d47e06178e08b6e7d6070635778b07739e5 | Shell | 1,492 | 66 | #!/usr/bin/env bash
MAKE_MESH=false
while getopts ':v:n:m' flag; do
case "${flag}" in
v)
PV="$OPTARG"
;;
n)
PN="$OPTARG"
;;
m)
MAKE_MESH=true
;;
:)
echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
if [ -z "$PV" ]; then
PV=9999
fi
if [ -z "$PN" ]; then
PN="mo... |
27c61f3d11fbe4cdc0034d74a000f8c722c773641780ec6c90245f884e147bdb | Shell | 1,492 | 29 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
e3739bcad4a206948a54fba31f26ac09e463aa3d2a578dcf78422c5a5e78348e | Shell | 1,492 | 45 | #!/bin/bash -e
if [ $# -ne 4 ]; then
echo "usage v1: srna-mad-qc.sh <annotation_gtf_gz> <quants_a_tsv> <quants_a_tsv> <out_root>"
echo "Calculates Mean Absolute Deviation and other stats on a pair of quantifications. Is independent of DX and encodeD."
echo "Expects extract_gene_ids.awk, sum_srna_expression... |
bb0e3415af9888622f5c17123ca608ca92e35b692a198bc60c7c77c86534968f | Shell | 1,493 | 69 | #!/bin/bash
SECONDS=0
echo "Launching all processes..."
cd /root/vsc/hnfc-dataset-agent/
if ls ./data/metamap_sent/*.xml 1>/dev/null 2>&1;
then
rm ./data/metamap_sent/*.xml;
fi
if ls ./data/metamap_sent/*.json 1>/dev/null 2>&1;
then
rm ./data/metamap_sent/*.json;
fi
if ls ./data/metamap_sent/*.txt 1>/... |
a710feee4ec72362281aff75b8521b755bb29622272a85d27b885607af5eb682 | Shell | 1,497 | 54 | #!/bin/bash
#SBATCH -J St1_k15_P100
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=12
#SBATCH --partition=pi_anticevic
#SBATCH --time=1-00:00:00
#SBATCH --output="/CAP_Time_Analytics/cap_codes/slurm_output/St1_k15_P100-%A_%a.out"
#SBATCH --array=1001-1010
module load miniconda
source activate pycap_env
for perm in... |
1a105f324df084939b6750e0c38f9e101f6dc69392b251441e54cc42705e9609 | Shell | 1,499 | 51 | #!/bin/bash
output_file_name=~/logs/viewoutput.csv
folder_name=$1
repress_completed=$2
log_name=${1%/}/status.csv
if ! test -w $log_name; then
# log file does not exist, create it and exit
exit
fi
#read the last line of the log
last_line=$(tac $log_name |egrep -m 1 .)
IFS=',' read -ra ADDR <<< "$last_line"
last_... |
ce126ba7b0f6e13210f87f6034d681e1118b317ca1d72cfc3bcf1d1b37cd2f50 | Shell | 1,508 | 49 | #!/bin/bash
#
# Complex_Inversion_Integration.sh
#
set -euo pipefail
##Input##
inv_resolved_vcf=$1
full_resolved_vcf=$2
##gzipped##
outputvcf=$3
##make bed of the inversion resolved vcf##
zcat $inv_resolved_vcf \
|awk '{if ($8!~"UNRESOLVED" || $1~"#") print}' \
|svtk vcf2bed stdin inv.resolve.bed -i MEMBERS
##mak... |
2ea5c00539223920269a0f13cc1b0ab08f967865069f47c24db0617287a053f0 | Shell | 1,512 | 31 | #!/usr/bin/bash
dataset=$1
run_id=$2
# --taxonomy_predictions /home/projects/cpr_10006/people/svekut/cami2_${dataset}_reassembled_1/results_taxonomy_predictor.csv \
vamb \
--model vaevae \
--outdir /home/projects/cpr_10006/people/svekut/cami2_${dataset}_reassembled_${run_id} \
--fasta /home/projects/cp... |
669b73588a78c113d34592973912f865de1b6491c72d593a9dd499cd096a268c | Shell | 1,519 | 31 | #!/usr/bin/bash
annotator=$1
# --taxonomy_predictions /home/projects/cpr_10006/projects/semi_vamb/data/sludge/vaevaeout_sp100/results_taxonomy_predictor.csv \
vamb \
--model vaevae \
--outdir /home/projects/cpr_10006/projects/semi_vamb/data/sludge/vaevae_${annotator} \
--fasta /home/projects/cpr_10006... |
3fa68f1ce9c7bdc36a8e642715a79cd3b539e58f4826d69159220078ac3812d3 | Shell | 1,521 | 44 | #!/bin/bash
# bam-to-bigwig-unstranded.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.1.0.tar.gz
... |
42695c219938e561fe2b7d3a2fdec7e33f3a9f8550b77391933e616591302ef3 | Shell | 1,522 | 38 | #!/bin/bash
#SBATCH -J DelSwitch
#SBATCH -p high
#SBATCH --exclude=node0[19-21,25]
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --array=0-20
#SBATCH -o /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.out
#SBATCH -e /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.... |
bb2bd0178377bc13467c5caa3d14e8a5b959549dba7a7cfa560f6f3f1c1098d9 | Shell | 1,524 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-02:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
b194310851023213c83f054b19148b0c653f8d9cbd4efb6c837b90055f5e0f9c | Shell | 1,526 | 38 | #!/bin/bash
#SBATCH -J DelSwitch
#SBATCH -p high
#SBATCH --exclude=node0[19-21,25]
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --array=0-20
#SBATCH -o /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.out
#SBATCH -e /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.... |
3b09b670bc40dfbbd41fb807969bdad5a5fa2c60b5d9e74bc74d05c9bab13d27 | Shell | 1,528 | 48 | #!/bin/sh
# Wrapper script to infer factor compositions of new participants with polarLDA model
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###################
# Input variables
###################
corpusDir=$1 # document corpus
modelDir=$2 # learned... |
e3fc2655ef5f7217b85b9b87d8bbce7b4aa28ca786775f605963b2d730df6ab3 | Shell | 1,528 | 28 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=184000 # Memory pool for all cores (see als... |
f90bea15fb1ecf935f99bf3cef4efef8a0781a4070f2eddabf48eceb7e64a3f1 | Shell | 1,528 | 38 | #!/bin/bash
#SBATCH -J DelSwitch
#SBATCH -p high
#SBATCH --exclude=node0[19-21,25]
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --array=0-20
#SBATCH -o /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.out
#SBATCH -e /homedtic/gjimenez/DADES/DADES/Delineator/Logs/%A-%a.... |
4991e98185ca117d0ef516e722bbeadb6b9139e43d864b911a56848c89933df9 | Shell | 1,529 | 45 | # Snapshot to spawn.
target_vm_snapshot = rv-parameterization
# Disk(s) to mount.
target_disk = annotated-cardiac-tensors-45k
# Base prefix name for the VM.
vm_base_name = pdiachil-rv-inference
# Username.
user = pdiachil
# Branch of ML4H to use.
ml4h_branch = pd_sf_blox
for j in {0..4}
do
start=$((j*10))
end=... |
b9340fdb505bfb145d6bdb714d016757f9734e31a53631cb846c475cdcbf6285 | Shell | 1,531 | 29 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
e45b0dbafa5005056f4d854eb4eec47c5c046cb28c98e034b51dcbb09a97fd2c | Shell | 1,532 | 59 | #!/usr/bin/env bash
set -euo pipefail
# Adapted from https://github.com/vllm-project/vllm/blob/main/tools/install_gdrcopy.sh
# Usage: install_gdrcopy.sh <GDRCOPY_OS_VERSION> <GDRCOPY_CUDA_VERSION> <uuarch>
# uuarch must be "x64" or "aarch64"
# Optional: set GDRCOPY_VERSION to override the libgdrapi package version (d... |
8de6355b718500a3753320a975f681092ba3b7af81463ab4a987c53957fe06b0 | Shell | 1,540 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-02:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
63f710106979a13463a0a29f09737ffa14f8c8c29d96f45f31ad82eeb0d29bcc | Shell | 1,544 | 35 | #!/bin/bash
[[ ${SLURM_NODELIST} ]] || { echo "SLURM environment not detected." ; exit 1 ; }
pdir=$(pwd)
profile="${SLURM_JOBID}_profile"
clog="ipcontroller_${SLURM_JOBID}.log"
#/mnt/xfs1/bioinfoCentos7/software/installs/python/2.7.10/bin/ipcontroller --profile=${profile} --ipython-dir=${pdir} --ip='*' > ${clog} 2>&1... |
39f1211754e6967e5020fc57d3ed9437c1b41745ddcedf77f3d58aa8cb64660e | Shell | 1,548 | 15 | #!/bin/bash
for graphtype in dag rulegraph
do
hippunfold ../../test_data/bids_T1w /tmp/out participant -np --modality T1w --${graphtype} | tail -n +3 | ./proc_subgraph.py out_${graphtype}/T1w
hippunfold ../../test_data/bids_T1w /tmp/out participant -np --modality T1w --${graphtype} --config autotop_labels=... |
32e5aed8ae3b5636b18e6a8ff106ab6a2d5321cc00960c531a06a69c28a03528 | Shell | 1,550 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
25c72bb10fb3ad83ac331e5fe644ed67aa5f288ff936b867a9044748aad0cd40 | Shell | 1,556 | 29 | for threshold in {33..100}
do
JUNC_BEFORE_SORT=/ccb/cybertron/khchao/splam-analysis-results/train/data/junctions_${threshold}.bed
JUNC=/ccb/cybertron/khchao/splam-analysis-results/train/data/junctions_${threshold}.sort.bed
sort -k1,1 -k2,2n -k3,3n ${JUNC_BEFORE_SORT} > ${JUNC}
MANE_dir=/ccb/cybertron/... |
776e61b17e180a8f2459e6875063a2845530240df6a0281cd67ab309173aa877 | Shell | 1,556 | 61 | #!/usr/bin/env sh
#PBS -A mnh5174_c_g_sc_default
#PBS -l nodes=1:ppn=20
#PBS -l pmem=8gb
#PBS -l walltime=10:00:00
#PBS -j oe
#PBS -M michael.hallquist@psu.edu
#PBS -m n
#PBS -W group_list=mnh5174_collab
cd $PBS_O_WORKDIR
export G=/gpfs/group/mnh5174/default
module use $G/sw/modules
#module load r/3.5.0
#module lo... |
dba6650ae79cc9bc02c204e0f41eacca35e0c21d27ebdee22711230e05c57fd7 | Shell | 1,556 | 75 | #!/bin/bash
# Usage:
# ./setup-ubuntu.sh [arm64 | amd64]
# Warning! This will override your sources.list file!!
arch=amd64
# Copy off old sources.list file
cp /etc/apt/sources.list /etc/apt/sources.list.old
echo "Backed up /etc/apt/sources.list to /etc/apt/sources.list.old"
# Copy over the new file
cp sources.list... |
312cb438947915eb16ea1784dd4c6d2502dab53207769c765d861796fdf8f9e2 | Shell | 1,557 | 63 | #!/bin/bash
# Generate preview images for all bundled brainchop models
# Run from niivue-desktop directory after building the app
set -e
# Determine app path based on platform
if [[ "$OSTYPE" == "darwin"* ]]; then
APP="./dist/mac-arm64/niivue-desktop.app/Contents/MacOS/niivue-desktop"
if [[ ! -f "$APP" ]]; then
... |
058939a6ccd2d9d56917a6b214477e38f655778668f0b950911fe42442553d89 | Shell | 1,563 | 39 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-04:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=60000 # Memory pool for all cores (see also... |
0a58b28918459b786626299cd33b85327a61f0f406cb412dd1ae23163f3d9e7e | Shell | 1,567 | 32 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
33d112d726a863fef6f564be13313546cda0134303603d7fdaf7839fffeefcbf | Shell | 1,567 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-08:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=84000 # Memory pool for all cores (see also... |
d1f1db1e97a9ae2d1e694173ddd2060c21fe2bc56506a89018479f7ed966c988 | Shell | 1,567 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-08:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=84000 # Memory pool for all cores (see also... |
dbbab795cb5ecd37750189af55202cdccfdae68259cac5652c43764add0818fa | Shell | 1,567 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-08:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=84000 # Memory pool for all cores (see also... |
f8490936f0acdef9b20d636626a05c4addd063672125dd4d9f4391d530cd2def | Shell | 1,567 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-08:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=84000 # Memory pool for all cores (see also... |
24440cbc7d155ef315d6de0f40c8cc370229d3b24fcbbcba97f0a7e7a68c3efa | Shell | 1,569 | 40 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=20gb # Memory pool for all cores (see also ... |
a6d735aa74412fdedaf77e1ecdb77d6d3d70732edb3e26ea732bb2c457efed9a | Shell | 1,570 | 28 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
f5972584dccba727a79a919d93eb2b71d31e0692ab39d01683ba4481008bf390 | Shell | 1,570 | 29 | SAMPLE=$1
# TARGET="NEG_noncan_junctions"
# for OUTPUTFILE in "./dataset/pos" "./dataset/neg_1" "./dataset/neg_random"
for OUTPUTFILE in "./dataset/pos" "./dataset/pos_MANE" "./dataset/pos_ALTS" "./dataset/neg_1" "./dataset/neg_random"
# for OUTPUTFILE in "./dataset/outlier_test"
do
for TARGET in "splam" "splic... |
385ea6a3eb98282026d84281badb7964e7e43bd931ba021cf1da9bfc2c93fff7 | Shell | 1,571 | 39 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
485de5d108f6af18a569f6733a1ce4e9c42788d58317f53f6172f7761a6bf80d | Shell | 1,579 | 26 | #!/bin/csh -f
set top_dir = top_dir/
cd ${top_dir}/3dMerge_Heatmap
set filename = 'heatmap_lexicalfactor_overlap_individuallevel'
# individual participant cluster heatmap, just the cerebellum - OVERLAPPING REGIONS
# Trying to create a cluster overlap map wherein at least 6 subjects have to have shared voxels for it to... |
52ed0d8ad6ef84f612b475e01149f11ec6c088de41b9a07563a3a1b7a3f1f2fb | Shell | 1,579 | 48 | #!/bin/bash
# merge-annotation.sh
main() {
# Now in resources/usr/bin
#wget https://github.com/ENCODE-DCC/long-rna-seq-pipeline/tree/master/DAC/GTF.awk
# If available, will print tool versions to stderr and json string to stdout
versions=''
if [ -f /usr/bin/tool_versions.py ]; then
versio... |
76952e13ab32fad4050eeb401bfe18cb063cc318f5944461fd293ffee3ee8644 | Shell | 1,580 | 42 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=5:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
3a86d6b570850f3e2afa9a5bb28b4e3509b412badb4dab3c9fc1867160f5a74c | Shell | 1,586 | 57 | #!/bin/bash
set -exuo pipefail
ARTIFACT_TYPE=${1:-wheel}
if [[ "$OSTYPE" == "msys" ]]; then
ARTIFACT_MOUNT="/c/artifact-mount"
else
ARTIFACT_MOUNT="/artifact-mount"
fi
if [[ "$ARTIFACT_TYPE" != "wheel" && "$ARTIFACT_TYPE" != "jar" ]]; then
echo "Invalid artifact type: $ARTIFACT_TYPE"
exit 1
fi
if [[ "$ARTIF... |
dbffae491525f228dee62a33153bc6f3d63c527075131fbb4a189d578b0f5e32 | Shell | 1,586 | 29 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=128000 # Memory pool for all cores (see als... |
974832deb571b46cac454b78e0ca19341146c378a93a42ebfad7b7d6c885e2d2 | Shell | 1,593 | 53 | python3 /project/run_vqvae.py run \
--training_subjects='/path/to/ukb/training_samples.csv' \
--validation_subjects='/path/to/ukb/validation_samples.csv' \
--load_nii_canonical=False \
--project_directory='/results/' \
--experiment_name='ukb_vqvae' \
--mode='training' \
--device='ddp' \
--distributed_po... |
f90ed538d311972a79ab266dd43302db6c54d73e08da3b12b3b4901f33d34b1c | Shell | 1,596 | 53 | python3 /project/run_vqvae.py run \
--training_subjects='/path/to/adni/training_samples.csv' \
--validation_subjects='/path/to/adni/validation_samples.csv' \
--load_nii_canonical=False \
--project_directory='/results/' \
--experiment_name='adni_vqvae' \
--mode='training' \
--device='ddp' \
--distributed... |
b298fc4d3859a4ada47ce85eefbe3d41867e066bbeb0694ea0181cc2040eb332 | Shell | 1,602 | 49 | #!/bin/bash
# Bump the CEBRA version to the specified value.
# Edits all relevant files at once.
#
# Usage:
# tools/bump_version.sh 0.3.1rc1
version=$1
if [ -z ${version} ]; then
>&1 echo "Specify a version number."
>&1 echo "Usage:"
>&1 echo "tools/bump_version.sh <semantic version>"
exit 1
fi
# Dete... |
dbcb83aef326714acecb6f6f53b8ab3b376ba71dca17dc0dd6b54d1d41907276 | Shell | 1,606 | 43 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=144:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1... |
4614aac10cae21d4b478ebf2cab05e5c02b623d731216c985e6c3f0c057b6960 | Shell | 1,608 | 55 | #!/bin/bash
#-------------------------------------------------------------------------------
# This script performs a test of the program a calculate-genotype-data.py
# in a Linux environment.
#
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Siste... |
ce87f6d8dfb51d40fad4a0b2755b398ef7c0d8999dcd6064685bf5d45a2ad6cf | Shell | 1,608 | 43 | #!/bin/bash
# 1_segmentation_overlap.sh
# Loop across sessions for data preparation
process_subject() {
sub=$1
echo "Processing subject: " $sub
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $session
echo "subject: " $sub "session: " $ses
#Directories
project_di... |
8558fcd7bb3bc58d330b5149de41b8f7c9d410660e8414dbe838937154eef01a | Shell | 1,611 | 35 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=5:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
106ae7ac4b151afab52117565646fe4e604a880571720a41032c694d101f0ee8 | Shell | 1,615 | 30 | #!/bin/bash
#BATCH -p DCU
#SBATCH -N 1
#SBATCH -n 9
#SBATCH --ntasks-per-node=9
#SBATCH -o %j.out
#SBATCH -e %j.err
pheno="Left_Dentate"
##RNASE12
gene='RNASE12'
i="14" # i denotes chr
for t in {1..26};do
Rscript /home1/Huashan1/SAIGE/extdata/step2_SPAtests.R \
--bedFile=/home1/Huashan1/UKB_WES_data/qcstep... |
efa41a9b2fec20ce137e382fc0b486c57a774a78c125101f1fd757ef07ef2e2f | Shell | 1,615 | 58 | #!/bin/bash
#-------------------------------------------------------------------------------
# This script performs a test of the program tab2vcf.py
# in a Linux environment.
#
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Recursos Natur... |
2e0d5d37eb907b163d4107e75e5ed2ed149e92c73c39f33abecdf9d9de415400 | Shell | 1,616 | 32 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
f1468d2897c5b183c27a95e1596870e04abe51a45354a95816307103d3e76d6d | Shell | 1,623 | 55 |
for maxSite in 5 10 20
do
for cutoff in 0.005 0.015 0.035 0.05 0.1
do
for peak in 600 1000
do
qsub -P trapnelllab -l mfree=32G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATA... |
0fe2b7eb750889853676118edbfc1683dcd4e17ea2ea33fc78730cab3e5098ef | Shell | 1,624 | 76 | #!/bin/bash -evx
export TURTLEBOT3_MODEL=burger
roslaunch emcl test_gui.launch &
sleep 15
### ESTIMATION RECOVERY TEST ###
rostopic pub /initialpose geometry_msgs/PoseWithCovarianceStamped "header:
seq: 0
stamp:
secs: 0
nsecs: 0
frame_id: ''
pose:
pose:
position: {x: -2.5, y: 0.0, z: 0.0}
orie... |
d58f374e1b120682e4537ef6b00702eb07214fab8e6a847e2b965b5a997f62ac | Shell | 1,625 | 37 | #!/bin/bash
#SBATCH -c 1
#SBATCH -p normal
#SBATCH --mem=12g
#SBATCH --time=12:00:00
source /com/extra/ucsc/2015-04-21/load.sh
# bedtools v2.27.1 fails due to a bug in BEDtools merge (not reporting strand after merge)
source /com/extra/bedtools/2.25.0/load.sh
# change directory to the local scratch-directory, and ru... |
d59d379c7ca307cb2562b4a254432d5b02a613bf9a3a4a4e181f3d085cecab39 | Shell | 1,625 | 42 | #!/bin/bash -l
#SBATCH --time=8:00:00
#SBATCH --ntasks=8
#SBATCH --mem=10g
#SBATCH --tmp=10g
#SBATCH --mail-type=ALL
#SBATCH --mail-user=molin239@umn.edu
export BCFTOOLS_PLUGINS=/home/jhwang/molin239/bcftools/plugins/
cd /home/jhwang/molin239/Desktop/bcftools_VCF/NEPC_Output_2-13-2024/sorted_VCF_annotationV4_Filter_W... |
d2f3f0eda03f07488d3a7f838f8bd8fbf49b9f0724a065d226a9044a384afb96 | Shell | 1,629 | 29 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=32000 # Memory pool for all cores (see also... |
a435b15fbc3458c59c31a6165128efa74ae8f2d13cb5b7599f29329b0c4ca02c | Shell | 1,630 | 57 | #!/bin/bash
folder_name=${1%/}
UpdateLog.sh $folder_name delete_tracks HEAD_NODE START Deleting_Analysis_Files
declare -a files_removed
count=0
files_to_remove=(
'processed.avi'
'processed.mp4'
'processed.mkv'
'tracking_deleted_tracks.mat'
'centerline_deleted_tracks.mat'
)
# remove all th... |
61412cf0ea185f56659b0aae05d32dd1321818636f818a9a5a0bbeff8b7f2afe | Shell | 1,637 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
46b8ee4f915f73ca3d9acb1b263b76143612b2dbc1cb81ee08532415da11abba | Shell | 1,639 | 23 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/assembly
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/assembly
echo mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoo... |
35a9217df190e3e531d7960838022458c99d7541a55c1e1d2c9521132d8bb6f6 | Shell | 1,640 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
051fcb3c81468e0b6d8e130439b2e99b255b0260f6679d56522c6a445eb89940 | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
50c2483268803bb14a66d60a11ed7439e811ff9d2f8c8e5472df6ecc40d07a76 | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
66ef7c2ca34adaf4ccf87d1f17074c980a32ff072a60b9afb198dfcd78c1d7f7 | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
8b3c23b94819906d31132e23d569f903a13c3e853a33c79bdf6b14bf996535cc | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
d73c3e08b2563e0b5967b87d5099851ff06fde9ee7baeb9393a14553e2f7948f | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
ded66fdb110e3ce1c687fa3dd39ca9306b88dfbe70f7da9c889386487c1993de | Shell | 1,641 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
b141c880553c2ab2027be251a68cda25f31694c5444deb0df48d90757e659816 | Shell | 1,643 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
e4aa199bfb137d7e72b9fdfd9fc93dafe527eb8bea2e2052991a32cfeab192dc | Shell | 1,643 | 41 | #!/usr/bin/env bash
# SETUP EXPERIMENT DIRECTORIES ----------------------------------------------
# Prepare experiment directories with necessary input files for DeepRVAT running
# Replace `[path_to_deeprvat]` with the path to your clone of the repository.
# Activate your virt-env before running script. i.e. $ mamba ... |
0f255c5d2879a172bb1a83000ca99e59ce14c157aaa46f416d59616a28ecd72c | Shell | 1,645 | 59 | #!/bin/bash
#-------------------------------------------------------------------------------
# This script performs a test of the program a vcf2tab.py
# in a Linux environment.
#
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Recursos N... |
4c4d11e86d373d0b4948700201bb09b7e38cb5eaf63d16dbf4e781f4fdfe6763 | Shell | 1,649 | 45 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
17f796c8cf97eea05b26b4d5f10f32e4da515ca1607ff775ddcb33abd63c9f40 | Shell | 1,651 | 19 | mkdir NEG_rev_junctions
gtf2bed --gtf ../../Dataset/MANE.GRCh38.v1.0.ensembl_genomic.gtf --bed ./NEG_rev_junctions/MANE.GRCh38.v1.0.ensembl_genomic.bed
sort -k 1,1 -k2,2n -k3,3n ./NEG_rev_junctions/MANE.GRCh38.v1.0.ensembl_genomic.bed > ./NEG_rev_junctions/MANE.GRCh38.v1.0.ensembl_genomic.sort.bed
bedtools merge -i ... |
7013e914efc2ce7ad71fbfb594f3043fa4ca629d270372c14e03d091cba25d81 | Shell | 1,651 | 54 | #!/bin/bash
# Build Python-agnostic ray-cpp wheel.
#
# The ray-cpp wheel contains only C++ headers, libraries, and executables
# with no Python version-specific content. This script builds a single wheel
# tagged py3-none-manylinux2014_* that works with any Python 3 version.
#
# Usage: ./ci/build/build-cpp-wheel.sh
#
#... |
165ba543c6ebda5f900abf9c0ee5cf1b83429a6f41afcf2f7cc8c5f2adba333b | Shell | 1,653 | 68 | #!/bin/bash
ASM=$1
ALN=$2
TRUTH_H1=$3
TRUTH_H2=$4
ID=$5
TC=16
if [[ -z "$5" ]] ; then
echo "usage: $0 ASM ALN TRUTH_H1 TRUTH_H2 IDENTIFIER"
exit 1
fi
echo -e "ASM: $ASM\nALN: $ALN\nT_1: $TRUTH_H1\nT_2: $TRUTH_H2"
sleep 1
set -o xtrace
minimap2 -ax asm20 -t $TC $ASM $TRUTH_H1 $TRUTH_H2 | samtools view -F 0x904 -... |
0eb511381b479c2c8d9491e0dbc72ac18b1cbc4570f456c8265b8e41410ad765 | Shell | 1,654 | 54 | #!/bin/bash
#$ -S /bin/bash
#$ -N bcf_cat
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=8G,h_rt=48:00:00
#$ -hold_jid normann
#$ -t 1:22
##===keeps biallelic within our dataset that are multiallelic
##concat by chr
##sort
##remove exact duplicates ... |
20fc0665e898aef90d4559af8ba5188752f3ef5ee0c6cba2a7c264b57e430154 | Shell | 1,662 | 44 | #!/bin/bash
#
# Run script to conduct age - expansion analyses #
# using parcellation (OPNMF or Davi130) #
# The R script requires 5 input arguments #
### 1 - Working directory (wd) where relative paths can be used to find files
### 2 - Cohort investigated
### 3 - Parcellation Image used for analyses
### 4 - Deforma... |
7388eb23874244e41b4bea86c051f176af2ba891b8f4ebc9d45442c64e817bc3 | Shell | 1,662 | 36 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=5:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
771615d5d5a597175551d4d246a202c2e8590222033a218cb9e2ad59ad16c45c | Shell | 1,662 | 53 | #!/bin/bash
#
# Path to the Nextflow processing run configuration file.
#
WORKING_DIR="/net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/2021_03_29_HM10_Human15_ResetPlates_nobackup"
CONFIG_FILE="$WORKING_DIR/experiment.config"
#
# Nextflow executable and pipeline script locations.
#
# Note: the bbi-demux r... |
cb2d7d185442cb079e47b1186abb48e2033c005f47cb65312a26d1d4a4bc7ef4 | Shell | 1,662 | 53 | #!/bin/bash
#
# Path to the Nextflow processing run configuration file.
#
WORKING_DIR="/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_06_07_prelim_DanaRula_BethMethod_nobackup"
CONFIG_FILE="$WORKING_DIR/experiment.config"
#
# Nextflow executable and pipeline script locations.
#
# Note: the bbi-demux r... |
edd6f0711b0c29ab236098100a73ba65b280bf200f85127f8e89f014dd3d5549 | Shell | 1,665 | 31 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-02:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
39c2ad0083603c02b8a3c5a8b5d6696ff97b79029f896cfbd8ba7e7287deb575 | Shell | 1,666 | 51 | #!/bin/bash
# Ultralytics YOLO 🚀, GPL-3.0 license
# Download ILSVRC2012 ImageNet dataset https://image-net.org
# Example usage: bash data/scripts/get_imagenet.sh
# parent
# ├── yolov5
# └── datasets
# └── imagenet ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_imagenet.sh --train --val
if [... |
4f07df026316b69f183ebec9861bff34ffb39a7855c95d3b6d20879aca47e55c | Shell | 1,669 | 43 | #!/bin/bash
# Bash script to run CNN-LSTM for 3D sleep classification project
export CUDA_VISIBLE_DEVICES=8
echo "$CUDA_VISIBLE_DEVICES"
# main arguments
mode=test
model=model_dau_nores
dataset=dataloader_sleep_tfrecords_local
seed=42
# dataloader arguments
data_path=/shared/planck/MRI/xiaohui/mouse_optical/sleep_s... |
5a44b1cfc5c18c13115e3beea37ce8e1c3d78fce4889cf812ff740a448aa6be4 | Shell | 1,673 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=32000 # Memory pool for all cores (see also... |
79dc6d7fdc0717a6b17d4da020d646ed8325bd3df53f53476da7f7c47fd0a6e9 | Shell | 1,673 | 39 | #!/usr/bin/bash
thres=$1
vamb bin default \
--outdir /home/projects/cpr_10006/projects/vamb/MATRIX_vamb_no_split \
--fasta /home/projects/ku_00200/data/matrix/mgx22_assembly/avamb_outdir/contigs.flt.fna.gz \
--rpkm /home/projects/ku_00200/data/matrix/mgx22_assembly/avamb_outdir/abundance.npz \
-l 32 \
... |
e4265153ed3efd39d5fe4d3e16f39506c8048c053dd992b4074682daa9af008a | Shell | 1,673 | 47 | #! /usr/bin/env bash
# compiles all
function usage() {
echo "usage: `basename $0` <Matlab Compiler>"
}
echo STARTED:
date
if [ $# -eq 1 ]; then
MCC_FILE="$1"
fi
if [ ! -e $MCC_FILE ]; then
echo "unable to locate matlab compiler"
usage
exit 1
fi
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null &&... |
22713265623e186a92da10f7f162db1a0b10ca5ba7a3f56a596beeaf00099536 | Shell | 1,674 | 76 | #!/bin/bash -evx
export TURTLEBOT3_MODEL=burger
xvfb-run --auto-servernum -s "-screen 0 1400x900x24" roslaunch emcl2 test.launch &
sleep 15
### ESTIMATION RECOVERY TEST ###
rostopic pub /initialpose geometry_msgs/PoseWithCovarianceStamped "header:
seq: 0
stamp:
secs: 0
nsecs: 0
frame_id: ''
pose:
pose... |
8a3e5c933211bbeb3137c1f0c7432828611d3f56ad71add4a14b603080338e7c | Shell | 1,678 | 32 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-08:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=72000 # Memory pool for all cores (see also... |
0178f7086cb4abc2506a5b1075c22a1cbee0e72be4bbfd0109477a89f23c9d86 | Shell | 1,681 | 49 | #!/bin/bash
wget -O models/ldm/celeba256/celeba-256.zip https://ommer-lab.com/files/latent-diffusion/celeba.zip
wget -O models/ldm/ffhq256/ffhq-256.zip https://ommer-lab.com/files/latent-diffusion/ffhq.zip
wget -O models/ldm/lsun_churches256/lsun_churches-256.zip https://ommer-lab.com/files/latent-diffusion/lsun_church... |
99ac60b4bc94c45d2ffec04cb3f85115a349f3d23d4db48c8ec6c2f96bc07711 | Shell | 1,692 | 34 | #!/usr/bin/bash
annotator=$1
thres=$2
# --taxonomy_predictions /home/projects/cpr_10006/projects/semi_vamb/data/sludge/vaevaeout_sp100/results_taxonomy_predictor.csv \
vamb bin taxvamb \
--outdir /home/projects/cpr_10006/projects/semi_vamb/data/sludge/vaevae_${annotator}_predictor_${thres} \
--fasta /home... |
df8804312b18d2118977f862dc13ef3369ca055a301e6335e2a272ad378a1a59 | Shell | 1,693 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
89ce4edefb13400cd0bf2feae50a6eadb2734473c9482c59480ef461a24fb232 | Shell | 1,694 | 50 | ##Partition GWAS summary data into 22 chromosome files
partition_chrs(){
map_file=~/Database/00-common_all.txt
cat ~/Database/GWAS/GWAS_metadata.txt |cut -f 1 |while read line; do
mkdir -p ~/Moloc/sumstats/${line}
zcat ~/Database/GWAS/Sumstats/${line}.sumstats.gz |\
awk -v OFS='\t' '{if(NR==FNR){a[$3]=$3;b[$3]... |
5b3822c520afccefbe88a08dab4d403e99692bd088d50fc872c10a357181699d | Shell | 1,695 | 42 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
93a6e74ae5e0dff71e5fdedacebb3b004c1d28dd77bba1333b1e57406283b430 | Shell | 1,698 | 32 | #####Bash script used to create training set. Example for ENCFF843MGJ.
#Requirements: Bowtie, macs2, samtools, bedtools, cutadapt, Allo, and cnn_training_gen.sh (provided on github)
#Getting files
wget https://www.encodeproject.org/files/ENCFF968ICP/@@download/ENCFF968ICP.fastq.gz
gunzip *gz
bowtie -q HG38_INDEX_LOC... |
99d9822657af0aed5ae339a9e201a5190ad0d57060486d1ac3946a301294254e | Shell | 1,703 | 30 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
9f784251bab6b79cbb3ec78a8f2c51ffbb6f727b73de6a5a0eabbe5a271127c5 | Shell | 1,703 | 17 | #!/bin/bash
#sbatch --export=atlas="/proj/mnhallqlab/projects/clock_analysis/fmri/pfc_entropy/masks/Schaefer_136_2.3mm.nii.gz" sbatch_medusa.bash
#sbatch --export=atlas="/proj/mnhallqlab/projects/clock_analysis/fmri/vmpfc_ah/vmpfc_ba_max_2.3mm_filled.nii.gz" sbatch_medusa.bash
#sbatch --export=atlas="/proj/mnhallqla... |
f3a8df344509fc3320eded4dfd30b029600c13af40839e29d4b868909c80362c | Shell | 1,703 | 33 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
#... |
8f948ac312d718e6799fa9180e6516093f5dd636b0f15d376038ffc80d5df6bd | Shell | 1,705 | 54 | #!/bin/sh
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
set -e
GENERATOR_VERSION="v6.0.1"
VERSION="2.80.1"
LIB_NAME="cvat_sdk"
LAYER1_LIB_NAME="${LIB_NAME}/api_client"
DST_DIR="$(cd "$(dirname -- "$0")/.." && pwd)"
DOCS_DIR="$DST_DIR/docs"
GEN_DIR="${DST_DIR}/gen"
POST_PROCESS_SCRIPT="${GEN_D... |
f02e50aa8a193c732fa5d98c492ffea1696a782a21d5bf3468f797df3b2288c9 | Shell | 1,705 | 58 | #!/bin/bash
#-------------------------------------------------------------------------------
# This script performs a test of the program a impute-md-naive.py
# in a Linux environment.
#
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Re... |
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