sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1a6c147fe558eaeb9f26ded30f465613b54983f42d031ae6ee67d0ca8d22a536 | Shell | 936 | 35 | #!/bin/bash
# Convert figure captions and supplementary tables from Markdown to PDF
# Check if pandoc is available
if ! command -v pandoc &> /dev/null; then
echo "Error: pandoc is not installed or not in PATH"
exit 1
fi
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Define the specific files to... |
6e3028c57081c95174542c495cd23262241361caf5104c86ffc667bf9811eab9 | Shell | 936 | 48 | #!/bin/bash
#Work around for the problem that
#I cannot get the linker to use /usr/X11/lib instead of /opt/X11/lib
#The issue is with Mavericks (10.7) that has an apple version of X11 already
#installed in /usr/X11 instead of xquartz which installs in /opt/X11 and has
#a symbolic link to /usr/X11
#Change all links of... |
6f60897151c2d3e3d3b5fffc168e6307af6d7305b1d0e7bf8ee388f20b32d0dd | Shell | 936 | 36 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
conda_env="scenicplus"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export MKL_NUM... |
8f566801aa4dae89e8a82d03efd0428e048f31a4ac36662afc5021272d499d43 | Shell | 939 | 28 | #! /bin/bash
step=1
## Copy files for MIND calculation
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
targ_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/STATS/T1/FSDATA
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist_init.txt... |
cc0ff56fd57afd7dbdbf44abea208c87896622e8dcded12f7f9519630e6bd7e5 | Shell | 939 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/taiwan16k/img_anisosmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
#mkdir /lustre/atlas/proj-shared/nro101/BigNeuron/taiwan_16k_valid_batch_run/anisosmooth/results/$filename
for i in {25..27}
do
# mkdir /lustre/atlas/proj-share... |
27ce94cb7a68c09937e0185e5028580b1204a90d8c2e325d6553cecc90f32462 | Shell | 940 | 34 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir="//infiltration_maps/model/Map"
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<... |
2ca437b2d4efb3c4f39a97d7cd661feaf5540ef2c8b5537716552dcfdf6bc535 | Shell | 940 | 9 | #!/usr/bin/env bash
# Run the pipeline (Mark Duplicates, BQSR, Haplotype Caller) on small data in GCS.
. utils.sh
time_gatk "MarkDuplicatesSpark -I gs://hellbender/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O hdfs:///user/$USER/small_spark_eval/out/markdups-sharded --sharded-output true" 8 1 4g 4g... |
0ccb91a822719d073d1cbeccb8e735bbc33c7beea7e08c6d655decc7224be933 | Shell | 941 | 39 | !#/bin/bash -v
################################################################################
#
# group_tractography
# ------------------
#
# Submit multiple jobs to constrct subject tractograms
#
################################################################################
#
# Usage : group_tractogr... |
331054343764a761d6dfad8d0bf95cdc585735799d07c854a26a034faba80f28 | Shell | 941 | 33 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=12:00:00
#SBATCH --job-name=shinobi_corrmat
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=48G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
# Get repository root - use SLURM_SUBMIT_DIR (directory where sbatch was... |
7fabce246e4abc9f2ea662d09b73f86f6aae078772bbb675962c30e471a4f94a | Shell | 941 | 33 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=01:00:00
#SBATCH --job-name=shi_subjlevel
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=32G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# Get repository root - use SLURM_SUBMIT_DIR (directory where sbatch was ca... |
b4da03f3fc801180ee9078e6974ce2b58a6cd03255a6158d66a6cf7a0a68a19e | Shell | 941 | 22 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 0-01:00 # Runtime in D-HH:MM format (was 10m, hit timeout 2026-04-28 — banc-ids.R needs ~13m per orchestrator history)
#SBATCH -p short # Partition to run in
#SBATCH --mem-per-cpu=8G ... |
93cc89beb91fde07b787662642e5f1a32ab38fe05c955b1a5309bddab9182c07 | Shell | 942 | 26 | #!/bin/sh
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export Project_dir=$1
export virus_index_file=$2
export case_control_id=$3 #tab delimited file: column1 - index names; column2 - 1 if case and 0 if ctrl
export NR_cases=$4
export NR_ctrl=$5
export pos_cutoff=... |
37f5e9077b2bb36598afd2043e1f18b07a930b134c1964b66b63486eacf55c12 | Shell | 943 | 6 | #!/usr/bin/env bash
# Downloads the HGNC data source from the HGNC website.
curl 'https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_locus_group&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=g... |
6d02e4e93cac6c13909ca0226b67314e28953d91504c7fb2afbaa4f0a1dac53e | Shell | 944 | 28 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=HAIL_matrix
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=100
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to cache dir... |
a3c070bd47f7754a2734e8a0cf097e7eb403fbb30210859129a92f68eaced002 | Shell | 945 | 20 | #bench4
PLDDTDIR=./plddt_metrics_bench4_af_std_and_hhblits_msas_model_1_recycle_10_
OUTNAME=./plddt_metrics_bench4_af_std_and_hhblits_msas_model_1_recycle_10_all_runs.csv
#python3 ./merge_plDDT_dfs.py --plDDTdir $PLDDTDIR --outname $OUTNAME
#Marks
#AF2+paired
PLDDTDIR=./plddt_metrics_marks_af_std_and_hhblits_msas_mode... |
ac3ba10bd03563cd08289473744edbe5087f3d774919ee84133d290dfb5cdf04 | Shell | 947 | 26 | #!/usr/bin/env bash
set -e
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
INPUT="$(readlink -f "$1")"
shift
OUTPUT="$(readlink -f "$2")"
shift
USERNAME="$3"
shift
PASSWORD="$4"
shift
unset CONDA_SHLVL
eval "$(conda shell.bash hook)"
conda activate rosettafold
mkdir -p ${OUTPUT}
HEADER="... |
074e68ace65c174b2d3f3625e62547e64956c98ef8ee9c3102cf36868e622c75 | Shell | 948 | 37 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
conda_env="scenicplus"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export MKL_NUM... |
e91ca15d96a8252dc26a4209794077292af5360febb9f93c84f348d15bbf9197 | Shell | 948 | 30 | #!/bin/bash
# Set paths
INPUT_DIR="../../../processed_data/cellbender"
OUTPUT_DIR_BASE="../../../processed_data/cellbender"
SAMPLES_FILE="${INPUT_DIR}/samples.txt"
echo "-----------printing samples file------------"
cat "$SAMPLES_FILE"
echo "--------------------------------------------"
# Loop over each sample name
... |
5e5600108a6a25e72c10fa3535f4432e058f3012ef11dcfc39d1d171d6d59ea0 | Shell | 950 | 37 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
conda_env="scenicplus"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export MKL_NUM... |
cdcf2d1ebac0f0410dcef16761751086488bd4aa8fac79c0cebab3d114e197e0 | Shell | 951 | 38 | #!/usr/bin/env bash
# Run all hidden-dim variant trainings (20 and 32). Original 2th/4th/NeuralRK4 are not touched.
set -euo pipefail
ROOT="$(cd "$(dirname "$0")/.." && pwd)"
export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}${ROOT}/src"
cd "$(dirname "$0")"
echo "PYTHONPATH includes: ${ROOT}/src"
run_py () {
local di... |
e60db6787c3cf4ac14dd645d66ec12942bdfe15529c1c06b92d524cc1cc7fa04 | Shell | 951 | 28 | #!/usr/bin/env bash
set -euo pipefail
unset PGPASSWORD # Use ~/.pgpass authentication; do not pass credentials here.
DB_HOST="${DB_HOST:-localhost}"
DB_USER="${DB_USER:-postgres}"
DB_NAME="${DB_NAME:-mimiciv}"
run_step() {
local step="$1"
echo "----------------------------------------"
echo "[$(date '+%F %T')... |
29ae1853e5212806ec7cb4a6ac6bd3a448c9f03675feab0e4c230d2435ce33fc | Shell | 952 | 37 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
conda_env="scenicplus"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export MKL_N... |
8d403e98b68e65b0abe5458367c949dfae4defdf2d9a954b55860ab69d4746a1 | Shell | 954 | 40 | #!/bin/bash
#PBS -P jh2
#PBS -q normalbw
#PBS -l walltime=00:30:00
#PBS -l ncpus=1
#PBS -l mem=4GB
#PBS -l jobfs=10GB
#PBS -l wd
#PBS -N comp_pypi_publish
#PBS -j oe
#PBS -m bea
#PBS -l storage=scratch/jh2+gdata/jh2+scratch/mk27
set -euo pipefail
# ========= Fill paths =========
PROJECT_ROOT="${PROJECT_ROOT:-/g/data/... |
ca3ee792d88ae4377b8432f4eea37a45bebb44f6857891613a2418b00a7fe0a1 | Shell | 955 | 44 | #!/bin/bash
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2022 Xilinx, Inc. All Rights Reserved.
# Copyright 2022-2025 Advanced Micro Devices, Inc. All Rights Reserved.
#
if [ -z "$PATH" ]; then
PATH=/opt/Xilinx/2025.2/Vitis/bin:/opt/Xilinx/2025.2/Vivado/bin
else
PATH=/opt/... |
f7ea0288a047a8fd2596f9d18deb5d8d14d9fadbe2f54928a100041ce637f6d4 | Shell | 955 | 27 | #!/bin/bash
#####################################################################
# Copyright 2023-2024 Blue Brain Project / EPFL
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http:/... |
06b1a13799e7481ab4bb01ed8a08a41ec527c9bfb7be81ca8a788e4bc383b2ba | Shell | 956 | 35 | #!/bin/bash
#SBATCH --partition=xnat
#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 24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/decoding_analysis/slurm-%A_%a.out
#SBAT... |
2b7b832f5f45c37d8efbe3c361e252bc07ec78b6c2cf589715aa2037e188b358 | Shell | 956 | 37 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
conda_env="scenicplus"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export MKL_N... |
dfb134c798d50a27f0519b493c48418f6a4521c72f50c24f960c6d935e5c14fa | Shell | 956 | 35 | #!/bin/bash
# This script returns a dataset for each variable amino acid site in each transcript. The dataset contains a column with species name
# and a second column with the allele variant: 0 for the major allele, and 1 for the minor allele.
# Ambiguous nucleotides are assigned an 'X'.
source Scripts/functions_b... |
400be96681608d2132ff8eebed3c0433ea96f8b5f8f213e1f46da85216571127 | Shell | 959 | 41 | #!/bin/bash
#SBATCH --job-name=mq
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=mq
#SBTACH --error=mq
#... |
ed47c503f6523d43b888ab00aaaab1dfa0c7c54fb156ccba6855781b2b67203b | Shell | 960 | 36 | #!/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)
container_home... |
23cbaad306458cbd7d958f577eefe72dc4755dea61b0f7c84059674b32220676 | Shell | 962 | 30 | #!/bin/sh
#PBS -V
#PBS -q sugon10
#PBS -N co2+ni100
#PBS -l nodes=1:ppn=24
source /share/home/bjiangch/group-zyl/.bash_profile
# conda environment
conda_env=PyTorch-190
export OMP_NUM_THREADS=6
#path to save the code
path="/home/home/zyl/pytorch/2021_8_1/eann-8/"
#Number of processes per node to launch
NPROC_PER_NODE=... |
eaf3012d8086b8406b1117554411a0000b2f5d82eb79b84e564e79eeeddc488d | Shell | 962 | 38 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sepoffRM
#SBATCH --error=joblog_error_%j.txt
#SBATCH --output=joblog_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# data source
path_biotools="/gpfs/sc... |
2f147679ead13563ca5699068dcdc1ebbeeef179340502adaa1396fb23279b95 | Shell | 964 | 25 | #####################################################################
# Copyright 2023-2024 Blue Brain Project / EPFL
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.o... |
305a5ab7bef85db3cb211f5792c79b8396579cbec60c88bf04b1e880bc5feb24 | Shell | 964 | 31 | #!/bin/bash
#SBATCH -p cpu
#SBATCH -N 1
#SBATCH -n 48
#SBATCH -t 124:00:00
#SBATCH --mem 20G
#SBATCH -o model_silva_mouse.out
#SBATCH -e model_silva_mouse.err
qiime micom build --i-abundance feature_table.qza \
--i-taxonomy classification.qza \
--i-models MCMG754_genus.qza \
... |
8a887e37a47b51559e39faa2afe5aba79f05fe80820530e29a692eaa6167b562 | Shell | 964 | 32 | #!/bin/bash
# Setup script for Superset Codespaces development environment
echo "🔧 Setting up Superset development environment..."
# The universal image has most tools, just need Superset-specific libs
echo "📦 Installing Superset-specific dependencies..."
sudo apt-get update
sudo apt-get install -y \
libsasl2-d... |
4443fa859c23bbf8f60ab19146fc63cc53abd31288af33251f98c1159eedeb4e | Shell | 965 | 48 | #!/usr/bin/env bash
# Smoke test for NEURON builds travis_build.sh relative/path/to/build if the
# environment variable CONFIG_OPTIONS is set, that is used for the ./configure
# script, otherwise a default is used
set -ex
BUILD_DIR=$1; shift
INSTALL_DIR=$(pwd)/$BUILD_DIR/install
if [[ -z $CONFIG_OPTIONS ]]; then
... |
5f4340cf71274fe652c7dc3a8895dc919c1f9a888c3c708c97742ed3ae0c5d53 | Shell | 965 | 32 | #!/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
sed -i 's/\.\/docs\/source\///' docs/source/getting_started.md
sed -i 's|src="\./resources/images|... |
7da40546123cc9f5c0d8702aa009fb297c459a4ae81bdbb49c33bcd84f067c0d | Shell | 965 | 56 | #!sh
# get the last argument
for last; do true; done
OUTPUTDIR=.
HASDIR=0
# if the last argument begins with --NEURON_HOME=
if [[ $last == "--OUTPUTDIR="* ]] ; then
OUTPUTDIR=${last#"--OUTPUTDIR="}
HASDIR=1
# remove the last argument
set -- "${@:1:$(($#-1))}"
fi
if test -f $1/bin/cygpath ; then
N="`$1/bin/cygpat... |
fcbabc129c4881573a2f242dc06755dad236c12350674c2b19f9c46e3137c5dd | Shell | 965 | 22 | #!/bin/bash
mkdir -p $3
for filepath in $1/*
do
for i in 1 2 3 4 5 6 7 8 9 10
do
sbatch --job-name="GRNBoost2_"$(basename "$filepath" .csv) --exclude gorilla4 --wrap=". /opt/miniconda3/etc/profile.d/conda.sh
conda activate GRNBoost2
python data-raw/arboreto_with_multiproc... |
98ec52bfab12a90cf6e8bc5f02964b10a958586a64efb48fe9f2d03d7c5e8d28 | Shell | 966 | 32 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=1
#PBS -N align_tnf5
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="py38_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
... |
df0dc4e1b0827422a8ec4f041c7630a7cd300b8539ceed42b3c416d4b21c2eac | Shell | 967 | 9 | #!/usr/bin/env bash
# Run the pipeline (Mark Duplicates, BQSR, Haplotype Caller) on exome data in HDFS.
. utils.sh
time_gatk "MarkDuplicatesSpark -I hdfs:///user/$USER/exome_spark_eval/NA12878.ga2.exome.maq.raw.bam -O hdfs:///user/$USER/exome_spark_eval/out/markdups-sharded --sharded-output true" 96 1 4g 4g
time_gat... |
1efa3f76db1b05d983a7817efec00e621984f8ec3207c686108e262cf1aa7366 | Shell | 969 | 27 | #!/bin/bash
####################################
# GET PTBXL DATABASE
####################################
mkdir -p data
cd data
wget https://storage.googleapis.com/ptb-xl-1.0.1.physionet.org/ptb-xl-a-large-publicly-available-electrocardiography-dataset-1.0.1.zip
unzip ptb-xl-a-large-publicly-available-electrocardio... |
48baad960913fa43591f1fec48cb4996b0e9293f9a7ec170acd3c420fc130e35 | Shell | 969 | 31 | #!/bin/bash
figlet "GRU-SVM"
printf "Operation: [1] Train [2] Test\n>> "
read choice
if [ "$choice" -eq "1" ] &>/dev/null; then
echo "Training GRU-SVM for intrusion detection"
if [ ! -d "./models/checkpoint" ] &>/dev/null; then
mkdir models/checkpoint_path
fi
python3 gru_svm_main.py --operation "train" \
--train... |
60345dbae3a145e941ee6207bada0a8191fe52b7c406f134bd9011075cf43cab | Shell | 970 | 43 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_repeat_modeler
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 2
#SBATCH -c 1
#SBATCH -t 24:00:00
#SBATCH -v
#SBATCH -o run_repeat_modeler.%j.out
#SBATCH -e run_repeat_modeler.%j.err
module purge
#module load bio/Flye/2.9.1-GCC-11.2.0
#source /home/tcolgan/met... |
db6d2bfb880e4be367280c142373ed7e3ec6c41fdca161dc58be8e644d1d91e3 | Shell | 970 | 19 | #! /bin/bash
# Download the data form the paper
#Altan E, Solla SA, Miller LE, Perreault EJ (2021) Estimating the dimensionality of the manifold underlying multi-electrode neural recordings. PLoS Comput Biol 17(11): e1008591. https://doi.org/10.1371/journal.pcbi.1008591
# The dataset contains high dimensional data from... |
eaa7c1a7ec2ef13530e9c0f5416e5a34ff73933c74c2a27124d75a66f7f60d17 | Shell | 971 | 27 | #!/bin/bash
#####################################################################
# Copyright 2023-2024 Blue Brain Project / EPFL
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http:/... |
3f84773cfeacdb341d06d3c3fd62b29cc842df0b2fdc2fc0a3ad34e6273b922f | Shell | 973 | 9 | #!/usr/bin/env bash
# Run the pipeline (Mark Duplicates, BQSR, Haplotype Caller) on small data in HDFS.
. utils.sh
time_gatk "MarkDuplicatesSpark -I hdfs:///user/$USER/small_spark_eval/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O hdfs:///user/$USER/small_spark_eval/out/markdups-sharded --sharded-output true" 8 1 4g 4g... |
5d146b3902c8c2b191a8984a80769dd2210926cc2cfa26c3f60afe6adfeb7e0c | Shell | 973 | 38 | #!/bin/bash
### This script runs NMF on each sample's myeloid cells in the CAREmut dataset ###
# Activate the conda environment for running NMF, if not currently active.
module load miniconda
conda activate NMFenv
### Input arguments ###
ARRAYID="`expr $1`"
# Identify where the expression matrices are stored
IN_PA... |
721de89894c71e7a38c1aa07e05c377c6428081d06aefef0dc32521ff7b8b1f8 | Shell | 973 | 21 | #!/usr/bin/env bash
set -euo pipefail
target="docs/README.md"
cp README.md $target
replaceTarget() {
# cross-platform for Linux and Mac, based off https://unix.stackexchange.com/a/381201/152866
sed -i.bak -e "$1" "$target" && rm $target.bak
}
# replace absolute links with relative links
replaceTarget 's/(https:\... |
4b566b541e50340f50bfd41f0446c2068858c51a082497034eb99f67933a5737 | Shell | 974 | 43 | #!/bin/bash
#SBATCH -A m2_jgu-funcpoll
#SBATCH -J run_repeat_modeler
#SBATCH -C skylake
#SBATCH -p parallel
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -t 72:00:00
#SBATCH -v
#SBATCH -o run_repeat_modeler.%j.out
#SBATCH -e run_repeat_modeler.%j.err
module purge
#module load bio/Flye/2.9.1-GCC-11.2.0
#source /home/tcolgan/met... |
3e0a07ddb714e772406df3b562d8c9e865694e98cac0ca86687654c63b42d701 | Shell | 975 | 37 | #!/usr/bin/env bash
set -euo pipefail
#############################################
# Run GenaLM fine-tuning job (multi-GPU)
# Usage:
# bash run_finetune_genalm.sh
# or for background run with log:
# nohup bash run_finetune_genalm.sh > finetune.log 2>&1 &
#############################################
# ==== ... |
f22b02ff1e77e048ac366e35d224018b12e3d5f03a6c15d8a02c8d5eda111f77 | Shell | 975 | 44 | #!/usr/bin/env bash
LEVEL=$1
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )";
cd ${DIR};
mkdir -p ../build/;
cd ../build/;
if [ -d "nglviewer.github.io" ]; then
cd ./nglviewer.github.io/;
git fetch --all;
git reset --hard origin/master;
cd ../
else
git clone "https://github.com/nglviewer/nglviewer.githu... |
70249038fa104a5e38f98a8ece7feb363d0674e35321e31954da3254e10c0617 | Shell | 977 | 17 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Example of built-in structural-conflict resolution.
# Four neurites grow straight apired into two planes. NeuroMaC
# does not allow inters... |
ae2896d5d8d873e8ce9904e1412661982988c185de1380347bbcc703eb3fbecc | Shell | 979 | 26 | #!/bin/sh
#####
# Example:
# $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG_diffusion_processing2022/AMICO/CBIG_DiffProc_runAMICO.sh \
# --subj_list /path/to/txtfile --dwi_dir /path/to/dwi_images \
# --output_dir /path/to/output --py_env name_of_AMICO_environment \
# --mask_output_dir /path/... |
223abd37836e5b9f862d26a38b4c7d01e5c5318b28fea90d6647ded57854c0d2 | Shell | 981 | 43 | #!/bin/bash
#SBATCH --job-name=dea
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=19cm51@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=
#SBATCH --error=
# Ti... |
55241cd86555eacd1974103c528ee8d26dae7063717cb6ed1fbdca71af3b92d1 | Shell | 981 | 23 | #!/bin/sh
#####
# This is a wrapper script to run reliability analysis for the split-half predictions in the HCP dataset.
# "BWA" refers to the univariate reliability analysis and "Haufe" refers to the multivariate reliability analysis.
#
# EXAMPLE:
# CBIG_ME_HCP_runReliability_wrapper.sh
#
# Written by Leon Ooi a... |
6166147e59c0f2261f93898eaa8aabf6cd63e4dc9ac0c93444dc0d1a49b76f32 | Shell | 981 | 43 | #!/bin/bash
#SBATCH --job-name=
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=
#SBTACH --error=
# Title... |
063c929d74c9cf9173f3e88ec5f961a1bda41621cbde73a70dae5ecec423ac69 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq6_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq6_2.out
#SBTACH -... |
249205b27d0347b914c2ff1d694b45d5abd339913792f687abf6ed365a6adaf3 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq4_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq4_1.out
#SBTACH -... |
281cc721fdb81b959ea3dd7527edd31a7c27d0b6bb3cca0c7b210cc2941b5228 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq7_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq7_2.out
#SBTACH -... |
4b1a340a0950f89b46197c3007100f8bdee4f7b11c4362e67aa89310de46d883 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq3_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq3_1.out
#SBTACH -... |
564c21ea7daf762fdceaa646a1b9f4c6b7679bd457eaef8bfbc1e9d488127b8d | Shell | 982 | 33 | #!/bin/bash
function svn_add(){
cd ../MLatom
svn add $1
cd -
}
function svn_del(){
cd ../MLatom
svn rm $1
# rm -r $1
cd -
}
export -f svn_add
export -f svn_del
for ver in `seq 460 479`; do
echo start submition: r$ver :
svn up -r $ver
cp -r * ../MLatom/
info=$(svn log --ve... |
66def201ed1f7444c14861e957dc7e788edd686452e0c714303ed906d09a21ee | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq3_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq3_2.out
#SBTACH -... |
6ba5231b490f8e7715fe6f3108fc36bdc33ed3911dfd4037af58268d27214d09 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq5_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq5_2.out
#SBTACH -... |
78755cecfe1f4062af2c98c71e3f2ec88dcbf1bd9ca632e8605e02ac17010e8d | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq4_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq4_2.out
#SBTACH -... |
d0764255c43ffa66c3af8cac8cf20b790c17926b1b769a4ec9607c1f97eb8e02 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq7_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq7_1.out
#SBTACH -... |
ef6fb448fba8ac09c16f8504f2f59f9bfa4ddc483d46ca4899b14247ca54f6af | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq6_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq6_1.out
#SBTACH -... |
ef72cb00d30e5cdcec12d33960a963017f244741b214f3c330ecaadb4c664b57 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq5_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq5_1.out
#SBTACH -... |
f5ca460ac3c3143d68c3bfaac225804f464f8081346db77b8d5425fcd40d98d1 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq8_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq8_2.out
#SBTACH -... |
ff01d91f250f6b1deb54305d29facb079b63f273e7a1bb2bfa0e2459a8ac7f33 | Shell | 982 | 31 | #!/bin/bash
#SBATCH --job-name=fq8_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq8_1.out
#SBTACH -... |
906b694ea8016a98e08e09b92b44c733c4f635ad34f6445d21f251a88ad20384 | Shell | 983 | 37 | #!/usr/bin/env bash
CABI_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
header_file_backup="$CABI_DIR/include/minijinja.h.backup"
function cleanup {
rm -rf "$WORK_DIR" || true
rm "$header_file_backup" || true
}
trap cleanup EXIT
WORK_DIR=$(mktemp -d)
cp "$CABI_DIR/include/minijinja.h" "$header_file_ba... |
2afdf0e5590d65457886b1435e97f0d7f64328bd23edf3eecd6c032f4b7be3b5 | Shell | 985 | 22 | #!/bin/bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); y... |
37f0460758ea7b30cfe89c2c42c69e12bd216b9ab97152b7153869111d55be23 | Shell | 985 | 23 | #!/usr/bin/env bash
# Run comp_pipeline_restructure with slugpy (read_cluster from SLUG2).
# Uses this project's .venv (has pyraf for 5-filter photometry). Set IRAF for full photometry.
# Requires: SLUG_DIR so slugpy finds lib/filters; PYTHONPATH so Python finds slugpy + cluster_pipeline.
set -e
ROOT="$(cd "$(dirname ... |
40b5d5dfa8d86c008fe3738958156546cedfe4f2fe15d5355a5416c7ea8e9a6f | Shell | 986 | 20 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="$CBIG_CODE_DIR/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
rep_data_dir="$C... |
084d997722d30b8bc074bc08789e97f4e8ad26f7cae8b97f31b9f111a1e2f58a | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq18_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq18_2.out
#SBTACH... |
2af0e4dc27f2c7d9a9fb9cd9c8a426d95ac698bec9ca684d32ce8a9d15e9e569 | Shell | 987 | 23 | #!/bin/sh
#####
# This is a wrapper script to run reliability analysis for the split-half predictions in the ABCD dataset.
# "BWA" refers to the univariate reliability analysis and "Haufe" refers to the multivariate reliability analysis.
#
# EXAMPLE:
# CBIG_ME_ABCD_runReliability_wrapper.sh
#
# Written by Leon Ooi... |
37ee5bea9a6344b81740fa64847745b2283860833a766c7b023bb05257df1c52 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq17_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq17_2.out
#SBTACH... |
5baaf748ba84e36cb554aa115c058f55b6fb7ebe6ffad82946a2f8acd073ee13 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq11_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq11_1.out
#SBTACH... |
68793114b9090caebee51890b1ff524a59d2de335c7066898621c4212abf852c | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq12_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq12_2.out
#SBTACH... |
8834201ff8ce5658229599c5b8d0e84c613bf1305e58e97d32eb3bf7dd864cb2 | Shell | 987 | 20 | #!/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 ${log_dir}
rep_data_dir="$... |
9ad409dcc784861dcbca1ce63af57f9fa83cba4ee34456edd3ad85ca8e621939 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq18_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq18_1.out
#SBTACH... |
9bd6508b6ce336726ec71a914af78cb114e479199eecf3aa47d058e9ad61e722 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq16_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq16_2.out
#SBTACH... |
9d32417ceb37450b873aae10fda35b1d67334af19ed465c3b1501a1f151ee32a | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq13_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq13_1.out
#SBTACH... |
b16a2538036c86d817cbf8d7f0e2abbe28c9ef0152c9f4e6a7919a433a37f2d6 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq17_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq17_1.out
#SBTACH... |
c6258d3771f35bab31182241e23c2195cd7425f75e45f8c4989d353f2073caa7 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq12_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq12_1.out
#SBTACH... |
d747bb4d6a0eda3ef66ef840e91b52ee7ff04d46ff43f0e74c6c1ab54e6a7927 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq13_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq13_2.out
#SBTACH... |
da1d299a72ea4a0681b0ccb41141c838c07831de3d9f5be55039727738f88182 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq11_2
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq11_2.out
#SBTACH... |
e374d3ac7d56c48a8dfe336d8df1ea40d1eda717a8ec5f9ea7cb51bec3524f15 | Shell | 987 | 31 | #!/bin/bash
#SBATCH --job-name=fq16_1
#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=10GB # Job memory request
#SBATCH --time=0-12:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=fq16_1.out
#SBTACH... |
40216c9b921d906a8831d285ac152abe3eec888f582bae0e6c2e19211294d667 | Shell | 988 | 31 | #!/usr/bin/env bash
# Starts a GCS cluster, runs scripts, then deletes the cluster.
# The cluster is only deleted if all the scripts run successfully, to allow for debugging.
# The cluster will automatically be deleted in any case after 3 hours.
if [ -z "$GCS_CLUSTER" ]; then
echo "Please set the GCS_CLUSTER enviro... |
71991232b7e64b67391cb0c4a6025982575edb6dbad9a25c76cb86d6102a1930 | Shell | 988 | 31 | #slurmjob
#!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=redo_do_kallisto_ipsc_npc
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir # TODO: set dir to cache dir
... |
f6611689009d9ffd9341bfa0f7f604a6ecd22e0b20a29a91d439567e0c368f8f | Shell | 988 | 24 | # -----------------------------------------------------------------
# Legacy exploratory analysis by a member of the Wilson Lab.
# Historical record only — not part of the bancpipeline release.
# -----------------------------------------------------------------
#!/bin/bash
#SBATCH -p short
#SBATCH -c 1 ... |
60632940885095ac2d5111a1b2b14b259aff43644a45d2f237658c9f73becdaf | Shell | 991 | 38 | #!/bin/bash
### This script runs NMF on each sample's malignant cells in the CAREmut dataset ###
# Activate the conda environment for running NMF, if not currently active.
module load miniconda
conda activate NMFenv
### Input arguments ###
ARRAYID="`expr $1`"
# Identify where the expression matrices are stored
IN_... |
f0cf027eb61ea636ce25d94d09e093355794841669910a7aa42989580e1a9362 | Shell | 991 | 38 | #!/bin/bash
# base name of the bench
# it reads $1.out
# and generates $1.pdf
WHAT=$1
bench=$2
header="rev "
while read line
do
if [ ! -z '$line' ]; then
header="$header \"$line\""
fi
done < $bench"_settings.txt"
echo $header > $WHAT.out.header
cat $WHAT.out >> $WHAT.out.header
echo "set title '$WHAT'" > ... |
ff005c1a089d62dc834a7c9e02e5241ea1c50dba207994ee1ebe64a5df6f0e8f | Shell | 991 | 36 | #!/bin/bash
#SBATCH --partition=xnat
#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_analysis/slurm-%A_%a.out
#SB... |
c6d91f602db5235db14810702b08e6c3b549a5b1b9199f4fd7b43b042791b53e | Shell | 992 | 23 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
mkdir $pd/data/neural_differentiation_dataset/cell_type_annotation_ref
cd $pd/data/neural_differentiation_dataset/cell_type_annotation_ref
# get barcodes, genes, count matrix and metadata from Rhodes et al. 2022
wget https://ftp.... |
9de5177b5977465b0e0d18d6b8c9d50a307700068f84215104371a6987eadb37 | Shell | 993 | 31 | #!/bin/bash
#SBATCH -p cpu
#SBATCH -N 1
#SBATCH -n 48
#SBATCH -t 124:00:00
#SBATCH --mem 20G
#SBATCH -o grow-agora.out
#SBATCH -e grow-agora.err
qiime micom build --i-abundance feature_table.qza \
--i-taxonomy classification.qza \
--i-models /agora201_gtdb207_genus_1.qza \
... |
c2035d5619d1f5937a3498ef0dec99d5b37b3e146e14be4e249deeeab94077b4 | Shell | 994 | 23 | #!/bin/bash
cd /lustre/atlas/proj-shared/nro101/BigNeuron/bigneuron_annotation_consolidated_20150715/gold166/
for foldername in `ls -d checked*`
do
echo $foldername
cd $foldername
# mkdir /lustre/atlas/proj-shared/nro101/BigNeuron/bigneuron_annotation_consolidated_20150715/gold166_ORNL/$foldername
for subfolder in ... |
fd1a3e01ebfa3f3b2be13e7c52b7e0960190c0065f73614930d5feadc39a1fcc | Shell | 995 | 44 | #!/bin/bash
set -e
# 项目配置
APP_NAME="gcta64"
BUILD_DIR="build/Release"
INSTALL_DIR="$BUILD_DIR/installed"
PACKAGE_DIR="${APP_NAME}-package"
EXECUTABLE_PATH="$INSTALL_DIR/usr/bin/$APP_NAME"
# 构建和安装
echo "[1/5] CMake 构建..."
cmake -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX="$INSTALL_DIR/usr" \
-B "$BUILD_DI... |
91b17e050800d83b2dcac36b43bf2960c26cfa3998ef68dfbab26dbb868a7af7 | Shell | 996 | 35 | #!/bin/bash
set -e
: "${SLOW_5_TOOLS_VERSION:=v1.3.0}"
: "${SLOW_5_LIB_VERSION:=v1.3.1}"
apt update
apt install -y libzstd-dev libhdf5-dev
wget "https://github.com/hasindu2008/slow5tools/releases/download/${SLOW_5_TOOLS_VERSION}/slow5tools-${SLOW_5_TOOLS_VERSION}-release.tar.gz"
tar xvf "slow5tools-${SLOW_5_TOOLS_V... |
33b7ac3cb163127881904cdd3d2944bd4a33c5e096690a339e403c8440cb88b6 | Shell | 997 | 24 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
mkdir -p $pd/data/neural_differentiation_dataset/mapping/hg38
mkdir -p $pd/data/neural_differentiation_dataset/mapping/gorGor6
mkdir -p $pd/data/neural_differentiation_dataset/mapping/macFas6
# map reads to all genomes using zU... |
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