sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
59b9c5c7b3a495234268aaa26f899c65e32bcaefebfd7e0193d1f5f928a71797 | Shell | 1,527 | 42 | #!/bin/bash -l
set -e
#cd in the directory of the script in order to use relative paths
script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P )
cd "$script_path"
WORKING_DIR=/home/runner/work/gatk/gatk
WDL_DIR=$WORKING_DIR/scripts/vcf_site_level_filtering_wdl
CROMWELL_TEST_DIR=$WORKING_DIR/scripts/vcf_site_level_fi... |
9fc91148e23b76c7870a53beadd1531fbdea859a1fd16b16af40febf070c2ba0 | Shell | 1,527 | 44 | #!/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
###########################################
# Usage
usage() { echo "
Usage: $0 -p <paramfile> -t <test_fold> -o... |
8d41a08087a4c36913d197b0919b27dfc9fa037a89fa76f40ddc5a8389dd05e4 | Shell | 1,529 | 42 | set -e
# Load conda environment
# ----------------------
#source /data/spurneyma/miniconda/etc/profile.d/conda.sh && conda activate lemon_preproc_py27_nipype
source /data/SFIMJGC_HCP7T/Apps/miniconda38/etc/profile.d/conda.sh && conda activate lemon_preproc_py27_nipype
# Load software needed by the pipeline available ... |
6ae527eab773b8daa34763ee0531a59e80612dc3027e18cdbc3bb497f62680ce | Shell | 1,530 | 43 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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.org/licenses/LICENSE-2.0
#
# Unless required by... |
e6ee2abd7886976bcf3e1e4cd126ccd0067ecfcb9e2eb1c1dfeab32e103fa059 | Shell | 1,532 | 41 | #!/bin/sh
#####
# This script calls the matlab function to run the univariate t-stats for KRR models.
# Specify the input directory with FC matrices, the output directory with the results,
# the version of the analysis that was run (either full or random), the number of minutes,
# sample size and index of the phenoty... |
1c897670f0e4974f6bf3cec6ac598783f7cd9748f3062fcfa049eb91b5b8a06f | Shell | 1,533 | 41 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 single subject unit test.
# Written by Xingyu Lyu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outdir=$1 # Your output directory
fmrinii_dir="$CBIG_TESTDATA_DIR/stable_projects/preprocessing"
fmrinii_di... |
58b8408b0c8c53fbf3b08f337a7db8914f6062afac14e08e1a0c038591355c8b | Shell | 1,535 | 24 | #!/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_Ooi2024_ME
# remove useless stable projects
rm -r Standalone_Ooi2024_ME/stable_projects/brain_parcellation/Kong2019_MSHBM
rm -r Standalone_Ooi2024_ME/stable_... |
7b54614935b25dbc39c8e8a2d7d0a718f9fffad1b5d34f75aa71a68a9c8a91ce | Shell | 1,535 | 40 | #!/usr/bin/env bash
#################################################################################################
## CCS SCRIPT TO PERFORM REHO COMPUTATION IN 3D VOLUME SPACE (INTEGRATE AFNI AND FSL)
##
## R-fMRI master: Xi-Nian Zuo. Feb. 18, 2015. at Institute of Psychology, CAS.
##
## Email: zuoxn@psych.ac.cn or... |
002af200e8305391cf85347baa1604e7a245aef7cdf7661e3e803627afdc4080 | Shell | 1,536 | 57 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=1
#PBS -N pseudo
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="bulk-seq"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
expo... |
7a56adddac2c735ec3a2283faa536d5f0822962f1287ca9ddd9287f4e426ccf3 | Shell | 1,536 | 34 | #!/bin/bash
set -e -u
echo -e "START: CreateDenseScalarASL"
Subject="$1"
ASLVariable="$2" #perfusion_calib"
ROIFolder="$3" #"${StudyFolder}/${Subject}/MNINonLinear/ROIs"
LowResMesh="$4" #"32"
RegName="$5" # MSMAll
GrayordinatesResolution="$6"
SmoothingFWHM="$7" #"2"
OutputAtlasDenseScalar="$8" #"${AtlasResultsFolde... |
11dc69e1ed2a5d2b8c31dcd40b0b521e9586afa6dd6fce678b28f3e0170694a9 | Shell | 1,539 | 30 | #!/bin/bash
# Download the macaque genome
cd /home2/gkonop/workdir/REFERENCES/FASTA_ONLY
wget https://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/bigZips/rheMac10.fa.gz
gunzip rheMac10.fa.gz
# Subset the small chromosomes (to test if the tool works)
cd /home2/gkonop/workdir/REFERENCES/TMP
/home2/gkonop/workdir/PROGR... |
f7f5e2a6c8402e5dccd6cc7f4a59f5019f445a9572089ac3aa521acba8d0f7a0 | Shell | 1,539 | 52 | #!/usr/bin/env bash
set -euo pipefail
# Parse command line arguments
BUILD_ARGS=""
while [[ $# -gt 0 ]]; do
case $1 in
--no-cache)
BUILD_ARGS="--no-cache"
shift
;;
*)
echo "Unknown option: $1"
echo "Usage: $0 [--no-cache]"
exit... |
5df54fee57a9155503e1d7db2202d3b119775198fe508abbfe8b0122f76089ba | Shell | 1,542 | 26 | #!/usr/bin/env bash
set -e
KNOWN_HOSTS_FILE=$(dirname "$0")/ssh_known_hosts
HEADER="# This file was automatically generated. DO NOT EDIT"
echo "$HEADER" > $KNOWN_HOSTS_FILE
ssh-keyscan github.com gitlab.com bitbucket.org ssh.dev.azure.com vs-ssh.visualstudio.com | sort -u >> $KNOWN_HOSTS_FILE
chmod 0644 $KNOWN_HOSTS_... |
77b12d1d6d66b34e3e5ab979d54053b9a91c55ac65bcd4cdb2ba6e085e50497d | Shell | 1,543 | 52 | #!/bin/sh
#
# This function check whether the input file is plumb and RPI orientation.
# If not, this function will deoblique the input file and change orientation to RPI.
# This check should always be applied to T1 before recon-all and fMRI before preprocessing.
#
# Example: CBIG_preproc_deoblique.sh -i input.nii.gz
#... |
94c84ab7e14da10ef98e5249c1ebffc37bf80a4780fa4280d646f3d3d50081da | Shell | 1,544 | 42 | #!/usr/bin/env bash
set -e
bcl=$(realpath $(which bcl.exe))
NTHREAD=12
FEATUREFILE='Atom1.object'
sdfs="$@"
if [[ $# -eq 0 ]]
then
echo "Usage: calc_descriptors.sh 1_combined.sdf [2_combined.sdf ...]"
fi
for sdf in $sdfs
do
parent_dir=$(dirname $(dirname $sdf))
out_dir=${parent_dir}/mol2d_atom1
mk... |
7829eed6c5aa22b8d27d3f037c6d40f44bb3f61035f66757ac43e47ce34947cc | Shell | 1,546 | 43 | #!/bin/bash
set -e
set -x
set -u
WORKDIR=${WORKDIR:-/work}
arr=$@
tmp_var=$( IFS=$' '; echo "${arr[*]}" )
example_id=${tmp_var//[^A-Za-z0-9_-]/_}
mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests ${WORKDIR}/crashfiles
echo "[logging]" > ${HOME}/.nipype/nipype.cfg
echo "workflow_level = D... |
28385629edee627113d85cf58f99150da1c25831e5604d43a4aa87c7df269347 | Shell | 1,547 | 39 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
908a33b3366ac5d267c81409ff9f7aadcb610dd55933141ceec0532d9c5ec68d | Shell | 1,547 | 42 | #!/bin/bash
# ANTs bimodal SyN warp CIT168 T1w and T2w head templates to MNI152 2009c nonlin asym T1w and T2w templates
#
# AUTHOR : Mike Tyszka
# PLACE : Caltech
# DATES : 2017-10-31 JMT Adapt from mirror_warp_calc.sh
# Key directories
cit_dir=./CIT168
mni_dir=./mni_icbm152_nlin_asym_09c
# Key files
cit_t1=${cit_d... |
9361cf4f5b4f07c2e811828cca6a6436de451220a0358f2b11502dcc7e7cc8a7 | Shell | 1,549 | 31 | python /mnt/d/Code/HeartModelling/s7_cleanScar.py \
--meshPath /mnt/d/Paper3/Models/invivo/mi/la/sample8/mesh_full_segmented.vtk \
--outPath /mnt/d/Paper3/Models/invivo/mi/la/sample8
python /mnt/d/Code/HeartModelling/s7_cleanScar.py \
--meshPath /mnt/d/Paper3/Models/invivo/mi/la/sample9/mesh_full_segmente... |
872201bde24b8951a330e246099f665fdfc090435e8dc79f13cb4f103f7467d6 | Shell | 1,550 | 52 | set -e
# Activating miniconda
echo "++ Activating miniconda"
if [ ${USER} == "javiergc" ]; then
echo " + User is javiergc";
echo " /data/SFIMJGC_HCP7T/Apps/miniconda38/etc/profile.d/conda.sh"
source /data/SFIMJGC_HCP7T/Apps/miniconda38/etc/profile.d/conda.sh
fi
if [ ${USER} == "spurneyma" ]; then
echo ... |
fff7a7d513c46e54d22352e97d40740bcc32635e8bd48366d3a6f829ccffa5a8 | Shell | 1,552 | 63 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_orca_from_mmff_finetune_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${... |
9c1518e69fe96f495fb8158fee61a84eafb57f10c2b0151568afa123cd16cd17 | Shell | 1,554 | 59 | #!/bin/bash
pd=/your/project/directory
input_dir=$pd/data/validations/ATAC_seq_BAM
output_dir=$pd/data/validations/ATAC_seq_coverage
mkdir -p "$output_dir"
for i in "$input_dir"/*.bam; do
sample_name=$(basename "$i" .bam)
if [[ "$sample_name" == *gorilla* && "$sample_name" != *_NCBI ]]; then
ncbi_b... |
fe339bbcad5727b4274612e17857259918096d86c2cf11ae67654cf3faffc0db | Shell | 1,555 | 63 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_mopac_from_mmff_finetune_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=$... |
2249cee5debf45b904d48171884356608096a889e7945801bd93e48cdf3dec6d | Shell | 1,556 | 63 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_orca_from_mmff_finetune_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${... |
063c96ba0ad14df492896eec9dce39b5ecb8fb0ea85b09bb0901b53de1c03cac | Shell | 1,557 | 61 | #!/usr/bin/env bash
set -euo pipefail
# Find unused images and videos under docs/ (basename matching).
# Exits with 1 if unused images are found.
#
# Requires: git, ripgrep (rg)
repo_root="$(git rev-parse --show-toplevel)"
cd "$repo_root"
if [[ -x "$repo_root/bin/rg" ]]; then
rg="$repo_root/bin/rg"
elif command -v... |
7b179fb565ed553bdffe691f9b119ac1ceaae8bbe3efd8782e414a34b28452e8 | Shell | 1,559 | 49 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/fs/wang_atlas_mapping-%A_%a.... |
d1b9a46fcde2e1d2bcb2b1ef10717b0d84ae98ad250b4aec88d3bdb0072e9a22 | Shell | 1,559 | 63 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_mopac_from_mmff_finetune_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=$... |
0ad8660d2aa183405642aff8242276355e74b8bfcd18b9fe61891aed003f257f | Shell | 1,561 | 40 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Tue Apr 28 2020 00:37:21 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
dbfe59e7af5a6298fbd8e00a126cc769b6961ad3990a73fae0283b1574df6c85 | Shell | 1,562 | 54 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Tue Apr 28 2020 00:37:21 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
3c66ccd8fb4fb71cc0aafe36a2f87007fb27af79af0e07e83cb4d4e49874c32f | Shell | 1,563 | 33 | #!/bin/bash
#SBATCH -p short
#SBATCH -t 0-1:00
#SBATCH -c 1
#SBATCH --mem=16G
#SBATCH -J banc_wb_dryrun_diff
#SBATCH -o data/scheduled_runs/wb_dryrun_diff_%j.out
#SBATCH -e data/scheduled_runs/wb_dryrun_diff_%j.err
###############################################################################
# Dry-run of banc-alignme... |
3b874592547108cd1ca18a791133b9160a6d70b0c1f836cd0af499c71d1e4741 | Shell | 1,565 | 67 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sepoffRF
#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... |
5ee996ed0b723e7aaa1018765bfb28b987d83307f328cc977bd4b19d54706565 | Shell | 1,567 | 41 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 motion correction unit test.
# Written by XUE Aihuiping and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outdir=$1 # Your output directory
fmrinii_dir="$CBIG_TESTDATA_DIR/stable_projects/preprocessing"
fmri... |
99c6f705732ad7e83fec3e5e57a953cf568abb32e5a72b8a9b32d8d491b6367a | Shell | 1,567 | 34 | #!/bin/bash
# Hi-Culfite script for making observed / expected matrices
# See README.md for more information
#Juicer tools, for running dump
juicer_tools=/aidenlab/juicebox
# Given a hic file that contains contacts divided by methylation status
# (via a simulated genome that repeats each chromosome; this allows us
#... |
b11675d0f0d1ee362d2318e70eaf06e1cfd2c15b1d4113a19bb12bf22e81c9c0 | Shell | 1,570 | 45 | #!/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"); yo... |
0781889a893d040bde759ecc9ebd19a9ea42e5b7d74e2b76bfc0182e9be7985d | Shell | 1,572 | 43 | #!/bin/bash
# A task for run merge of BGEN liftover chunks. This will also create index
# files for bgenix and bgen-reader (simple and complex). This expects the job
# array file to have the following columns IN THIS ORDER:
# 1. rowidx - sequential row index number, required by every job array file
# 2. infile - This ... |
f630c8bd308d5c11e828f3abc3bdd60370a6b42cde62944838dff884293df38a | Shell | 1,574 | 42 | #!/bin/sh
#####
# This script calls the matlab function to run the univariate t-stats for KRR models.
# Specify the input directory with FC matrices, the output directory with the results,
# the version of the analysis that was run (either full or random), the number of minutes,
# sample size and index of the phenoty... |
cd350c7620ed4e45b5072bf6c755be65c871f35fcbb331f6d7bc0181083759a3 | Shell | 1,577 | 54 | #!/usr/bin/env bash
set -euo pipefail
: "${X_NPY:?Need X_NPY}"
: "${META_NPZ:?Need META_NPZ}"
: "${LABEL_KEY:?Need LABEL_KEY}"
: "${GROUP_KEY:?Need GROUP_KEY}"
: "${POOL_ROOT:?Need POOL_ROOT}"
: "${SCARCITY:?Need SCARCITY}"
: "${OUT_DIR:?Need OUT_DIR}"
mkdir -p "$OUT_DIR"
for seed in 0 1 2 3 4; do
for fold in 0 1 ... |
2433a3890e684a74a905f8914c81d8cd56578b0c3fcdc187e2dfebcfb888a77e | Shell | 1,580 | 48 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
aa29e2fc864ca0c61aefcbd9a96b243cadc1681b19c41fd0dbd8b697f393600b | Shell | 1,580 | 48 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
e3701963f09054c86c06032bfca97715e22f1da184531c3b5a4d219d06c0ecca | Shell | 1,584 | 48 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
f05ed5193f6defca61a056a788113c62c3c5cb8eed3d86a8ace3ca5b4161b221 | Shell | 1,585 | 13 | #!/bin/sh
wget https://github.com/JingyunLiang/SwinIR/releases/download/v0.0/003_realSR_BSRGAN_DFO_s64w8_SwinIR-M_x4_GAN.pth -P experiments/pretrained_models
wget https://github.com/JingyunLiang/SwinIR/releases/download/v0.0/004_grayDN_DFWB_s128w8_SwinIR-M_noise15.pth -P experiments/pretrained_models
wget https://gith... |
f80d29bdd310278bfc6bd02836b19cf06472c7b2876f7af5cf4a2174ca732577 | Shell | 1,588 | 55 | #!/bin/bash
#PBS -P jh2
#PBS -q expresssr
#PBS -l walltime=24:00:00
#PBS -l ncpus=104
#PBS -l mem=500GB
#PBS -l jobfs=400GB
#PBS -l wd
#PBS -N comp_pipeline_photo
#PBS -j oe
#PBS -m bea
#PBS -l storage=scratch/jh2+gdata/jh2+scratch/mk27
#PBS -M janet.tang@anu.edu.au
#PBS -o /scratch/jh2/jt4478/output/comp_pipeline.o
#P... |
602a4447a5015a3b0df095a995db38c218bd2e997fa65b940ed75ac41afcc79c | Shell | 1,589 | 46 | #!/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"); yo... |
70451d24729d00051af5c7b715c244631cc655a69c8fd880c314f7137a46e0fe | Shell | 1,589 | 44 | if [ -n "$GCS_CLUSTER" ]; then
HDFS_HOST_PORT="${GCS_CLUSTER}-m:8020"
else
# leave empty and pick up from local Hadoop configuration
HDFS_HOST_PORT=""
fi
time_gatk() {
GATK_ARGS=$1
NUM_EXECUTORS=$2
EXECUTOR_CORES=$3
EXECUTOR_MEMORY=$4
DRIVER_MEMORY=$5
if [ -n "$GCS_CLUSTER" ]; then
SPARK_RUNNER_A... |
80acf4989a5c3123dd7a7d030efa858fa7cf09b38c0823b212196254aa9dfce5 | Shell | 1,590 | 60 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
SRCP_DIR=src
RUN_MODE_1=diverse_conf
RUN_MODE_2=sanity_check_for_raw_data
RUN_MODE_3=extract_by_index
RUN_MOD... |
23e33b3b76b582e7924771cb1b3e5f2f4e371b78a9285d1e308ecb9c606af0b4 | Shell | 1,592 | 42 | #!/bin/bash
set -eu
if [[ "$#" -ne 6 ]]; then
echo -e "Please provide:"
echo -e " [1] local directory of GATK build (required)"
echo -e " [2] cluster name (required)"
echo -e " [3] absolute path to the output directory on the cluster (required)"
echo -e " [4] absolute path to the BAM on the cl... |
6db1eb87dd9d68ef7ce7692cce63bd36a228a0488984df6ef90a294f8018aa46 | Shell | 1,592 | 59 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step1.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_block_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/family 7
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export working_dir=$1
export family_dir=$2
export km... |
a46fcab672dc83ae73265042c217d0312a065d47560710026fd1a4197340078f | Shell | 1,595 | 58 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
771314610acaec196638ce81879469b7039f022eff12ce8d6d51bba3834c3403 | Shell | 1,596 | 35 | ### assumes you have the $fsav subject in your exampledir, might be changed when we use freesurfer 5
#!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#wb=/data/users/aschaefer/src/workbench_centos/workbench/bin_rh_linux64/wb_command
workingDir=${1}
segment_na... |
663dfcaefcec4b39799de68b7e025d0369cf1e403eb640827e65c5cb7daf8f27 | Shell | 1,597 | 55 | #!/usr/bin/env bash
# This script contains utility functions and initialize exmaple scripts.
# Eg: run_python_examples.sh, run_distributed_examples.sh
BASE_DIR="$(pwd)/$(dirname $0)"
EXAMPLES=$(echo $1 | sed -e 's/ //g')
# Redirect 'python' calls to 'python3'
python() {
command python3 "$@"
}
ERRORS=${ERRORS-""}... |
164692079927b2cdc7616db8d83aa6aee1c1cdb603877f67d40e4f1cb6f26756 | Shell | 1,599 | 57 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download COCO 2017 dataset http://cocodataset.org
# Example usage: bash data/scripts/get_coco.sh
# parent
# ├── yolov5
# └── datasets
# └── coco ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_coco.sh --train -... |
aa978d8f488984346c9dfbe37fd74a08299f2a275d48d349e927085e6323351d | Shell | 1,600 | 48 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -o job_$JOB_NAME.$JOB_ID.out
#$ -l h_rt=1:00:00,h_data=64G
#$ -pe shared 1
# --- Script Arguments ---
# The first argument to this script will be the Python script to run.
PYTHON_SCRIPT_TO_RUN="$1"
# Check if a Python script name was provided
if [ -z "$PYTHON_SCRIPT_TO_RUN" ]; then
ec... |
cac2054aae5687ffcb4dc1b6c06ccb2d66e7d1c7bf9f0e163f6e3ac3d16d7b51 | Shell | 1,601 | 55 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --job-name=strngtie
#SBATCH --error=log_stringtie_error_%A_%a.txt
#SBATCH --output=log_stringtie_output_%A_%a.txt
#SBATCH --array=0-22
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname... |
0bef10df1d63d265a732a11f42f69cce715d5160c1ee81de19bc2bbad61e4f0e | Shell | 1,608 | 58 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=1:00:00
#SBATCH --job-name=shi_mvpa_agg
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=16G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
# Arguments from task launcher:
# $1 = subject (e.g., sub-01)
# $2 = n_permut... |
061fa2a04a8dc293086befc84f56a8841add7a74b018151f5d855c902afdb548 | Shell | 1,613 | 41 | #!/bin/bash
# get MM2 home
MM2_HOME=$1
EMU_VERSION="1.1"
if ! [ -d "$MM2_HOME" ]; then
echo "[$MM2_HOME] is not a directory."
else
# tests if mvn is installed
command -v mvn >/dev/null 2>&1 || { echo >&2 "Failed to call mvn, are you sure Maven is installed?";}
# tests if the Micro-Manager jars are present and... |
928038d23c8142cdff5a52474fe97df8b96b628a2a6cc2d2ca41b52de4b18bcd | Shell | 1,613 | 41 | #!/bin/bash
# get MM2 home
MM2_HOME=$1
EMU_VERSION="1.1"
if ! [ -d "$MM2_HOME" ]; then
echo "[$MM2_HOME] is not a directory."
else
# tests if mvn is installed
command -v mvn >/dev/null 2>&1 || { echo >&2 "Failed to call mvn, are you sure Maven is installed?";}
# tests if the Micro-Manager jars are present and... |
f1b5067535129bc79422cbb6740321b8be8c49f3a4e4af0adcc68bcb0a664ad7 | Shell | 1,614 | 60 | #!/bin/bash -l
#PBS -N cde_extract
#PBS -q debug
#PBS -A SolarWindowsADSP
#PBS -l filesystems=home:grand:eagle
#PBS -l nodes=2
#PBS -l walltime=00:60:00
module use /soft/modulefiles
module load conda
module load nvhpc-mixed
module load craype-accel-nvidia80
conda activate
source /grand/SolarWindowsADSP/dingyun/venvs/c... |
5545d47be2e7d5e9b5486068045390b81d8c03edf19436b27a4303cdef3f2015 | Shell | 1,615 | 43 | #!/bin/sh
#####
# This script calls the matlab function to run the Haufe inversion for KRR models.
# Specify the input directory with FC matrices, the output directory with the results,
# the version of the analysis that was run (either full or random), the number of minutes,
# sample size, type of regression and ind... |
e102d7cde05e1decd8f00d37ec276a3749f03e0f16ceef90fe4480e4175d3de7 | Shell | 1,616 | 38 | #!/usr/bin/env bash
set -euo pipefail
repo_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cleanup_sql="${repo_root}/sql/cleanup_sofa_gov_20260619_intermediates.sql"
test -f "${cleanup_sql}"
rg -F "I_APPROVE_SOFA_GOV_20260619_INTERMEDIATE_CLEANUP" "${cleanup_sql}" >/dev/null
rg -F "set_config('app.confirm_cl... |
f003b979c4af7446398c5002f472fe79cef7a0f53a17278315006ef0b3c4447b | Shell | 1,616 | 37 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
45538bf2544df0824731a76d41b4633174d31fb58ea7f1ed691cf6443d036d38 | Shell | 1,618 | 54 | #!/bin/bash
#conda activate ldsc
indir=outMarkerP_LDscore
outdir=outMarkerP_h2
path_ldsc=ldsc
path_data=ldsc/data
path_resource=ldsc_ph/resources
path_gwas=resources/GWAS
BASELINE_1000G=$path_resource/1000G_EUR_Phase3_baseline/baseline.
WEIGHTS_BASE=$path_resource/weights_hm3_no_hla/weights.
FREQ_BASE=$path_resource... |
86233fd7886504e8334db6019e269a40fd0be438681a274498e79704f47e50f1 | Shell | 1,618 | 54 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Tue Apr 28 2020 00:37:21 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
6aebb7402ebac0f23a99f3da7d2507b2c21f74615c6dd1cc1e3668151ca404d4 | Shell | 1,619 | 43 | #!/bin/sh
#####
# This script calls the matlab function to run the Haufe inversion for KRR models.
# Specify the input directory with FC matrices, the output directory with the results,
# the version of the analysis that was run (either full or random), the number of minutes,
# sample size, type of regression and ind... |
059b3a0bc3a67c58e1315f50444a727eeb2e093f5aebda85aa93ba578d017ba5 | Shell | 1,622 | 48 | #!/usr/bin/env 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 "Licens... |
526e4cb0db0bc304e19f3d75acb69f2ab54e321414f7a2766fbc759812ce01ae | Shell | 1,624 | 46 | jupyter nbconvert Train.ipynb --to python
jupyter nbconvert recon_inference_mi.ipynb --to python
jupyter nbconvert final_evaluations_mi_multi.ipynb --to python
jupyter nbconvert plots_across_subjects.ipynb --to python
jupyter nbconvert plots_across_methods.ipynb --to python
export CUDA_VISIBLE_DEVICES="0"
for subj in ... |
e4797db7a9f803268c650a436adfd404063e62aa0d4965ef4e8eb6ecdba325ab | Shell | 1,624 | 54 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# aranges them in the CHANGELOG txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage:
#
# $ /bin/bash update_changes.sh v0.0.1
#
# Originally authored by @oesteban (github.com/oesteban) for fmriprep, licensed
# unde... |
2746f0d23d05664fe4de36f2f349d024ecd052e79e3578a3629a7bc5f2e8b44d | Shell | 1,625 | 46 | jupyter nbconvert Train.ipynb --to python
jupyter nbconvert recon_inference_mi.ipynb --to python
jupyter nbconvert final_evaluations_mi_multi.ipynb --to python
jupyter nbconvert plots_across_subjects.ipynb --to python
jupyter nbconvert plots_across_methods.ipynb --to python
export CUDA_VISIBLE_DEVICES="1"
for subj in ... |
2929c7020f142d2d76e6acececb4ccc48480c39c72e33b8d1075e9d74c103815 | Shell | 1,625 | 51 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psy... |
a8b32dea79dc96ebf059e6be3fa61d9b71822c496539a1ef2bc804f16b802fbb | Shell | 1,626 | 26 | #!/bin/bash
## Creating hic file for use in methylation analysis
## In this example done for only one chromosome
## MethylDackel looks only at CpGs
MethylDackel perRead -o chr14_perRead -@ 4 /aidenlab/references/Homo_sapiens_assembly19.fasta chr14.bam
## Must gather the reads since read names are printed more than o... |
9b6d3fcc7a4223c8a20861e50b937162925216545031da548a713cec7967c2af | Shell | 1,627 | 85 | #!/bin/sh
auditprogpath=`dirname $0`
pid=$1
auditdir=$2
tmpdir=$auditdir/$pid
tardir=$auditdir/TAR
if [ ! -d $tmpdir ] ; then
echo "$0: tmpdir:$tmpdir does not exist"
exit 1
fi
datefile=$tmpdir/datefile
date > $tmpdir/datefile
commandfile=$tmpdir/commands
xopenlist=$tmpdir/xopens
diffile=$tmpdir/diffile
savefile=$... |
2a6b7d0be4b3be38de004254a8f85e332d5d631a99aeff53979839f2958fd694 | Shell | 1,628 | 46 | #!/bin/bash
# This script runs CBIG_fMRI_Preproc2016 single subject unit test within a Docker container.
# ! Warning: Since Docker is not installed on the compute nodes, this unit test runs directly on the compiler.
# ! Therefore, please choose a time when the compiler is not busy to run this unit test.
#
# Wr... |
a5b172568929bfe7a58dd16308dd45deefd02b9e2b656d3edae164d297a5a07e | Shell | 1,629 | 39 | # Moderate effect size genes project
# Author: Madison Caballero
# Desription: A set of steps to annotate and extract variants in the non-neuro cohorts.
# These steps were used for 1kGP, BioMe, and All of Us
# For speed, I just extract one sample. This keeps all loci even if 0/0
bcftools view --threads 4 -s [random_sa... |
dea4a049be7b9030bd16d999459a3e3b0bf0a14a4311470465f8050610e78176 | Shell | 1,630 | 51 | #!/usr/bin/env bash
# Manual deploy from your laptop to the EC2 app host.
# Use this until the OIDC + GitHub Actions deploy role exist and
# .github/workflows/deploy.yml can run.
#
# Prereqs:
# - publish-images.yml has finished pushing sha-<commit> tags to GHCR
# (it uses GITHUB_TOKEN; no AWS needed, runs on ever... |
c63a210a8469ecc53298a1438c931c66da33812be007592bad165f5f528a4b93 | Shell | 1,634 | 38 | # to call from root
# clean up
rm docs/source/sonata-network.rst
rm -rf docs/source/sonata-network_files
rm docs/source/nmc-portal.rst
rm -rf docs/source/L5TTPC2_files
rm docs/source/load_nwb.rst
rm -rf docs/source/load_nwb_files
rm docs/source/extrafeats_example.rst
rm docs/source/multiprocessing_example.rst
rm docs/... |
38af3ecc93c3536c76cbe1b75fe8073e25c881e95b9cc89e37e7824117ca136c | Shell | 1,635 | 52 | #!/bin/bash
# A query to get the regulatory statistics for regualory features in a gene
# flank
GENE="$1"
FLANK="${2:-1000000}"
CORE_DB="homo_sapiens_core_95_37"
FUNCGEN_DB="homo_sapiens_funcgen_95_37"
mysql -u"anonymous" --host ensembldb.ensembl.org --port 3337 <<EOF
select rf.regulatory_build_id,
ra.regulatory_a... |
0edf9343789e875343fb597aeaf207a648e00853076f8c63313359714acd130c | Shell | 1,638 | 48 | jupyter nbconvert Train.ipynb --to python
jupyter nbconvert recon_inference_mi.ipynb --to python
jupyter nbconvert final_evaluations_mi_multi.ipynb --to python
jupyter nbconvert plots_across_subjects.ipynb --to python
jupyter nbconvert plots_across_methods.ipynb --to python
export CUDA_VISIBLE_DEVICES="2"
for subj in ... |
19da5cc7d6a47d5b0a69def54adeb549676269c3d0e29573877832fdf3557e68 | Shell | 1,638 | 55 | #!/bin/tcsh
set ANTSPATH=$argv[1]
set targetnii = $argv[2]
set patidnii = $argv[3]
set patid = reg_out
set tmpPath = $argv[4]
@ coregtype= $argv[5]
set ANTS = ${ANTSPATH}/antsRegistration
set WARP = ${ANTSPATH}/antsApplyTransforms
######## compute warping maps
set cmd0="${ANTS} -d 3 --float 1 --verbose 1 -u 1 ... |
807f8fcd7adca45333e0ab653118d2711cfb1c43a32c664c220bb42b598dcaed | Shell | 1,638 | 62 | #!/bin/bash
set -e
set -x
MPI_LIB_NAME="$1"
case "$TRAVIS_OS_NAME" in
osx)
brew cask uninstall oclint
brew update > /dev/null
brew install flex bison modules
brew upgrade python3
# NOTE: brew installed python3 on OSX has known issue
# See https://stackoverflow.com... |
20951e3056123cde983b7b85f0286116fe944e052ed0ea679323e3557d2a9874 | Shell | 1,639 | 48 | jupyter nbconvert Train.ipynb --to python
jupyter nbconvert recon_inference_mi.ipynb --to python
jupyter nbconvert final_evaluations_mi_multi.ipynb --to python
jupyter nbconvert plots_across_subjects.ipynb --to python
jupyter nbconvert plots_across_methods.ipynb --to python
export CUDA_VISIBLE_DEVICES="3"
for subj in ... |
d7a3bc991901e57b51fb28acd9b1d657d78bc57dd4d272fafb179fcf425b9170 | Shell | 1,641 | 40 | #!/bin/bash
#####
# This script estimates the fibre orientation directions and generates the tractogram.
#
# Written by Leon Ooi and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
###############
# set up environment
###############
sub=$1
sub_outdir=$2
diff_dir=$3
algo=$4
ma... |
1464b85259d453693973f3e544bc0ca096a96ddf83501546955a411940638330 | Shell | 1,646 | 56 | #!/bin/bash
# A query to get the regulatory statistics for regualory features in a gene
# flank
GENE="$1"
FLANK="${2:-1000000}"
CORE_DB="homo_sapiens_core_95_37"
FUNCGEN_DB="homo_sapiens_funcgen_95_37"
# mysql -u"anonymous" --host ensembldb.ensembl.org --port 3337 <<EOF
# SELECT count(*) FROM ${FUNCGEN_DB}.peak_calli... |
fbb926e96b5dee6bcbbc64788985814b8f8fb1e03f0316eece38593e8d2c0e44 | Shell | 1,647 | 46 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step3.sh /media/StorageOne/HTS/PublicData/nt_pb/ffp_7_final /media/StorageOne/HTS/PublicData/nt_pb/virus_genomes_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/ssDNA_clean_list.txt /media/StorageOne/HTS/PublicData/nt_pb/VIR_unique_taxa_1000.txt
export path_htsa_dir=/me... |
d917e501714dbde932454ecc098199fdb62e5887a281c4b6bd4de291bfb6c03d | Shell | 1,648 | 70 | #!/bin/bash
set -e
# Deployment script for our sphinx/doxygen/breathe documentation
#
# Expectations:
# - Called from the MIES repository (full clone)
# - The boundary commit on the gh-pages branch exists. This commit separates
# the commits we can throw away (old documentation) from the ones we want to keep
# (s... |
b764794a22e6b852c0ac72f442d3a4ef8eacfa58c1d7b5a77f72d61dcaf33d21 | Shell | 1,649 | 41 | #!/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... |
9048788cd60890733a33552fe5de53b9fd3fb35638e0eac60901efa5dc307c2d | Shell | 1,651 | 57 | #!/bin/sh
#Last-modified: 29 Jan 2020 11:02:25 AM
####################### Module/Scripts Description ######################
#
# Copyright (c) 2020 Yunfei Wang <tszn1984@gmail.com>
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the BSD License (see the file COPYING ... |
f52efa347c4f9f1cbf299c3020ac261fac8d840989f49403f7b3c7031fa01b96 | Shell | 1,652 | 47 | #!/bin/bash
if [ $# -eq 0 ]; then
echo "Usage: $0 START_DATE (format: YEAR-MM-DD) END_DATE [LABEL] [BRANCH1,BRANCH2] [LIMIT]"
exit 1
fi
START_DATE="$1"
END_DATE="$2"
if [ -z "$3" ] || [ "$3" = "all" ]; then
LABELS=("core" "extractors" "preprocessing" "sorters" "postprocessing" "metrics" "curation" "widget... |
a1898110c0bffe24f2dbabd83d3a031945073ab0a02f51a69af6b4e00013bc91 | Shell | 1,656 | 45 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step2.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_species_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/virus_block_ffp_7 species
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step3.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_genomes_ffp_7 /media/StorageOne/HTS/Pub... |
d0a391b841320d08ae149551b65a41ca272fb1722417a0ac9faedd27b0f1cb57 | Shell | 1,656 | 55 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2013-12-13 #
#compares sequences to custum viral databases #
###################################################################
#sudo /media/storage/HTS/VirusMeta... |
41603da9e20b109d2e6f6a4c4e95a2d00c1e273f3531319b8cd9a2734d9f6f5d | Shell | 1,661 | 51 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
9f75e70efac46d08ce7c45f1e26aa56ca1e5eb7114c631c8411e6411b92c20c7 | Shell | 1,661 | 51 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
ca6eb34ec19b53b51f347533dadf464fe9c857c90e15f058abf3204ba68a7582 | Shell | 1,661 | 51 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
4607dfc190d672d6285782a4801b469bf8f8a174b0a2b9e8120c1fa7f04ef8ee | Shell | 1,663 | 47 | #!/bin/bash
# generate_scaffold_beds.sh
# Generates BED files from scaffold .fai index files for both assemblies.
# Optionally filters to only chromosome-scale scaffolds above a size threshold.
#
# Usage: bash generate_scaffold_beds.sh [min_length_bp]
# min_length_bp: optional minimum scaffold length to include (def... |
abc3e71da8e604eec5db93f9a4ad0abf5629916532a38b27e79dc05fe95f5f3a | Shell | 1,671 | 54 | #!/bin/bash
set -eux
# get the directory of the script
script_dir=$(realpath "$(dirname "${0}")")
# define required package
REQUIRED_PKG="singularity"
# check if singularity is already installed
if [ -n "$(which $REQUIRED_PKG)" ]; then
echo "$REQUIRED_PKG already installed"
else
# if not, install singularity an... |
a86fa8e184ac2a9743fd37cc00d3ee8256fe814d2999ed19f337d2e7b7d5e064 | Shell | 1,672 | 42 | #!/usr/bin/env bash
# This script trains the PRISM dataset in the random split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5; do
python train.py \
--gpu 0 \
--dataset_dir "data/PRISM" \
--num_workers 4 \
--dataset_name PRISM \
... |
f96fa8ca4bcc334c122b23f996543342052605ea02ac508f1fc1022ddc2a1efe | Shell | 1,675 | 25 | #!/bin/bash
#SBATCH -N 1 # Number of nodes. You must always set -N 1 unless you receive special instruction from the system admin
#SBATCH -n 48 # Number of CPUs. Equivalent to the -pe whole_nodes 1 option in SGE
#SBATCH --mail-type=END # Type of email notification- BE... |
23daac6512993795672a72a93e2a02212cee9933461e4edac428756345830804 | Shell | 1,677 | 54 | #!/bin/bash
# ------------------------------------------------------------------------------
# LDSC Summary Statistics Munging Script
# Description: Formats GWAS summary stats for LD Score Regression (LDSC)
# ------------------------------------------------------------------------------
# PBS Configuration
#PBS... |
9c64892e4640c41be9fbeb1fa3119306372910eb3bc55f9c035d8e7ec5a80754 | Shell | 1,681 | 56 | #!/usr/bin/env 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 "Licens... |
0a7b4f29961815b3bcddbe640a268fcc5cf282a76dfc3671a52984cfcf38673c | Shell | 1,685 | 43 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=gnomad_CNV
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/iPSC_corrine/CNV/src
#SBATCH -o logs/4_intracohort... |
69c38c93e8838603491b56341bc4dde9a997221821e1dcd5e15d3f329967c3d7 | Shell | 1,685 | 44 | #!/usr/bin/env bash
# This script trains the GDSC dataset in the random split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5; do
python train.py \
--gpu 0 \
--dataset_dir "data/GDSC" \
--num_workers 4 \
--dataset_name GDSC \
... |
bec0e11008f12d62f96b34974233556135416aa03c347b06d252e676e0268bf3 | Shell | 1,685 | 52 | #!/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:/... |
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