sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b19932cdf832dc716bd1c0e71f4d0668ef4a5c620e515e397ee7213bc9357b7a | Shell | 1,451 | 39 | #!/bin/bash
parse_cost_args() {
local -n cost_stay_ref=$1 # Reference to cost_stay variable
local -n cost_switch_ref=$2 # Reference to cost_switch variable
while [[ $# -gt 2 ]]; do # Skip first two args (they're the reference names)
case ${3} in
--cost)
cost_stay... |
92eaefc38e7245c51e587921e13845f7b7275a26ac9e42838f4b950712c17b77 | Shell | 1,452 | 33 | #!/bin/bash
umask u+rw,g+rw # give group read/write permissions to all new files
## GENERAL SETTINGS
main=/your_path/ # to data directory
main_root=/your_path/ #to output directory if different
morf_dir=/path_to_mmorf/ #input path to where you have downloaded mmorf
script_dir=$main/scripts/Template #or change to your... |
dd15713f346e72401f6325e477ec1fae268ef7f008314eab53547e61cd09a048 | Shell | 1,453 | 62 | #!/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 ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/refe... |
94140e5a6ef3e80cc43614485e0842511a1d3656fcffeb73b53916cb9fd59975 | Shell | 1,454 | 45 | #!/bin/bash
# =============================================================================
# STARsolo CLI — installer
# =============================================================================
# Adds the starsolo command to your PATH by symlinking into a bin directory.
#
# Usage:
# ./install.sh ... |
3550a2b3637d8d117eff416552e3f9d5bb553d27a0da3fd899b9988f30ba6d6d | Shell | 1,456 | 46 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sepoffRC
#SBATCH --array=0-1
#SBATCH --error=joblog_error_%A_%a.txt
#SBATCH --output=joblog_output_%A_%a.txt
path_biotools="/gpfs/scic/software/biotools"
path_subread="${pat... |
648f273f6c5fe32b90214963b634a257556ac4a25ae9f85fac2b0b4830b1259b | Shell | 1,456 | 54 | #!/bin/bash
if (( $# == 0 ))
then
echo "USAGE: ./cleanup_wget_downloads.sh <URLs.list>"
echo "Please provide the list of URLs used for original download!"
exit 1
fi
URLS=$1
KK=`cat $URLS`
AC=0
DC=0
if [[ -d done_wget ]]
then
echo "Found directory named 'done_wget', will use it to move completed downloads!"
... |
05599ba7c13b8b1923db49199b7ffa9ca0d2961b2a2f161b6a04f1ed4aecdb96 | Shell | 1,458 | 41 | #!/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: $0 -p <paramfile> -t <test_fold> -o... |
32b35180899033223a3f1c3cd21b2a807d73143adedda4db1126a20f08470d71 | Shell | 1,461 | 50 | #!/bin/bash
#SBATCH --job-name=indexGenHisat2
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=10
#SBATCH --mem=400GB # Job memory request
#SBATCH --time=0-10:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=indexGen... |
bf42b913751b2eaca3caac9d104837d22bb20dd29817aec342ba091687cf3941 | Shell | 1,461 | 47 | # ---- PRELIM: Set all variables up front for easy copying/editing ----
export PETSC_VERSION=3.23.4
export SLEPC_VERSION=3.23.2
export PETSC_SRC=$HOME/petsc-$PETSC_VERSION-src
export PETSC_INSTALL=$HOME/petsc-$PETSC_VERSION
export SLEPC_SRC=$HOME/slepc-$SLEPC_VERSION-src
export SLEPC_INSTALL=$HOME/slepc-$SLEPC_VERSION
... |
750c0707bcf93a02044e127d72152a6406a3f67d237d7ad669201079cb881aba | Shell | 1,463 | 58 | #!/bin/bash
# search_repo.sh - Search codebase with best available tool
#
# Usage: ./scripts/search_repo.sh <pattern> [path] [options]
#
# Examples:
# ./scripts/search_repo.sh "TODO"
# ./scripts/search_repo.sh "function.*login" src/
# ./scripts/search_repo.sh "error" --type ts
set -e
PATTERN="${1:-}"
SEARCH_PAT... |
22f04e643c68021839504a15c90f7feb36061b92ff0991c62f02bee493850a4b | Shell | 1,465 | 29 | #!/bin/bash
input_path=$1
output_path=$2
mkdir -p "$output_path"
temp_dir="${output_path}/tmp"
mkdir -p "$temp_dir"
# specific options (-c zstd -s svb-zd) must be provided to slow5tools to create compression comparable to vbz
# also number of processes/threads must be set to 10 to match with default value in pod5_c... |
ef2050dca0385e99cb23357574e1aed97451d863ac8678e19d26ea3980d9b1e6 | Shell | 1,466 | 36 | #!/usr/bin/env bash
# App host bootstrap. Runs once on first boot via cloud-init.
# Templated by Terraform — variables ${git_repo}, ${git_ref}, ${db_private_ip}.
set -euxo pipefail
exec > >(tee /var/log/user-data.log) 2>&1
# --- Docker + Compose -------------------------------------------------------
dnf install -y do... |
f7844f941989eaa4c78be18290bfdbf79fa2c2c04954fe3c13127fd987442577 | Shell | 1,468 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_mca_rmsd_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/... |
2e03829fff908d4f6d3b363754d74a9a00aa3f82cae9b159b8a5e04b83f3f438 | Shell | 1,471 | 47 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=2
#PBS -N macs2
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}
expor... |
3220bde7aa724c04fe22c87ee785188f4e845f7c8af6e8a36c9f3c963a957b10 | Shell | 1,471 | 62 | #!/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 ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_mca_gth_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/r... |
3fe1baa95f14ed78aa354e25258e6a9cc02fd0d5049633cce8cfad81356742f6 | Shell | 1,471 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_orca_from_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}... |
25965e6acd37c20bc8fcff57a5ce20bd1cf4ecd5f0e331e9ebf1894522e30950 | Shell | 1,472 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_maa_rmsd_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/... |
a252234feae98634f02d9603885c6b87a5dfcd01709b6fbfbdd5225e28380206 | Shell | 1,474 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_mopac_from_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT... |
1de79203b9fa012f34e5f7ff6969627b44e172b55b9c6ff67523b97c9d79da78 | Shell | 1,475 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_maa_gth_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/r... |
74587de37c21d75afb22e7f44b72d2451964b49936d391d1829c5c078f55fb5d | Shell | 1,475 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_orca_from_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}... |
9abaef72bba27a307f3ef906bd42511268cab3af25bd2554c2cb7f9623d89543 | Shell | 1,476 | 45 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# A wrapper to preprocess macaque structural images, looping over subjects.
# 1. brain extraction
# 2. bias correction
# 3. reference registration
# These steps are dependent on each oth... |
ae48bd57af998e431681b7ea584cd5d6b2ac1460b8fc9e9fb2ed2fc7de9b97f1 | Shell | 1,477 | 45 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-18:00
#SBATCH -p medium
#SBATCH --mem=200G
#SBATCH -o jobs/banc_data_push_v3only_%j.out
#SBATCH -e jobs/banc_data_push_v3only_%j.err
# One-shot v3 rebuild after banc-data.R was patched to:
# - persist v3 spatial-NN pre_label/post_label into the enriched parquet
# (Section 3 v3... |
79d682144a0df0a17dd772a6021a6010347629cc49710edbf0812d2b5c77f990 | Shell | 1,478 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_mopac_from_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT... |
918245800eaa7cfa64b64d8adb58b0efd95c1b8026c875cf290f90207370c8b9 | Shell | 1,478 | 42 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=dumpstr
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=50G
#SBATCH --chdir /data7/ipsc/16p12_1_del/str_calls # TODO: set dir to projec... |
1bfeb1fa748125859189d40393bf70ad1010b7dd4ec67730389b6f06ce28546b | Shell | 1,479 | 45 | #!/bin/bash
# this function generates all non-Python and non-R based figures for the TRBPC project
#
# Written by Angela Tam and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outdir=$1
code_dir=$CBIG_CODE_DIR/stable_projects/predict_phenotypes/ChenTam2022_TRBPC/figure_utilities
... |
9fb43a2503ec65f07496bd34ee6737261d3389ff2bf87f4e5eb6657dc44ed923 | Shell | 1,480 | 33 | #!/usr/bin/env bash
# Download all required data for small BAM and store in HDFS. Use this for non-GCS clusters.
TARGET_DIR=${1:-small_spark_eval}
hadoop fs -stat $TARGET_DIR > /dev/null 2>&1
if [ $? -eq 0 ]; then
echo "$TARGET_DIR already exists. Delete it and try again."
exit 1
fi
set -e
set -x
# Create data... |
019e3cdbaaaec0161d838502b05cb514b370fd05dd564fa87aa0f1a03ba6730e | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-07
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
06d903af0ad2caa33265746ea948aca9b2cdf0efc6c8ea4353d98c3dd77edf85 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-09
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
07cb7b1a8bc70ccbf6e8156b23c8de79f90a311ed0e9354dcb28310b896ef928 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-10
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
17bb384af2f65ad4eb4928c37c3c27c95a0f2a5c7a6ec099576379ff0ad49018 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-03
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
1e77866aebcce6c5683e2bd0e39a7ddf494f3215f9cd8b7268da3e2f1894f658 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-11
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
2e7eda42df79a82cfce34d8b287dd07eb158f3002f4812d0a8cf82172f74a13c | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-05
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
40423edc3f2edcf15c521e53eacba6d1a86f5b846609da564af86afd96c918a0 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-05
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
408dc9bfa26ef8e6e9511fb4c8d6928369a0af0d86a5845046394edeb2aaabfd | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-03
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
4bcc82261b124d59efd254198a0e5a0ceb39f9b46526d73d535bb57e53387deb | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-11
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
57183117ebe96a4edbb828d5496d91100a12ee6d50d2b5af99281d7e517e9af9 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-12
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
609a7d5fa7ef67027110f5422cf7dbd662d9d9493233c13f06e2f44714eab322 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-10
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
71483fb48635c43ef09a370d8115d2a88dea9c6faf6764265b43eed96444b070 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-09
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
71a2029018283893841b1d7d9c14b3fdc14379f505483cc28f075350c533fa89 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-02
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
72ba6da67d57f2999cc003c9cf88b36d91e7cbe670e50ca090d46bf39f8785f3 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-04
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
753cb7167621ef206611989e3e91e41c259870f50b7bd4ba90ffe0c82bb66c0c | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-02
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
808f6f59fabc20f297d218e7c21c950037ebf5617ce52d767c287d110057d322 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-01
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
81604bc2eb11d6a96f4552b5a60c5109b17108eacd2308075d54bdeb46ffce10 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-02
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
894f384d21fff287423d66d04de586fec9c25fa61d15f098aaf6e9ecbf535442 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-09
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
8f80a257c5cc2a52065d68cc46456f78c4f35db8b717bbe9771d4ed1fc3c8e03 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-01
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
913ddb357e84b58e55a5cf834a1fcc362335da3e52b48cf82516895ac82bbe3c | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-08
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
98a8ca5c663074e0482e9108f6addd914fdd11a0e30be848a094e14314886940 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-06
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
993a4d34633507c289377c42f6a8f6aba6dd907b0ae1e1b754648c9ee6055ec9 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-08
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
a1ced92d13977c80e86fc5716f94de02d893ec53c8f976e7c60d866264b28ecb | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-04
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
a9bbfc5869dc8b8001813e86e968c9717055f8d5987d5ce256dd8ecbcc282b5e | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-10
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
ab2fb81ca32fa366faf33df3a97b3898a5d27015ec3020a25a1d05cf536cf414 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-07
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
af880485e2bdf0637d000f606b37121ed80586b53a45f49a0fcae534eb14123f | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-07
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
b266fe58f5fc8de10ea7fd51b04fea0ad032159db14af4816c75b2a15800dd44 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-05
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
b6838933958f6914574979dd80a6df07f294763dfd1e2ff9bc626555100d3d21 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-12
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
bd3e93aa0e89602989fba46f419967e04d89e274327e94c5fefbec5d29ab54da | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-03
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
bfe2d8740a461af3f65732ac6703a79f9a5c203348150cc75187d7083467fb1e | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-08
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
d1e4a30b51f4bc2c023623fac3ec2e0f4ff37bd941777447202ac4ae5e75b723 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-11
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
e1e9e2f15742efde4770def0e491028749c909c31428f024ef956b422af2571a | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-04
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
f3acc6794335e8d2c8dbace93a405c73ea4f86532ba8c4aae92a7aa92e73f7d3 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-105-ses-06
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
f4c8db411d3ddb73a5331803ca036f4a6604d8cd6130100ac1124c9eeab2b6aa | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-01
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
fdae480897bb7af21e69785be9089fd5f7b4fd8d59af5698063b4d8ab45c4768 | Shell | 1,481 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-104-ses-06
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
fd39df0111123e0a85f8aacf462cab22788aa3a3f5ec29c25a5d7c7a1b4df360 | Shell | 1,482 | 44 | # Author: Javier Gonzalez-Castillo
# Date: June 16th, 2022
#
# Description:
# This script will do most pre-processing that happens after all spatial transformation matrices
# have been computed using Nipype
#
set -e
# Load software needed by the pipeline available as modules in biowulf
# -----------------------------... |
bcc0ac837922e05104b834e49aeae6cae8c843e31be4d6537da6b44875d81298 | Shell | 1,483 | 50 | #!/bin/bash
include_samples=("2xMBD2" "2xMeCP2" "4xMeCP2" "NTD-MeCP2-IDR" "pA" "5mC")
material=('nuclei' 'gDNA')
mkdir -p 04-analysis/ANA01-mCT_construsts/peaks_upset/
for mat in "${material[@]}"; do
prefix="${mat}_pA5mC"
files=(04-analysis/ANA01-mCT_construsts/peaks_replicates/*${mat}*optimal*)
# Onl... |
487ae9f091880273f47e37631a5d5f2623ec9a5c654d55871b050f09375f179e | Shell | 1,485 | 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... |
031a2e0f2ed7f6ce98e7561a7ea5bb917f2dcf49759341c3ce0e0cf2a1078642 | Shell | 1,491 | 38 | #!/usr/bin/env bash
# One-time maintainer script — run OUTSIDE this dev container, where you have
# SSH/gh access to the toolkit repos. Creates and pushes annotated tags at the
# exact commits behind the published v2.1.1 results, so a fresh clone can always
# fetch them (a bare SHA not reachable from any ref may fail t... |
2e528d063e657cab7be2db019b637272865ded7c5052ee6f7bce2516f32a04f5 | Shell | 1,491 | 34 | #!/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
# "Lic... |
9085907d34039cd53897cb78d7f5492faebed1e6cef0928fcdd6742d0e022d1c | Shell | 1,491 | 51 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_block_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
exp... |
052fafb3b47353e47510de250d69ffcb0942b426116638c88a6fc0b42b7668f2 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-02
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
0d643024cc359cf854a13cd4413b3ff63c048658106a32194c17c578ce7c01e8 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-11
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
15421ba4da1e02769ffe0de24139184d26d5c688bbb1c19c9e378408713f04e8 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-01
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
1be8caec0fd33f5f742a96c5081c9b010cf9883794f900cb45095678c648634c | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-08
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
29468ebcca48697a1e445c998a697f6a62716ff7bed90110404d84c7d86dc4f3 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-09
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
57cca1957b555f89a943c217e330a31ba923efa812a08ca8e3bebcdd4118e43e | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-103-ses-12
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
5ce448ccc19847bf8202f0a2c91019f1a4920c7519142acc5d93a9a64ec62fb2 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-10
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
6bfe61238aa8171590e4c36802b5d3c855589f9f0c6be294ced7256174367ebd | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-06
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
ad77b678bd3b30be7cc087fcf21cf09d47325d51e1cfe50ace4327eefc447610 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-03
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
b2410747f92ff8c9b26ee1a9693017bfb836e15342a5f6a8865913cbf8a25fa4 | Shell | 1,493 | 43 | #!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N fmriprep-sub-101-ses-07
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug8742... |
3299eae52ed205ec1691c256154bf5b90485911c2a82be2c05f6cfdba66f738c | Shell | 1,494 | 42 | #!/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... |
ec66b788b7f43098c47d8901c84a972bce47012cc710af1b063d63e50e21eb50 | Shell | 1,494 | 56 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
studyDir="/Volumes/rsfMRI/structural/proc"
instructFile=$studyDir/instruct/instructProcStr... |
5da4bb4e4f30e06fcb936aa38893dfdd7ba85d9d38a53408272fee5f82c19501 | Shell | 1,498 | 69 | #!/bin/bash
# Usage: $0 [-p <name of pxp to run against>] [-v <igor version string>]
# https://stackoverflow.com/a/246128
ScriptDir=$(cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd)
usage()
{
echo "Usage: $0 [-p <name of pxp to run against>] [-v <igor version string>]" 1>&2
echo " Igor Pro... |
e68a0d47184e68056c407a8aae234500664c04630bb289c556f9a50faf1f3021 | Shell | 1,499 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_mca_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/... |
f460c32e180e0a5c6d954bd9b23ef9b2343b26a7216cc145bf535b3556d293ea | Shell | 1,499 | 34 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 0000-00-00 #
# .... #
###################################################################
export path_htsa_dir=$1
export PB=... |
f48ff5ca9b39827576d4fa500dba3b31da232d8a9c7d2a465c6f677e5e9aa07f | Shell | 1,500 | 40 | #!/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 "Licen... |
b9b535c6fda58fa9de52a9b860460faf0d7b304237f316c999f53586c18a930d | Shell | 1,501 | 40 |
# Download Mol2D QSAR dataset in SDF format and WelQRate dataset in SDF and CSV format (containing SMILES)
scripts/download_qsar_datasets.sh
scripts/download_welqrate_datasets.sh
# Construct molecules from SMILES strings and kekulize
WELQRATE_SDF_DIR="welqrate/sdf"
mkdir -p ${WELQRATE_SDF_DIR}
for dir_csv in welqrate... |
a6046936cf22be877429920b09d75271d02d3a5dc35ba2d2d55bba1b05a3f7b1 | Shell | 1,502 | 62 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_maa_mmff_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=train
BASE_DIR=${WORK_ROT}/data/... |
826664acbd1f8d4a19188a21f5877d121c0a4102929e8646b3eac401837749da | Shell | 1,503 | 37 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 0-02:00
#SBATCH -p short
#SBATCH --mem-per-cpu=8G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_ol_ind_smoketest_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_ol_ind_smoketest_%j.err
###############################################################################
# OL ind_weigh... |
e6686df211c8b1166b437ec5e990ea438a3d727b045b6d3b9f289c7fce89b488 | Shell | 1,505 | 53 | #!/usr/bin/env bash
# Hook to enforce using 'uv' instead of 'python', 'python3', 'pip', or 'pip3' directly.
# This ensures consistent virtual environment usage across the project.
set -euo pipefail
# Skip if jq is unavailable
if ! command -v jq &>/dev/null; then
exit 0
fi
# Skip if uv is unavailable
if ! command ... |
16f51ce4ff1938345f71360ecaa3c92e274495ff02a1e58a8028efc0a0ba346e | Shell | 1,509 | 56 | #!/bin/bash
# DeepPlaque Inference Script
#
# Usage: ./run_inference.sh <input_images/folder> <output_dir> [score_threshold]
#
# Examples:
# ./run_inference.sh /path/to/images /path/to/output
# ./run_inference.sh /path/to/images /path/to/output 0.45
set -e
# Get script directory
SCRIPT_DIR="$(cd "$(dirname "${BAS... |
8aceaecf895082e8742a2d5877fadd0d09bdeb07cfd4fb4666382b0c90828e4c | Shell | 1,509 | 43 | #!/bin/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 applica... |
aae8aad158f997162ac713812f7585f3d5a99c36f18b16dc171924614dabb123 | Shell | 1,510 | 53 | #!/bin/bash
#PBS -l walltime=8:00:00
#PBS -N mriqc103
#PBS -q normal
#PBS -l nodes=1:ppn=28
#PBS -l mem=100gb
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
umask 0000
# New base directory
mydir=/gpfs/scratch/tun47039/night-owls
dsroot=/gpfs/scratch/tug87422/smithla... |
02213636e0ad95c9ef78c66f3abd33b142aa99e9f103f9f23a1ca78ce8a3dc44 | Shell | 1,511 | 40 | #!/bin/bash
# this is an example script of what was done to assemble the registration fusion results
# into a single file. The resultant file is what's shared on figshare
set -x
OUTDIR=/dartfs-hpc/rc/lab/C/CANlab/labdata/projects/bogdan_atlas/results/glasser/subject_parcellations/
for SPACE in MNI152NLin2009cAsym MN... |
e7746c13bd134298dba8d389fd74056a722b8ed5dfffdd39052a63d6332b8465 | Shell | 1,512 | 44 | # Path to binary for wb_command
WB_COMMAND=$1
# Path to director containing HCP S1200 subject data
HCP_DIR=$2
# Path to HCP subject IDs
SUBJLIST=$3
OUTPUT_DIR=$4
declare -A TASK_COPEIDS=( ["LANGUAGE"]="1 2 3" ["RELATIONAL"]="1 2 3" ["SOCIAL"]="1 2 6" ["EMOTION"]="1 2 3" \
["WM"]="1 2 3 4 ... |
c47cf52678c68d8b95c15665052862c7418a20891c3ad187c3ac9be75ae5547e | Shell | 1,515 | 49 | #!/bin/bash
###############################################################################
# Convert WB alignment seeds.csv → seeds_production.csv (no holdout).
#
# Flips every is_holdout=TRUE → FALSE so all GT cells become anchors. Use
# this for the final 100% GT production alignment run after a re-prep.
#
# is_hold... |
21898a9c2a92be51505d02530f9b927d974ea359e3c9dc49dabffccddf663b05 | Shell | 1,516 | 25 | workdir="/histor/sun/wangtao/0_user/3_shixh/singlecell/choline/ATAC/data/chromap"
inputdir="/histor/sun/wangtao/0_user/3_shixh/singlecell/choline/ATAC/data/rawdata"
outputdir="/histor/sun/wangtao/0_user/3_shixh/singlecell/choline/ATAC/data/chromap"
outdir="/histor/sun/wangtao/0_user/3_shixh/singlecell/choline/ATAC/data... |
2946c8a2d1d6402a8f836d48073123f2217544d48d82101964518c8e57febb73 | Shell | 1,516 | 18 | # Environment
KERNEL_NAME="JAMIE"
# Results
# jupyter nbconvert --execute --to notebook --inplace sample.ipynb --ExecutePreprocessor.kernel_name=$KERNEL_NAME ;\
# jupyter nbconvert --execute --to notebook --inplace scGEM.ipynb --ExecutePreprocessor.kernel_name=$KERNEL_NAME ;\
# jupyter nbconvert --execute --to noteboo... |
31425f455ca1a24b9ae23db91b38a922f00dccf185e9abd1d2d97c50a647051b | Shell | 1,520 | 22 | #!/bin/bash
# Download the chimp genome
cd /home2/gkonop/workdir/REFERENCES/FASTA_ONLY
wget https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips/panTro5.fa.gz
gunzip panTro5.fa.gz
# Subset the small chromosomes (to test if the tool works)
cd /home2/gkonop/workdir/REFERENCES/TMP
/home2/gkonop/workdir/PROGRAMS/s... |
4157e17892211a92d3b0ced35ac4d91f3d9006955ca9c85660dfaf798db190f2 | Shell | 1,521 | 83 | #!/usr/bin/env bash
set -ex
function retry-with-backoff() {
for BACKOFF in 0 1 2; do
sleep $BACKOFF
if "$@"; then
return 0
fi
done
return 1
}
while :
do
case "$1" in
# Install skinny dependencies
--skinny)
SKINNY="true"
shift
;;
# Instal... |
4617a9385a6d8eeb7533858214cb5370c1ab920e18097683c30eca703f1155d6 | Shell | 1,522 | 43 | #!/bin/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 applica... |
04750def50ae9a242f9b609b935410c4b601f64061212ca6d2cc62226d49a4bb | Shell | 1,524 | 57 | #!/bin/bash
# change to the dir of the script
cd $( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# change to the dir to the project
cd ../..
title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
test_config=AI/test.yaml
output_dir=${OUTPU... |
79fabe9c9e7ed10db1d21f571248c2f278763a5a858463b668c02ba202120ecc | Shell | 1,524 | 44 | #! /usr/bin/env bash
# Usage: bash measure_power.sh {logdir}
LOGDIR=$1
# Set LOGDIR to logs if it's not supplied
LOGDIR=${LOGDIR:=logs}
mkdir -p ${LOGDIR}
POWERLOG=${LOGDIR}/power_jetson.log
TIMERLOG=${LOGDIR}/times_jetson.log
CPUTIMELOG=${LOGDIR}/times_cpu.log
rm -f ${POWERLOG} ${TIMERLOG} ${CPUTIMELOG}
# Warm-up r... |
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