sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cdf2ef9678c596ea3d4f658ffa2a3b1dd59ef16ca5a33ed77434511101f736c0 | Shell | 847 | 21 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/nanopore_BAM_merged
output_dir=$pd/data/validations/nanopore_GFF
mkdir -p $output_dir
# reconstruct transcripts per species and cell type
for i in `ls $input_dir`
do
sample_name=`cut -d . -f ... |
997deaa2c9be9acebd3434df13cfbf14078e6aea0f6bb44bf9cbc316c0cfd15e | Shell | 848 | 27 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=5
sta_i_Kir=1
end_i_Kir=31
sta_i_batch_KM=1
end_i_batch_KM=31
n_batch_KM=1
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo " $i_pCaLs"
for i_Kir in $(eval echo "{$sta_i_Kir..$end_i_Kir}")
do
... |
45be99e2408e714559a1c2f85befb56b2d0b48bdbec0388f1087be62e7b7fcd2 | Shell | 852 | 23 | #!/bin/bash
# Navigate to your masks directory if needed
# cd /home/fs0/jdf650/scratch/DPhil-Human-fMRI/DPhil-Human-fMRI-Data/fsl/data/masks/1mm
# Create a binary mask that represents the overlap between SN and VTA
fslmaths SN.nii.gz -mul VTA.nii.gz SN_VTA_overlap.nii.gz
# Subtract the overlap from the original SN m... |
bcec04d11c219a1cfee7444f50760524e36326059246cba4f5ca30523345dc05 | Shell | 852 | 23 | #!/bin/bash
#SBATCH --mem=40G
#SBATCH --ntasks=15
#SBATCH --job-name=Regr_GenNet
#SBATCH -p long
#SBATCH --gres=gpu:1
#SBATCH -t 30-00:00:00
#SBATCH -o /data/scratch/avanhilten/GenNet_logs/out_%j.log
#SBATCH -e /data/scratch/avanhilten/GenNet_logs/error_%j.log
# Load the modules
module purge
module load Python/3.7.4-... |
a15057f8f1638f492ce0c152992fe6d94e1b5274c0958158fce63c096e689857 | Shell | 853 | 26 | #!/bin/bash
basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA/Longitudinal_VIPD/SESSION1"
cd ${basedir}
mapfile -t allsubs < /mnt/y/PROJECTS/GMmicrostructure/DATA/Batch.txt
template=/mnt/y/PROJECTS/GMmicrostructure/DATA/fsaverage/fsaverage_brain.nii.gz
for sub in ${allsubs[@]}; do
subdir=$basedir/$sub
cd $subdir
... |
1a53aa592becf9d44fe59079508380a2775d034aba77ba56f307ded2badb3d2e | Shell | 855 | 14 | # ===========================================================
# 2d loss contours for ResNet-56-noshort
# ===========================================================
mpirun -n 4 python plot_surface.py --x=-1:1:51 --y=-1:1:51 --model resnet56_noshort \
--model_file cifar10/trained_nets/resnet56_noshort_sgd_lr=0.1_bs=128... |
8576b92ed0527f3698b7a655bef3986dd42cc739eb150f2ec507d81b09424910 | Shell | 855 | 29 | #!/bin/bash
set -eu
if [[ "$#" -ne 4 ]]; then
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 (HDFS,required)"
echo -e " [4] absolute path to the 2 bit reference on the cluster (HDFS,r... |
29fd9ba739930e3bc09a09ddc09326f924a42578b3949d29ad520b4fb37ad26c | Shell | 856 | 25 |
# Move to the directory where the script is located
cd "$(dirname "$0")"
ATLAS_FILE='template/HCP_atlas_MNI152.nii.gz'
ROIS_FOLDER='rois'
mkdir -p $ROIS_FOLDER
# Loop from 1 to 180 (both included)
for i in $(seq 1 180); do
# Create the ROI file name. Save as HCP_atlas_MNI152_ROI_001.nii.gz
# The number is p... |
60f8477b5fc3d2ac36fe6aef43c782f650e5ee8aec6607992bcc4cca74e6a49a | Shell | 856 | 31 | usage() {
cat <<EOF
Usage: $(basename "$0") <bedpost_dir> <prefix> [nsqrt]
bedpost_dir completed bedpostx directory
prefix name of output file
nsqrt number of times to square root for contrast adjustment (default: 1)
Script takes a bedpost directory as input and outputs a fake T1 image.
... |
69166f5c33c6ca144aefb99a3cf50484e9ea489697db9e29fc534aec7a6f6a12 | Shell | 857 | 28 | #!/bin/bash
DATA_DIR="/.../EMBARC/03_FSL_FEAT/Whole-data"
# Find all subject/session directories
TASK_LIST=($(find $DATA_DIR -mindepth 2 -maxdepth 2 -type d -name "ses-*"))
missing_files=()
for TASK_PATH in "${TASK_LIST[@]}"; do
subject=$(basename $(dirname $TASK_PATH))
session=$(basename $TASK_PATH)
E... |
e75cf474265dbc65e5e2145872927ddcfdf86085d46d704287c7b3a4acda4591 | Shell | 858 | 26 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-04:00
#SBATCH -p short
#SBATCH --mem=64G
#SBATCH -o jobs/nblast_compile_%j.out
#SBATCH -e jobs/nblast_compile_%j.err
# Standalone re-run of banc-nblast-compile.R only (no NBLAST recompute, no
# CAVE push, no GCS share). The script wraps its body in local({...}); local
# does NOT s... |
2e7ea90697b4b6db25c9238abd3f137910fbfd687660ccf22b67232d800b8b3e | Shell | 859 | 16 | #!/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_CBIG2022_DiffProc
# remove useless stable projects
rm -r Standalone_CBIG2022_DiffProc/stable_projects/brain_parcellation
rm -r Standalone_CBIG2022_DiffProc/... |
5f12e723c15713b83cc6781c73cabce9b22a8c378d7644c322bf5bc31ff3971c | Shell | 861 | 29 | #!/bin/bash
# A script to initialise the dock building within the docker container. This
# is not designed to be run by gitlab , rather for local tests of gitlab
# CI/CD scripts inside the docker container.
# It is assumed that you are in the repo mounted as the working directory
if [ -e ./docs/build ]; then
rm -r ... |
a8d784216d462d48e3907639e5522cc27cff783bd566c6f28b7cf158e8219ed9 | Shell | 861 | 24 | #!/bin/bash -x
#SBATCH --account=inm7
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=06:00:00
#SBATCH --partition=dc-cpu
#SBATCH --output=logs/outputs/%x_%j.out
#SBATCH --error=logs/errors/%x_%j.err
source /p/project/cinm-7/bi1/miniconda3/etc/profile.d/conda.sh
conda deactivat... |
25fb774aca318f1fa00e2c5525cbe14ff31fd623352481d5246b8f24c089122b | Shell | 864 | 24 | #!/bin/bash
# =============================================================================
# bbduk.sh — adapter/polyA trimming helper
# =============================================================================
# Usage: bbduk.sh <sample_id> [adapters_fasta]
#
# Requires BBMap (bbduk.sh) in PATH.
# =================... |
1f0175dac7981afbe33a9fe65584f3874e0c3bb65d7bf2d7fd2a2a3cb4219146 | Shell | 866 | 10 | surf_name=$1 ; surf_ext=$2 ; mkdir -p ${surf_name}
convert ${surf_name}.${surf_ext} -crop 800x600+140+180 ${surf_name}/lh.lateral.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 800x600+140+1060 ${surf_name}/lh.medial.${surf_ext}
convert ${surf_name}.${surf_ext} -crop 640x580+130+1920 ${surf_name}/anterior.${surf_ex... |
4d8fde999e1d803e4025f0f902675168f6c99cbed613be40069dc916c51d5f63 | Shell | 867 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/icbeb/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--dataset icbeb \
--pretrain_path $pretrain_path \
--ratio 1 \
--learning-rate 0.001 \
--backbone $backbone ... |
7517cec2785dc555102f2ae9c4852e5908570917cd6c80177b6850deee62c892 | Shell | 867 | 36 | #Path of Age-Specific Templates (output Path in step 1 template construction)
ASTPath=$1
#AST prefix
AST=$2
#Path of individual brain image
source=$3
#individual ID or prefix
prefix=$4
#output path
OutputPath=$5
target=`ls ${ASTPath}/${AST}*template*`
outdir=${OutputPath}/${sub}
antsRegistration \
-d 3 \
--float 1 \
-... |
ad217e9633d4d8b2b995eeb0e91750b9c8935bdfbe91d8e75bde82238d1676cd | Shell | 867 | 34 | #!/bin/bash
########################################
#MEGAHIT
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export megahit_work_dir=$3
export diginorm_work_dir=$4
cd $project_work_dir
echo "starting megahit assembly..."
if [ -d $megahit_work_dir ];
then
rm -r $megahit_wo... |
b1b500825c02fa4db7189f80e49c20580563eaf7d95fdfc8c60b8893a64cd6d1 | Shell | 867 | 32 | #!/bin/bash
echo "Enter the parent folder location: "
read parent
if [ ! -d "$parent" ]; then
echo "Error: Parent folder '$parent' does not exist."
exit 1
fi
echo "Enter the input subfolder name (inside parent folder): "
read input_subfolder
input_path="${parent}/${input_subfolder}"
if [ ! -d "$input_path" ... |
fa06d88c54c95f195873c617b52a281ea51fb69b57100df389aff8c1d33c2cff | Shell | 867 | 33 | #!/bin/bash
set -e
DOCKER_USER="${DOCKER_USER:-1000:1000}"
USER_ID="${DOCKER_USER%:*}"
GROUP_ID="${DOCKER_USER#*:}"
HOME_DIR="${DOCKER_HOME:-/home/boa}"
XDG_CACHE_HOME_DIR="${XDG_CACHE_HOME:-$HOME_DIR/.cache}"
XDG_CONFIG_HOME_DIR="${XDG_CONFIG_HOME:-$HOME_DIR/.config}"
mkdir -p "$HOME_DIR" "$XDG_CACHE_HOME_DIR" "$XDG... |
3196521f8089469aefb43a528faa8bfc1af2e189b9475e969db35faf2ac877ba | Shell | 868 | 44 | #!/usr/bin/env bash
function error_handling() {
echo "Error occurred in dev-env-setup.sh script at line: ${1}"
echo "Line exited with status: ${2}"
}
trap 'error_handling ${LINENO} $?' ERR
set -o errexit
set -o errtrace
set -o pipefail
shopt -s inherit_errexit
set -x
err=0
REPO_ROOT=$(git rev-parse --show-topl... |
87b588bff0e8b0ae16deb13bb7e822a41c8b97f27726397d5a518a050066335d | Shell | 868 | 29 | #!/bin/bash
# Author: Andrew Hamel
# Mass. Eye and Ear, Harvard Medical School
# Date: June 2022
# This is a shell script that contains a sample run of GeneEnrich.
# Input genes are target genes of GTEx artery aorta eQTLs with coronary artery disease (CAD)
# CARDIoGRAM C4D GWAS P<0.05
# User must supply GENCODE gtf ... |
7b712a34a7718b51955f83361d433ed0485d21154963dde3584b206f0215c5f4 | Shell | 869 | 22 | #!/bin/bash
#####################################################################
# Copyright 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.... |
894b740170f388bdccd356906b3d9607fe2892bde2c94fc4f87e62df6ee9b9fa | Shell | 869 | 32 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=12
#PBS -N Intg-ssv4
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="r4_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
ex... |
248d553004964a1a70628d6c903fba1b8d7cf2d60d54f619f09f23f752dd261c | Shell | 870 | 25 | #!/bin/bash
set -eu
# This script initializes the master and worker nodes on a Google Dataproc
# Spark cluster to prepare them to run the GATK-SV pipeline.
#
# On the worker nodes we copy the bwa index image file
# from a bucket to each node's local disk.
REFLOC=$(/usr/share/google/get_metadata_value attributes/refe... |
9a15db0631ba0d7d793b50a7f20b29dc2e328179671cffd6a54359399db40e7d | Shell | 870 | 27 | #!/bin/bash
# Source directory containing the directories with files
src_dir="/Users/arman/Desktop/DARSI/new_run_plots/model"
# Destination directory to copy files
dest_dir="/Users/arman/Desktop/DARSI/new_run_plots/saliency_maps"
# Loop through each subdirectory in the source directory
for dir in "$src_dir"/*; do
... |
1eaef3f93d00df1caf340933618a8fbe4f7a467172432a31593937fd520c1861 | Shell | 873 | 13 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="$CBIG_CODE_DIR/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
cmd="cd ${rep_di... |
53614b40f512c10e4f7b2e8bbb6532cfcde4a34e125c4ec3d7df3e50577e3cc2 | Shell | 873 | 32 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=12
#PBS -N Intg-ssv4
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="r4_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
ex... |
933ea17cd54f34f633b521a05820d0acd5c6ed235fbc720fe7bfccd30537525b | Shell | 873 | 18 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Many to pia demo
# Multiple branching structure growing towards the pia
# For demonstration purposes, putative synapse locations are record... |
e91e35eb6f96179cc47079fa76fae773ded32d13d485ebd4c7acc55b4f31c20b | Shell | 874 | 36 | #!/bin/bash
# 定义源目录和目标目录
SOURCE_DIR=./
TARGET_DIR=../report/figures
# 定义文件列表
FILES=(
"ns_traj_error_new.png"
"error_grid_1s_new.png"
"error_grid_1.5s_new.png"
"error_grid_2s_new.png"
"error_grid_2.5s_new.png"
"omega_error_grid_1s_new.png"
"omega_error_grid_1.5s_new.png"
"omega_error_g... |
54b0a6c051c9edf2d69608743d67933f32fe7f9c13d98f3bb27933d6ab229285 | Shell | 875 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/chapman/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--dataset chapman \
--pretrain_path $pretrain_path \
--ratio 1 \
--learning-rate 0.001 \
--backbone $backb... |
a35c542ed78bc0f648e45c19ab2a515583ee858b7e665395bc0ece0d29bb245d | Shell | 876 | 19 | if [ ! -d $HOME/mcr ]
then
echo "destinationFolder=$HOME/mcr" > $HOME/mcr_options.txt
echo "agreeToLicense=yes" >> $HOME/mcr_options.txt
echo "outputFile=/tmp/matlabinstall_log" >> $HOME/mcr_options.txt
echo "mode=silent" >> $HOME/mcr_options.txt
mkdir -p $HOME/matlab_installer
wget -nc http://www.mathworks... |
4cf21ebcb2dae5972d12acb622801cc1082dbf801ed4b2eceddc9a1580b4f5a0 | Shell | 877 | 35 | #!/bin/bash
# Exit immediately if a command fails
set -e
# Create a new conda environment and activate it
conda create -n DKdMRI python==3.12 -y
source activate DKdMRI
# Install necessary packages via conda
conda install pytorch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 pytorch-cuda=12.4 -c pytorch -c nvidia -y
c... |
708e5c79c21788e072ca7f8e25d44f1ed51a154cfe04e34de375568466fb2675 | Shell | 877 | 8 | #omp_flags= "-D PKG_USER-OMP=ON -D BUILD_OMP=ON"
#bulid_type="-D CMAKE_BUILD_TYPE=RELEASE "
#build_mpi="-D BUILD_MPI=ON"
#shared_flags="-D CMAKE_SHARED_LINKER_FLAGS='-O3 -DNDEBUG' "
#cmake -D BUILD_MPI=ON -D BUILD_OMP=ON -D CMAKE_SHARED_LINKER_FLAGS='-O3 -DNDEBUG' -D CMAKE_BUILD_TYPE=RELEASE ../cmake
#cmake -D LAMMPS... |
26b3230222019e79dd6c4dd369c6f5f6d11793e3cf37293650a62c304455f6b0 | Shell | 880 | 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/i... |
b7086de99f9bf2334ca0564b1f93af90fb82d52482cb237afb28e09ada66a5e9 | Shell | 883 | 20 | #!/bin/sh
### Launch the code for the times 0-5 and using 5 cores
### and save the magnitude of the projected violating triangles \Delta_v at the level of edges
### on the file "edges_projection.hd5"
##The code needs to be launched from the directory "High_order_TS_with_scaffold" in order to include the
##different ... |
60dcb86ec38d4519280716ea02aa63eb0cf29ca5063392ba00d6f89392d5c6a5 | Shell | 884 | 32 | #!/bin/bash
# Parameters
# $1 - fixed phantom number
# $2 - moving phantom number
# $3 - metric (NCC in quotes)
# $4 - mask 1/0
rm -rf /tmp/test_affine.mat /tmp/src_reslice.nii.gz
if [[ ${4?} -eq 1 ]]; then
MASK="-gm phantom01_mask.nii.gz"
fi
# Perform the registration
echo ../../../xc64rel/greedy -d 3 \
-m $3 ... |
fdb23270f7fd05c08cf1fe6560786de81b69b7a0d9db687cf44efa35f03d9886 | Shell | 887 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/ptbxl_form/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--ratio 1 \
--dataset ptbxl_form \
--pretrain_path $pretrain_path \
--learning-rate 0.001 \
--backbone ... |
2e8a33e43711d96a2b640cae17ff25a1bdb1497146ff5d4ea385a75ae9057e5a | Shell | 888 | 39 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${IndexPath_100}
DataPath=${FastpPath}
FASTQ1=${FASTP1} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath}
AllOutPath=${AlignAllPath}
Read_len=100
... |
ee0f1b098827e1d4a12bd838408785b5dfba4dbe756986fe42d44f9c63f67875 | Shell | 888 | 23 | #!/bin/bash
# Define the feature combinations and targets
feature_combs=("Sleep" "Cov" "Brain" "CT" "SA" "Subcor" "Sleep_Cov"
"Sleep_Cov_Brain" "Sleep_Cov_CT" "Sleep_Cov_SA" "Sleep_Cov_Subcor"
"Sleep_Brain" "Sleep_CT" "Sleep_SA" "Sleep_Subcor"
"Cov_Brain" "Cov_CT" "Cov_SA" ... |
0e7d91b196a7df2b4ff8aac56405481cf163886a76ad6ae29311c3271da39e64 | Shell | 889 | 39 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${IndexPath_150}
DataPath=${FastpPath}
FASTQ1=${FASTP1} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath}
AllOutPath=${AlignAllPath}
Read_len=150
... |
82c2af641ac46a98802ea98fe2bc3660e4f8aded2a78945c8948c0db9c5f0c14 | Shell | 889 | 40 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${IndexPath_125}
DataPath=${FastpPath}
FASTQ1=${FASTP1} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath}
AllOutPath=${AlignAllPath}
Read_len=125
... |
5b25f56f37a30bc54c20d0791948bf6b3d5890d1f969fb49f101a1167032c5f6 | Shell | 890 | 66 | #! /bin/bash
[ $# -lt 5 ] && { echo 'Usage :
$1 = MNI152 image
$2 = patient prefix
$3 = lesions folder
$4 = disconnectomes folder
$5 = resultFolder
$6 = lower threshold for disconnectomes'; exit 1; }
echo $@
fileName() {
name=$(basename $1)
name=${name%%.*}
echo -n $name
}
disco=`ls $4/*$2*`
les=`... |
23cc29e0aceda125cc92a97a59bc18d973254fa56e5637cfe8880820d95347e0 | Shell | 891 | 36 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=8 -l mem=100G
#PBS -N ImputeATAC
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}
exp... |
9d8218c8adcc8011e73d7deac353fa609b7e4fce1aebf2206b2eff9e4d69e021 | Shell | 891 | 19 | #!/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... |
9fd601f3c538b30849c9d0137d3bcfc41c5a669d8f6a9af7ae6a8b1d0de9d91b | Shell | 891 | 33 | #!/usr/bin/env bash
# Install pyenv:
#
# https://github.com/pyenv/pyenv#automatic-installer
#
# Install pyenv in ~/.pyenv:
#
# git clone https://github.com/pyenv/pyenv.git ~/.pyenv
#
# Optionally, try to compile a dynamic Bash extension to speed up Pyenv.
#
# cd ~/.pyenv && src/configure && make -C src
#
# Get... |
04615617fd69d89d3eb49a3bd731b13530e8a1164da233328fc2331c3294afee | Shell | 892 | 23 | #!/bin/bash
# Define the feature combinations and targets
feature_combs=("Sleep" "Cov" "Brain" "CT" "SA" "Subcor" "Sleep_Cov"
"Sleep_Cov_Brain" "Sleep_Cov_CT" "Sleep_Cov_SA" "Sleep_Cov_Subcor"
"Sleep_Brain" "Sleep_CT" "Sleep_SA" "Sleep_Subcor"
"Cov_Brain" "Cov_CT" "Cov_SA" ... |
7ef220dfaef7102aa5df8f9d2d01d9eb3e194f791efc1a6467915b04740c818f | Shell | 892 | 24 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh # Change the path to your conda.sh file
conda deactivate
conda activate XGBoost
# Check if an argument is provided
if [ -z "$1" ]; then
echo "Error: No argument supplied. Please specify the validation folder (e.g., Liege)."
exit 1
fi
# Define th... |
97f50b58c0d036f97e40db12bd91c4d98570493e8af0bd3944184a0d2765bfd9 | Shell | 893 | 31 | #!/bin/bash
#SBATCH --job-name=run_seurat
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --cpus-per-task=5
#SBATCH --mem=30MB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=run_seurat.out
#SBATCH --error=run_seurat.err
# Title: Run Seurat analysi... |
7e0d42bedf50e20c064c210c160c4c1d6a2cbaf2c4d7d59f7924fd00e075675e | Shell | 895 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/ptbxl_rhythm/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--ratio 1 \
--dataset ptbxl_rhythm \
--pretrain_path $pretrain_path \
--learning-rate 0.001 \
--backb... |
4bdc1d9df8416e84e141b5368108c0bdacd2d56fe5754926ce7f563e817d8fd5 | Shell | 896 | 40 | #!/bin/bash
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2022 Xilinx, Inc. All Rights Reserved.
# Copyright 2022-2025 Advanced Micro Devices, Inc. All Rights Reserved.
#
if [ -z "$PATH" ]; then
PATH=/opt/Xilinx/2025.2/Vitis/bin:/opt/Xilinx/2025.2/Vivado/bin
else
PATH=/opt/... |
43287169cf0a7c23470e0fed51c487b3bd77ff1fdc394cbe8340649a25d8ea18 | Shell | 897 | 16 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Update environment demo
# One process grows straight and "drops a cue" / "secretes a cue" at \
# some point. Another growing process senses... |
9da0bb1e8878a001c7866f5851727b4b8b1c00b4c970c7850e21cf668255b048 | Shell | 897 | 23 | #!/bin/bash
# Define the feature combinations and targets
feature_combs=("Sleep" "Cov" "Brain" "CT" "SA" "Subcor" "Sleep_Cov"
"Sleep_Cov_Brain" "Sleep_Cov_CT" "Sleep_Cov_SA" "Sleep_Cov_Subcor"
"Sleep_Brain" "Sleep_CT" "Sleep_SA" "Sleep_Subcor"
"Cov_Brain" "Cov_CT" "Cov_SA" ... |
97c448f88ae1cdc09c6a5a64f0eb3bd91c129d56b2bba576908c798919931efd | Shell | 898 | 44 | #!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
# set -o xtrace
output_sku=$1
auditwheel_platform=
if [ $# -gt 1 ]; then
auditwheel_platform="${2}"
fi
CURRENT_DIR=$(pwd)
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
REPO_ROOT="${SCRIPT_DIR}/../"
cd "${REPO_ROOT}"
pod... |
89fdfaa2b9ffd57e9a55a536125c94763443d412111683f400a2227146584b10 | Shell | 899 | 33 | #!/usr/bin/env bash
# Push HTML files to gh-pages automatically.
# Fill this out with the correct org/repo
ORG=AthenaEPI
REPO=dmipy
# This probably should match an email for one of your users.
EMAIL=demian.wassermann@inria.fr
set -e
# Clone the gh-pages branch outside of the repo and cd into it.
cd ..
git clone -b g... |
97722540c585baceb2193da2b9f28a0ee720168c446a1d225e34be5761990b86 | Shell | 902 | 27 | #!/bin/bash
#SBATCH --job-name=symbolic_regression_robustness
#SBATCH --output=logs/estimate_%A_%a.out
#SBATCH --error=logs/estimate_%A_%a.err
#SBATCH --array=1-100 # Adjust the range as needed (seeds 1-100)
#SBATCH --time=08:00:00 # Adjust time limit as needed
#SBATCH --mem=16G # Adjust memory as needed
#SBATCH --c... |
e9ebf25db17fd705586dedcaa2f08f743bd9cb1df5eb430256319dc386654288 | Shell | 902 | 32 | #!/usr/bin/env bash
# this script will convert your BIDS *events.tsv files into the 3-col format for FSL
# it relies on Tom Nichols' converter, which has been copied to our scriptdir to preserve modularity
# https://github.com/bids-standard/bidsutils
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>... |
2827de33305682c2ba7cff9c8862e1102b881f372ff00403143623c319dedd4d | Shell | 904 | 10 |
# rm -r results/smiles_lstm_hc_1 results/smiles_lstm_hc_2 results/smiles_lstm_hc_3 c
# scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/smiles_lstm_hc/results.run.1 ./results/smiles_lstm_hc_1
# scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/smiles_lstm_hc/resul... |
744909152041f1066bd59c64ecd11736cfe6178de06431d0449179a1e0bf232b | Shell | 904 | 24 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh # Change the path to your conda.sh file
conda deactivate
conda activate new_autogluon
# Check if an argument is provided
if [ -z "$1" ]; then
echo "Error: No argument supplied. Please specify the validation folder (e.g., Liege)."
exit 1
fi
# Def... |
a2b8fae7109dd8a94c33b40534aecdff7004cdcb36df32a0a51be431abaaf215 | Shell | 904 | 18 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Random walk
# Not truly a rondom walk as the generated structure will terminate \
# when a structural overlap occurs. Detecting and avoidin... |
d85739f9d480bef2687b4985576e7c5018c985c719d557d1c6eb0c5c3bf2cfd7 | Shell | 905 | 25 | #!/bin/bash
# This script auto-grabs 4dfp tools from the offical ftp server
# and places them in the current directory.
HOST=imaging.wustl.edu
USER=anonymous # User must be set to anonymous
ftp -inv ${HOST} <<EOF
user ${USER}
cd pub/raichlab/4dfp_tools
get 4dfp_scripts.tar
get nil-tools.tar
get refdir.tar
bye
EOF
# ... |
c7ce9f86f599aafaa8528b766e406a4600c42726dea97e5ccda8de618dc8bd32 | Shell | 906 | 27 | #!/bin/bash
mkdir concorde
cd concorde
mkdir qsopt
cd qsopt
# Download qsopt
if [[ "$OSTYPE" == "darwin"* ]]; then
curl -O http://www.math.uwaterloo.ca/~bico/qsopt/beta/codes/mac64/qsopt.a
curl -O http://www.math.uwaterloo.ca/~bico/qsopt/beta/codes/mac64/qsopt.h
curl -O http://www.math.uwaterloo.ca/~bico/qs... |
80e4a8de9cb400449f860cf7f9c424e0c094ec75cfa2e6ce11bfb89062f7aa57 | Shell | 907 | 13 | working_dir=$(cd "$(dirname "$0")" && pwd -P)
echo "Compiling formatting scripts"
g++ "$working_dir"/Promoter_Windows.cpp "$working_dir"/STARE_MiscFunctions.cpp -std=c++11 -O3 -o "$working_dir"/Promoter_Windows
g++ "$working_dir"/ReplaceInvalidChars.cpp -std=c++11 -O3 -o "$working_dir"/ReplaceInvalidChars
g++ "$workin... |
cd7644eaf9296c2c749e94c234bb883648cdb968405573b22ae82bf6f5986d86 | Shell | 907 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/ptbxl_sub_class/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--ratio 1 \
--dataset ptbxl_sub_class \
--pretrain_path $pretrain_path \
--learning-rate 0.001 \
-... |
dfb377d2a019d45eef5ab25feb274822c6d98323cac751078f096a5fc31fd596 | Shell | 908 | 35 | #!/usr/bin/env sh
set -eu
case $1 in
init)
kubectl delete role jenkins --ignore-not-found
kubectl create role jenkins --verb=create,list,watch --resource=workflows.argoproj.io
kubectl delete sa jenkins --ignore-not-found
kubectl create sa jenkins
kubectl delete rolebinding jenkins --ignore-not-fo... |
f288fe2040bebdb9d9515513edd62ea48a3fb0bef39b6fc0b2e7d69d65243989 | Shell | 908 | 32 | #!/bin/bash
# A script to initialise the dock building within the docker container. This
# is not designed to be run by gitlab , rather for local tests of gitlab
# CI/CD scripts inside the docker container.
# It is assumed that you are in the repo mounted as the working directory
# echo "[info] current dir (start)"
# l... |
7aeb37e3b36e05ab094cd762d0e587410e9d2c3418ba352f9321cc7af32a2a2d | Shell | 911 | 39 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soBusco
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# inputs
file_fa_input="$1"
path_output="$2"
... |
8daa758fe712f7097c16bc7c34474fa52cabcb2702bba22eba3d7df1bc6d2f76 | Shell | 911 | 35 | #!/bin/sh
set -e
# set -x
old_tag=$(git describe --tags --abbrev=0 --match "Release_*")
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
for path in $(ls $top_level/Packages/MIES/*Macro.ipf)
do
file=$(basename $path)
for revision in HEAD ... |
904d5cb0e37779f74180093eab741127670d05f0f08fa568ed5b86f509aada6e | Shell | 911 | 29 | #!/bin/sh
a=$1
if test "$a" = "" ; then
a=.
fi
cd $a
if git log > /dev/null && test -d .git ; then
describe="`git describe --tags`"
branch="`git rev-parse --abbrev-ref HEAD`" # branch name
modified="`git status -s -uno --porcelain | sed -n '1s/.*/+/p'`" # + if modified
gcs=`git log -... |
bf9a6a99ac3d8870297a87fb47f7b2d46f6e9f25be4fec5f2e330de0be9d61bf | Shell | 913 | 29 | #!/bin/bash
#nohup /media/StorageOne/HTS/viralmeta_bioifo/blast_module/nt_blast.sh /media/StorageOne/HTS/HPV_center/nt_blast /media/StorageOne/HTS/HPV_center/HPV_L1.fasta
##
if [ -d $1 ]; then
rm -r $1
fi
mkdir $1
cd $1
##
export path_htsa_dir=/media/StorageOne/HTS
export work_fasta=$2
export filename_extention=$... |
17ef7542f3641b5c914c7248f83f255f3fcf35c55546a69e7c2ed871ca86bcad | Shell | 914 | 17 | #!/bin/bash
echo "Installing dependencies..."
sudo apt-get update && sudo apt-get install -y build-essential uuid-dev libgpgme-dev squashfs-tools libseccomp-dev wget pkg-config git cryptsetup-bin
export VERSION=1.12 OS=linux ARCH=amd64 && wget https://dl.google.com/go/go$VERSION.... |
bcaf8f0ad269529478c2df39b7d74eac6698a58e0cfb1aa3f3c42c6996a74eb2 | Shell | 915 | 33 | #!/bin/bash
#
# A script that builds the GATK base image locally (but does not push it anywhere).
#
# Usage: build_docker_base_locally.sh <docker_image_version>
#
# After building the image, you should test it with GATK before actually releasing it
# using the release_prebuilt_base_image.sh script. You can test it by m... |
d318f5bed3b65af795aa5898addc84d48f33c8d5d7f488e0a55edf0daf76d545 | Shell | 915 | 32 | #!/bin/bash
#SBATCH --job-name=optimal-policy
#SBATCH --output=logs/optimal-policy_%A_%a.out
#SBATCH --error=logs/optimal-policy_%A_%a.err
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G
#SBATCH --array=0-35
# Parse arguments
source scr/submit/parse_args.sh
declare cost_stay cost_switch
parse_cost_a... |
f0156b09441c1c78aa5bf908fa69c0a989477912865a248e3ac86ab32b24673d | Shell | 915 | 37 | task_name=$1
backbone=$2
pretrain_path=$3
ckpt_dir="/home/cl522/github_repo/ETP/finetune/ckpt/ptbxl_super_class/$task_name"
python main_single.py \
--checkpoint-dir $ckpt_dir \
--batch-size 16 \
--ratio 1 \
--dataset ptbxl_super_class \
--pretrain_path $pretrain_path \
--learning-rate 0.001 \
... |
9bc0261431bb9f8e626ffb2039fe6f5372aeb8b5b87b7306c11edfb57b0aa1e5 | Shell | 916 | 34 | # importing packages
library(httr)
library(XML)
library(dplyr)
url = "https://data.nemoarchive.org/biccn/grant/u01_feng/mccarroll/transcriptome/sncell/10Xv3/marmoset/raw/2019-04-26_BI005_marm027_Spencer_Put_rxn2/"
# making http request
resource = GET(url)
# parsing data to html format
parse = htmlParse(resource)
# ... |
eb1cea0cd61a5ba99250b71885b23f1107fc24c3b980b10b594fea09520a5602 | Shell | 916 | 22 | #!/bin/bash
###############################################################################
# A quick and dirty way to get drugs/targets for indications from the database#
# #
# ARGS: <USERNAME> <INDICATION> <OUTFILE> <PORT> ... |
591ff4c0d16e76a3adf2b35119137287165a65c6697074e2eb9febb593d2734a | Shell | 917 | 33 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sescDNA
#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/sci... |
5a0d5af59f8454e761738ce62830977196a0d25dcacc54c3764c859e35297c4b | Shell | 917 | 33 | #!/bin/bash
# filepath: compare_folders.sh
# Usage: ./compare_folders.sh <folder1> <folder2>
# For each file in folder1, compare with file of the same name in folder2.
# Only compare as many rows as the file in folder1 has.
folder1="$1"
folder2="$2"
echo "Comparing files in $folder1 with files in $folder2 ..."
for f... |
b6a54da80ddf14320f7e5fc06956b426b763449ec489beeaa0398966713a2bbe | Shell | 918 | 26 | #!/bin/bash
set -ex
HPACKER_VENV_DIR="${1:-"${HOME}/.hpacker_venv"}"
HPACKER_REPO_DIR="${2:-"${HOME}/.hpacker"}"
# Clone the hpacker repo if it doesn't already exist
if [ ! -d "${HPACKER_REPO_DIR}" ]; then
git clone https://github.com/gvisani/hpacker.git "${HPACKER_REPO_DIR}"
fi
# Create a virtualenv for hpacker... |
bbeb7cfaccce58c763d77426e0315bef0a2b8611a2611fc2d0df5a4fe55b2546 | Shell | 918 | 26 | #!/bin/bash
head_img=$1
mask=$2
odir=$(dirname ${head_img})
echo ${odir}
base=$(basename ${head_img/.nii.gz/})
echo ${base}
fslmaths ${head_img} -mas ${mask} ${odir}/${base}_brain_raw.nii.gz
#
3dUnifize -overwrite -input ${odir}/${base}_brain_raw.nii.gz \
-prefix ${odir}/${base}_brain_unifized.nii.gz \
-ssave $... |
d1b4c43b68df92c0cfeb3085608be7f4cbe98f0d33495ea3ac56c165d7d520db | Shell | 918 | 21 | #!/bin/bash
# Author: Yamil Vidal
# Email: hvidaldossantos@gmail.com
module purge
module load AFNI
# Define input files directory
input_dir=/mnt/beegfs/XNAT/COGITATE/fMRI/phase_2/processed/bids/derivatives/masks/ICBM2009c_asym_nlin
master=/mnt/beegfs/XNAT/COGITATE/fMRI/phase_2/processed/bids/derivatives/fslFeat/group/... |
074c04df4c25fd3ce5e79256469ed949c1a6cdddaa0219fa354ae7c0cbd8ffd4 | Shell | 921 | 27 | #!/bin/bash
# exit early if any command fails
set -e
# Install great_expectations using the airflow constraints file for our minimum supported version
AIRFLOW_VERSION=2.5.0
PYTHON_VERSION="$(python --version | cut -d " " -f 2 | cut -d "." -f 1-2)"
CONSTRAINT_URL="https://raw.githubusercontent.com/apache/airflow/con... |
84b13c668033abf05f10fcf24b14654fb22b7a2905dfee11f185726fab7e3853 | Shell | 921 | 15 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_gaussiansmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_gaussiansmooth/$filename
for i in {1... |
f1b83a33666c1078c22ab4f2449f9c7c29bea5569e7f2ccf21d050627888779e | Shell | 921 | 33 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=24:00:00
#SBATCH --job-name=shi_viz_seslvl
#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 c... |
4ae5a5cff18848dae7ff9ea1830a792c7166a19e4b4c007cd09954eadde64612 | Shell | 922 | 33 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=12:00:00
#SBATCH --job-name=shi_viz_sublvl
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=12G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
# Get repository root - use SLURM_SUBMIT_DIR (directory where sbatch was ... |
dd78acd119379d66188a33cae25252395142c86572d5192554ec6976004195b4 | Shell | 922 | 21 | #!/bin/bash
# Scans Python files changed relative to origin/develop under great_expectations/ and
# tests/ for linter/type ignore directives (e.g. noqa, type: ignore) that lack an
# explanatory comment. This does not run mypy and does not affect its exclusion config;
# it is a separate, narrower check on why an ignore... |
5e20f84d7a67bd38d83f95a17a724546b5db1a9f31bb07b3b243d5e1d35eefbf | Shell | 923 | 9 | #!/usr/bin/env bash
# Run the pipeline (Mark Duplicates, BQSR, Haplotype Caller) on genome data in HDFS.
. utils.sh
time_gatk "MarkDuplicatesSpark -I hdfs:///user/$USER/q4_spark_eval/WGS-G94982-NA12878-no-NC_007605.bam -O hdfs:///user/$USER/q4_spark_eval/out/markdups-sharded --sharded-output true" 256 1 4g 4g
time_g... |
6977e9d38d51162a344b4743fb9f93502b65f72ad94aeb5f1bc7d273559e8eee | Shell | 923 | 36 | #!/usr/bin/env bash
TRIES="$1"
shift
DIRS=("$@")
TS=$(date +%Y-%m-%d_%H-%M-%S)
TS_DAY=$(date +%Y_%m_%d)
for dir in "${DIRS[@]}"; do
mkdir -p "${dir}/log"
mkdir -p "${dir}/log/${TS_DAY}"
echo "--- Trying in ${dir} ---"
passed=0
for i in $(seq 1 ${TRIES}); do
logfile="${dir}/log/${TS_DAY}/r... |
a1ee6340441001deb2fbd3d349229d448519e73f5f40cbca0f53ff8e01518518 | Shell | 926 | 34 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
wd=$pd/data/neural_differentiation_dataset/FASTQ
mkdir -p $wd
cd $wd
# download files
HOST=ftp.ebi.ac.uk
USER=anonymous
DIR=biostudies/nfs/E-MTAB-/695/E-MTAB-15695/Files
lftp -e "
cd $DIR
mget *.fq.gz
bye
" -u $USER, $HOST
# con... |
c8441aae1b996eae97293b3f5e7429f2a2533f520bc38121f588ffa015ca7589 | Shell | 926 | 15 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_gaussiansmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
# mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_gaussiansmooth/$filename
for i in... |
3ae5f2a29d72a5527fce77bf5fc32f916d80576b469d37fcedddd049b0999afc | Shell | 929 | 27 | #!/bin/bash
set -xe
get_version() {
python -c "from continuous_integration.versions import get_oldest_pypy_package_version; print(get_oldest_pypy_package_version('$1', '$2'))"
}
get_python_versions() {
python -c "from continuous_integration.versions import get_adjacent_python_versions; print(*get_adjacent_py... |
fcbd90293f90cde863c1e519992c2027323fe2fbf4d9f0189b559939c8a883b7 | Shell | 929 | 28 | #!/bin/bash
#SBATCH -c 10 # Request cores
#SBATCH -t 0-12:00 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem-per-cpu=8G # Memory per core
#SBATCH -o jobs/banc_split_%j.out # File to ... |
9523143f1379efff1f59e091f4774c13e8f22e98dc83fbd1bdd7c5649a70cd86 | Shell | 930 | 34 | #!/bin/bash
set -e
set -x
GIT_DESCRIBE_TAG="${PKG_VERSION}"
CPATH="${LIBRARY_PREFIX}/include"
export GIT_DESCRIBE_TAG CPATH
mkdir -p build/afni_data
cd build || exit 1
# shellcheck disable=SC2086
cmake ${CMAKE_ARGS} \
-DCOMP_COREBINARIES:BOOL=ON \
-DCOMP_RSTATS:BOOL=OFF \
-DCOMP_ATLASES:BOOL=OFF \
-D... |
9eb498dfa90c5b0a0256645e152c46610ed0494794dcb7f225ac1332b4095e46 | Shell | 930 | 32 | conda activate SComatic
myPath=/media/MaleBRCA
OUTdir=$myPath/result/OUT_SComatic
cd $myPath
SCOMATIC=SComatic
REF=reference/genome/hg38/hg38.fa
editing=$SCOMATIC/RNAediting/AllEditingSites.hg38.txt
PON=$SCOMATIC/PoNs/PoN.scRNAseq.hg38.tsv
mkdir -p $OUTdir
cd $OUTdir
if [ -f $myPath/SComatic.list ]; then
rm $myPath... |
837944608a4156a9077a5fc4b74412a0d329cb6891afcba41cbb381fc3512084 | Shell | 931 | 30 | #!/bin/bash
#####################################################################
# Copyright 2024 Blue Brain Project / EPFL
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.... |
7929ac0f3fa0276bf28b391b227f6ca54af04f40e8cf7e35a9e097207688444f | Shell | 932 | 36 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=30
#PBS -N TopicModel
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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... |
551a9bbd3eb3c0d178e192f274ec1d8412db7c75a4f07d2beef1439f28a00296 | Shell | 935 | 41 | #!/usr/bin/env bash
# create binary masks of grey, white and combined borders
# Lennart Verhagen
# give help
if [[ $# -lt 1 ]] || [[ $# -gt 5 ]] ; then
echo ""
echo "create binary masks of grey, white and combined borders"
echo ""
echo "GMWMborder.sh <GM> <WM> [kernelSize] [outputBase] [outputAppend]"
echo... |
8d3320f0bf5e6bc85aa1bcc4cb30616acad95b6d4b4cc639a02fc15299997e0b | Shell | 935 | 29 | #!/bin/bash
# This script is used to create a local database from PacBio assemblies for BLAST searches
# makeblastdb version 2.16.0+
# blastn version 2.16.0+
path_ref_genes="Data/02.Local_Database_Blast/in/Referece_Genes/"
path_database="Local/path/to/databases/"
gene_array=( OT OTRa OTRb VT VTR1Aa VTR1Ab VTR2Aa VTR2... |
e988931b205c1245bebad1c8e9422e26b04076fb2e1c917abfb5fcd9b1edb5d5 | Shell | 935 | 36 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=16
#PBS -N RegionalDEG
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="r4_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
... |
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