sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
581cf1cffb4832edecc4c082eed3ff79081c9804cd32fb59af984cbe4f3aedcc | Shell | 1,797 | 37 | #!/usr/bin/env bash
# pre-build.sh: setup commands to run before building anything.
# Invoked by the Makefile automatically.
# If this script fails, the build will fail.
set -e
# We don't want to put dependency checks here because we run before `make
# get-deps` can do any dep-getting.
if which protoc >/dev/null 2>&1... |
ac5eac4d7a55486af71b0c5d1dfb61b52b407699ac047c8228dc0ee6715fb562 | Shell | 1,803 | 70 | #!/bin/bash
prdmeasures=$1;
resmeasures=$2;
bform=$3;
preds=${*:4:$#};
if [ -z "$preds" ]; then
preds_STR="";
preds_add_STR="";
preds_ablate_STR="";
else
until [ -z "$4" ]
do
if [ -z "$preds_STR" ]; then
preds_STR=($4);
else
preds_STR+=($4);
fi;
if [[ $4 =~ ~.* ]]; then
new=${4:1};
if [ -z "$... |
d356a2baf392c7542e423c76ead45b399842861ab7bcf1684b2c159b9f599195 | Shell | 1,808 | 51 | #!/bin/bash
######################################## BSUB Headers ###########################################
# Begin LSF Directives
#BSUB -P BIF135-TWO
#BSUB -W 02:00
#BSUB -nnodes 1
#BSUB -q batch
#BSUB -alloc_flags "gpumps"
#BSUB -J train_test_gcpnet
#BSUB -o job%J.out
#BSUB -e job%J.out
###########################... |
6895911d148fa4a245c080fad6e90776337fa3c2a8bc3febcf3b4ad477234ff3 | Shell | 1,811 | 51 | #!/bin/bash
######################################## BSUB Headers ###########################################
# Begin LSF Directives
#BSUB -P BIF135-TWO
#BSUB -W 24:00
#BSUB -nnodes 1
#BSUB -q batch-hm
#BSUB -alloc_flags "gpumps"
#BSUB -J train_test_gcpnet
#BSUB -o job%J.out
#BSUB -e job%J.out
########################... |
165dc3e36294657c2421c7f9f3a70866b76f330f4871286e6cc0fe92e53eba0f | Shell | 1,819 | 69 | #!/bin/sh
#============================================================
# JSONLAB inline documentation to wiki convertor
#
# Author: Qianqian Fang <q.fang at neu.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} / this file is part of EasyH5/ {exit} \
/-- ... |
c31b52b93489601fe04dc96879e6d0c5765fa834ba27320630d7c7108a9a2f57 | Shell | 1,828 | 67 | #! /bin/sh
# Usage: ./i1-hmmbuild.sh <hmmbuild binary> <MSA file> <tmpfile prefix for filenames>
#
# Verifies that hmmbuild builds HMMs reproducibly (no stochastic run-to-run variation by default).
#
if test ! $# -eq 3; then
echo "Usage: $0 <hmmbuild binary> <MSA file> <tmpfile prefix>"
exit 1
fi
hmmbuild=$1; i... |
59027b780013408d0373d788c186c4e73ebfc63398d5541ac1a5b033e7f0d3b4 | Shell | 1,848 | 57 | #!/bin/bash
function runGAJob {
CDGA_INPUT_PARAM=$1
shift
NEGATIVE_RADIUS=20
MASK_THRESHOLD=20
REQUESTED_CORES=$((${CORES_RESOURCE:-0}))
CPU_RESERVE=$((${CPU_RESERVE:-1}))
CONCURRENCY=$((2 * REQUESTED_CORES - CPU_RESERVE))
if [ ${CONCURRENCY} -lt 0 ] ; then
CONCURRENCY=0
f... |
0ccb55b4b0dbdce8ea941e82b75bab855b5ed0e5bff51f54a651186b1e2cb9b3 | Shell | 1,877 | 61 | #!/bin/bash
# rest only analyses
datasets=("PNC" "HCPD" "HBN")
measures=("GBC")
script_dir="/cbica/projects/network_replication/manuscript/code/connectivity_measures"
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
# Loop through each dataset
for dataset in "${datasets[@]}"; do
# Loop thro... |
7fe55d73b5e17f9179a81f52a2d323b7f220ef9b9e97f1e0816f785201c9521c | Shell | 1,881 | 54 | #!/bin/bash
# BASALT 1.2 Installation Script
set -euo pipefail
# 1. Ensure the Conda environment is activated
if [ -z "${CONDA_PREFIX:-}" ]; then
echo "Error: Please activate your Conda environment first."
exit 1
fi
if [ ! -d "$CONDA_PREFIX/bin" ] || [ ! -w "$CONDA_PREFIX/bin" ]; then
echo "Error: $COND... |
d90d2f03df39c0b204c24797caefd3648281c14b06b9d7f47fd8178c0cc71fb1 | Shell | 1,882 | 70 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# Calculating Enrichment score for
# cluster-based mthods
#======================
# Parameters for running
# InputLoop = loop file in bedpe format
# ValidPet = uniquely valid pet file in bedpe format
... |
958468b117015028f22e35fe3873e4b95952bff6aea61e76d0e7a1527e0cb51b | Shell | 1,884 | 66 | ## Get Freesurfer summary statistics of ROI.
# Import previously defined ROI and extract Freesurfer summaries.
#
# Vinding, M. C., Eriksson, A., Low, C. M. T., Waldthaler, J., Ferreira, D., Ingvar, M., Svenningsson, P., & Lundqvist, D. (2021). Different features of the cortical sensorimotor rhythms are uniquely linked ... |
d3b801b1674dce9753acec9df3546a6b7aec2b9e55c2adbf9af74db4462baf14 | Shell | 1,890 | 46 | #!/usr/bin/bash
MDL_VAR=$1
source ~/.bashrc
cd ~/modelblocks-release/workspace
#####################################################################
# (0) copy the lme formula for the pereira fmri corpus to the
# designated directory in the pipeline
##############################################################... |
b2ad0ff44e15ade0a28eaf78552a49cab95ee75215dc3284bbc88365c269893b | Shell | 1,911 | 87 | #!/usr/bin/env bash
# Set bash to 'debug' mode, it will exit on :
# -e 'error', -u 'undefined variable', -o ... 'error in pipeline', -x 'print commands',
set -e
set -u
set -o pipefail
log() {
local fname=${BASH_SOURCE[1]##*/}
echo -e "$(date '+%Y-%m-%dT%H:%M:%S') (${fname}:${BASH_LINENO[0]}:${FUNCNAME[1]}) $*"... |
b2234b493be7e174c8c96e4103edf37d7b3ceaa3c4eaf6c83f06f963bc88606e | Shell | 1,916 | 65 | #!/bin/bash
#
# Tries ports incrementally, starting with the given argument, and when it finds a free port runs an Xvfb instance in the background.
#
# Evaluate with `source` before starting GUI operations in your script.
#
# At the end of this script, the following state will be set:
# XVFB_PORT: the port that Xvfb ... |
42000b6773357aa5bba6496232a158ea218741dbf6578eaf6cad6af78970e4b2 | Shell | 1,938 | 25 | # parameter exploration settings
# select params
export paramexp_type=" \"tm\""; # choose iz (izhikevich) or tm (tsodyks-markram) parameters exploration
export fdr_prefix="param_explore_tm_" # folder name prefix
export run_on_hopper=1 # run from hopper's system
export local_run=2 # local run number
export use_hopper_... |
562747e4e59e6d0ac0d8be63c647eeb5ada6361e61ba8c8e9fd1695454bf8b1a | Shell | 1,948 | 44 | #!/bin/bash
path="path/to/file"
sample="GE_meis_IP"
input="GE_meis_input"
# cutadapt
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -o $path/raw_data/"$sample"_cutadapt.fastq.gz \
$path/raw_data/meis_GE_IP.fastq.gz \
--minimum-length 30 --cores=1 &> $path/out/"$sample"_cutadapt_report.txt
cutadapt -a AGATCGGAAG... |
54b8361866e23935b1d7b0dcf08e18c3a6920c394b2384f9367dd7b5d1f32ba7 | Shell | 1,965 | 25 | # parameter exploration settings
# select params
export paramexp_type=" \"tm\""; # choose iz (izhikevich) or tm (tsodyks-markram) parameters exploration
export fdr_prefix="param_explore_tm_" # folder name prefix
export run_on_hopper=1 # run from hopper's system
export local_run=2 # local run number
export use_hopper_... |
2e24a4272be5fcc7798f4bea827fa961dfe8531c6f678af20b96df6eccec268f | Shell | 1,969 | 68 | #!/bin/bash
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
functions_dir="/cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/"
###############################
# Fit GAMs for GBC, rest only #
###############################
datasets=("PNC" "HCPD" "HBN")
# Loop th... |
74bd01e7c4d2d9af3eecdd2f8dcd2957ba073a4060fa2ff7c11f9c6fd67aaeb3 | Shell | 1,998 | 73 | #!/bin/bash
# Builds a macOS app in a DMG container using PyInstaller and an app launcher.
# usage (append e.g. "App" to name to avoid naming conflicts with the library):
#
# osx_build_app.sh AppNameApp [AppVersion]
#
# Notes:
# - AppVersion is optional (used for name of DMG container)
# - This script must be calle... |
f1f39f9deb5bd4ffb7f98e66fe43c7ee33b5155a2834a3104da5a1ae4b49de7c | Shell | 2,020 | 63 | #!/usr/bin/env bash
# Set bash to 'debug' mode, it will exit on :
# -e 'error', -u 'undefined variable', -o ... 'error in pipeline', -x 'print commands',
set -e
set -u
set -o pipefail
lang=turkic
train_set=train_${lang}
valid_set=dev_${lang}
test_sets="test_az_lid test_ba_lid test_cv_lid test_kk_lid test_ky_lid test_... |
7c5109695f8d19e623315c24f4da73e601f6d9e3baf86a9705c85387a478812c | Shell | 2,028 | 48 | #!/usr/bin/bash
MDL_VAR=$1
source ~/.bashrc
cd ~/modelblocks-release/workspace
#####################################################################
# (0) copy the lme formula for the natural stories corpus to the
# designated directory in the pipeline
###########################################################... |
bad60f12d0953025a2c3d352df6391a257f2f7e0d5d6511a81abe98d70c25952 | Shell | 2,028 | 60 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# Function description
# Benchmark of ChIA-PET tools
#===============
raw_dir=$1
prefix=$2
out_dir=$3
# Set your own configurations
config=$4
source ${config}
echo ${thread}
# Running CPT2
mkdir $... |
093456a229dcd12299044c5efbcdfa835f75bedde195c128378268714d0a01f4 | Shell | 2,036 | 39 | #!/usr/bin/env bash
# Unit tests for the grpy module. Independent of the SOMO qmake build: compiles against the
# module headers (..) only.
#
# ./run.sh
#
# The solver itself is NOT tested here -- it is a separate GPLv3 program (ehb54/grpy-cpp)
# with its own golden tests against the original Fortran. What lives here... |
d4ae4766333ed1cceeba513245f1089a2ab5debfcb37a46f58627d277bcde429 | Shell | 2,044 | 72 | # Automatically modify simulation parameter settings for parameter explorations
# Use matlab's linspace (e.g., linspace(0,128,5)) to find param ranges.
# This version is for Izhikevich params
# Note: the target line to be changed with regex must be converted to 1 line not
# multiple lines.
# params
source ./config_fil... |
ea0429cb54311d5463dda803cda7e91db4628049b2129e962f6ea2c90b518b24 | Shell | 2,054 | 42 |
cd ../data/recount3/recount3_fix_download
#download the counts
wget http://duffel.rail.bio/recount3/human/data_sources/tcga/gene_sums/AD/PAAD/tcga.gene_sums.PAAD.G026.gz
wget http://duffel.rail.bio/recount3/human/data_sources/tcga/gene_sums/HC/LIHC/tcga.gene_sums.LIHC.G026.gz
wget http://duffel.rail.bio/recount3/hu... |
a5a911d6db4478e7a5c23328b53ec4cccd83d670b072aa720e9717ae2bbd4de8 | Shell | 2,057 | 75 | if [ $(uname) == 'Linux' ]; then
echo "Detected Host System: Linux"
# Setup xauth file location; Remove if exists
echo "Setting up X11 forwarding for User: ${USER}"
XTEMP=/tmp/.docker.xauth.${USER}
if [ -e ${XTEMP} ]; then
rm -f ${XTEMP}
fi
# Create new xauth file
touch ${XTEMP}... |
ca12f4eb39babf324a05a95a4efcd5e99b27743ebb92b135c04c8eae0caf83da | Shell | 2,066 | 65 | #!/usr/bin/bash
# copypkg-win - copy files for packaging - Windows-64
SRCDIR=/cygdrive/c/Users/gegorbet/us3_git/ultrascan3
SOMOBASE=${SRCDIR}/us_somo
QTBIN=c:/msys64/mingw64/bin
QTPLG=c:/msys64/mingw64/share/qt5
DESTDIR=/cygdrive/c/dist
SYSTYPE=`uname -o`
if [ "${SYSTYPE}" != "Cygwin" ]; then
echo "$0 requires a... |
9b9f616bb4979e5552348467c77a3b5e400ba6c494a06c5f7ba05f9cb495c8eb | Shell | 2,100 | 93 | #!/bin/bash
# Set up some stuff for getopts
OPTIND=1
home_dir=$(pwd)
version=2
usage() {
echo -e "Usage: $0 [OPTIONS] DIR0 DIR1 ..."
echo -e " DIR0 DIR1 ... Case directories"
echo -e " -v [2, 3]\n\tCSV version (2 default)"
echo -e " -h\n\tPrint this help and exit"
}
while getopts "v:h" opt; do
... |
45b00833734da73961bbe6cb79bbb250c2077fd2e49ff148cc03dea762189024 | Shell | 2,118 | 47 | #!/usr/bin/env bash
# Runs clang-tidy (config: .clang-tidy) on the CHANGED LINES since <base-ref> only.
#
# usage: scripts/run-clang-tidy-diff.sh [--fix] <base-ref> [compile-db-dir]
# --fix apply the auto-fixable style fixes to the worktree (modernize-*)
#
# Output: tidy.log (raw) and GitHub annotations on stdout (... |
b992585db0df5ed29ac2a46e6dbabd479e3d3817d821cedad24e6bc424ac98f4 | Shell | 2,175 | 45 | ### Load required modules
module load samtools/1.9
module load bedtools/2.26.0
module load trimgalore/0.5.0
module load python/cpu/2.7.15-ES
module load star/2.7.7a
DIR=/gpfs/data/depledgelab/scRNASeq-Reanalysis
### Generate Hybrid Genome index comprising MM10 and HSV-1 strain McKrae (MN136524.1)
STAR --runThreadN 1... |
ae9b44b18a45f5e394ed281afb486eb76b7030538112f388b462bb88291829ca | Shell | 2,188 | 54 | #!/bin/bash
# This script simulates reads using ART (Huang et al. 2012) that was modified to add adapter sequences
# (Jiang et al. 2014). We simulated ~1M 125 bp PE reads (0.1x genome coverage) using the empirically
# determined quality score profile (based on data derived from real HiSeq 2500 sequencing reads) -
# whi... |
2ba22cab80af157e888680ddc7a083bdf7629a7e37b892227a5d14bf1c81e25c | Shell | 2,224 | 57 | #!/bin/bash
# Generate APA for significant loops
# Created by LiTang
# tangli_csu@csu.edu.cn
# Process bedpe file
# Parameters for running
# bedpe = input bedpe file with at least 7 columns: chr1 str1 end1 chr2 str2 end2 pval/count
# hic = the path of .hic file for the respective genome
# lift = [1,0] 1 run liftover; ... |
49d297bb60520ef521d88fcca206be40b2d79b0a9eef80265f6804211a78d0c0 | Shell | 2,228 | 65 | #!/bin/bash
function runCDSJob {
MASK_INDEX=$(($1))
TARGET_INDEX=$(($2))
shift
shift
MASK_OFFSET=$((MASK_INDEX * MASKS_PER_JOB))
TARGET_OFFSET=$((TARGET_INDEX * TARGETS_PER_JOB))
REQUESTED_CORES=$((${CORES_RESOURCE:-0}))
CPU_RESERVE=$((${CPU_RESERVE:-1}))
CONCURRENCY=$((2 * REQUE... |
58dd892918614d3407bdb4617562a173b2a883c74c82ca856017d387efb35ba8 | Shell | 2,231 | 51 | #!/bin/bash
echo "choose the group you want to process and press [ENTER] :"
ls /work/cascades/bz10/VCU_mouse/data
read GROUP
cd /work/cascades/bz10/VCU_mouse/data/$GROUP 2> /dev/null
##############################################################################
until [ "$PWD" == "/work/cascades/bz10/VCU_mouse/data/$G... |
3ce2dda4875ed462de53ff9116c6a0dac163168650b8d8beb99f155060382b7a | Shell | 2,271 | 95 | #!/bin/bash
JAR_VERSION=3.0.0
AREA=brain
# EXPORT_TYPE can be one of:
# EM_MIPS, LM_MIPS, EM_CD_MATCHES, LM_CD_MATCHES, EM_PPP_MATCHES
EXPORT_TYPE=EM_PPP_MATCHES
OUTPUT_DIR=/nrs/neuronbridge/v3.0.0/${AREA}
CONFIG="--config local/proddb-config.properties"
RUNNER=
# Typically no change is required below this point
E... |
37ad5ae88192dd04260bcce720062d747f2daba7aa5f975581fb0129a8b619bf | Shell | 2,286 | 65 | #! /bin/bash
# Setup a SIGINT handler. Not sure why, but this is necessary for SIGINT (Ctrl-C) to cancel this script.
handle_sigint() {
echo "Caught SIGINT (Ctrl+C). Exiting..."
exit 130 # Exit with a specific code (128 + signal number)
}
# Trap the SIGINT signal and call the handle_sigint function
trap handle... |
2615e0fe2bb58dc6e0a0564f568b3aa770b8b9f4abfc2b16847cddcb0d70e530 | Shell | 2,288 | 54 | #! /bin/bash
#install docker, adapted from here: https://docs.docker.com/engine/install/ubuntu/
#NOTE this assumes you don't have docker installed already. If it's already there, it might get overwritten!
sudo apt-get update -y
sudo apt-get install -y ca-certificates curl gnupg lsb-release unzip bzip2
#install dock... |
1c0affee210e6779217f53a5b0d205ca60e2cd8f2d5d6437d72d325206c43ad1 | Shell | 2,289 | 65 | #!/bin/bash
# --- Configuration ---
ENV_NAME="glstm_env"
PYTHON_VER="3.5"
# Using CUDA 10.0. Change 'cu100' to 'cpu' if you don't have a GPU.
TORCH_WHL_URL="https://download.pytorch.org/whl/cpu/torch_stable.html"
#TORCH_WHL_URL="https://download.pytorch.org/whl/cu100/torch_stable.html"
# Stop script on first error
#s... |
b10ed92dae4aa030ef5cd137de5ec7ce783e8a6f67b0c1f4d2c9d0975962d334 | Shell | 2,307 | 84 | S3_BUCKET=janelia-neuronbridge-data-devpre
S3_DATA_VERSION=v3_0_0
LOCAL_DATA_DIR=/nrs/neuronbridge/v3.0.0
MIPS_DIR=mips
CDS_RESULTS_DIR=cdmatches
PPPM_RESULTS_DIR=pppmatches
PER_EM_DIR=em-vs-lm
PER_LM_DIR=lm-vs-em
LM_MIPS=lmlines
EM_MIPS=embodies
AWS="echo aws"
AWSCP="$AWS s3 cp"
uploadMIPS() {
local region="$1"... |
c0715c601accc0a4e1736528f0988fc33c4b20c45a558e7f227255c4fb3fe0d5 | Shell | 2,317 | 50 | #! /bin/sh
#
# Verify that phmmer/jackhmmer runs are reproducible (no stochastic variation),
# unless the RNG seed is deliberately varied.
#
# Example sequences here are carefully chosen to exercise stochastic clustering
# algorithm in domain postprocessing pipeline. [xref 2019/0410-h3-test-failures]
#
if test ! $# -eq... |
e70504420e5e5295af1d366499105e836cdbacef5979266d9a5594eab4bfd26b | Shell | 2,359 | 14 | ## Train CRI, Spring N5K2, change the parameter --train-examples [100, 500, 1000, 5000, 10000] to use different number of simulations for training
CUDA_VISIBLE_DEVICES=0 python train_CRI.py --input-dir ../dataset/sim_springs/K_2/particle_5/30000_train_5000_valid_5000_test_BalancedTypes_2/ --save-folder trained_CRI_spri... |
6baead552e3d33dc1043cb413d992732a7c09cff5523a5441acf5461a781f806 | Shell | 2,384 | 89 | #!/bin/bash
# This script will install debian pkg dependencies and activate
# the reat-time conda environment (rt) defined by environment.yaml
# Notes
# - this has only been tested on Ubuntu 18.04
# - libevent-2.1-6 was already installed on my machine,
# so assuming it comes default with Ubuntu 18.04
RED="\e... |
7200ddbab386c9e6bdc1c07f2a2ced211b4ed7a5bda397e00295183070626636 | Shell | 2,392 | 36 | #!/bin/bash
set -euo pipefail
readlinkf() { perl -MCwd -le 'print Cwd::abs_path shift' "$1"; }
SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# This script loads data and runs a server using the globally installed `pheweb`.
# It's helpful when you're modifying the code and want to quick see the results.... |
5f37539f3bc8115967cf8b087e56b0231ea6a6c8c1e1b97abbc0680583abd5fd | Shell | 2,397 | 34 | #!/bin/bash
# measure command execution time
measure_time() {
start_time=$(date +%s.%N)
eval "$1"
end_time=$(date +%s.%N)
elapsed_time=$(echo "$end_time - $start_time" | bc)
echo "Command '$1' took $elapsed_time seconds"
}
# define checkpoint paths
lba_model_ckpt_path="checkpoints/LBA/model_1_epoc... |
c2a02c64d0a2c8382ab63edca14fab9381f43d10a9b7be809cbb227749f735a7 | Shell | 2,477 | 69 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# Calculate peak occupancy for peak-based methods
#===============
# bedtools need to be installed in system path (https://bedtools.readthedocs.io/en/latest/)
# loop = called loops in bedpe format
# pea... |
712d5ef9161b3f7ece713f395798d82f2ecc7a4f8da1b3206ba200f4fb6c61dd | Shell | 2,488 | 71 | #!/usr/bin/env bash
# Checks (or fixes) the UltraScan III code style (.clang-format) on CHANGED LINES only.
#
# Also runs scripts/check-conventions.py (connect syntax, EOF newline, guards, \file header; needs pygments).
#
# usage: scripts/check-format.sh [--fix] [--staged | <base-ref>]
# --staged check the staged ... |
5d05c47812e323da1b17c95daf2d0963c70aecccbc8c7c0e134cb882757c395a | Shell | 2,511 | 15 |
## Train Var-CRI, Spring N5K2, change the parameter --train-examples [100, 500, 1000, 5000, 10000] to use different number of simulations for training
CUDA_VISIBLE_DEVICES=0 python train_VarCRI.py --input-dir ../dataset/sim_springs/K_2/particle_5/30000_train_5000_valid_5000_test_BalancedTypes_2/ --save-folder trained_... |
c97b3be15a4e16d729fef15925e758f186c7d6a163814df47590589426848fae | Shell | 2,516 | 56 | #!/bin/bash
#SBATCH --partition=p_waksman_0
#SBATCH --job-name=trimmomotic
#SBATCH --nodes=1
#SBATCH --ntasks=3
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2000
#SBATCH --time=12:00:00
#SBATCH --output=AXXC.slurm.%N.%j.out
#SBATCH --error=AXXC.slurm.%N.%j.err
#SBATCH --export=ALL
set -x
cd /scratch/hht25/gse101/f... |
c939775622f8bde747f596471d26a5fbc35c82b0b5c4eaa9344b9981ad099896 | Shell | 2,545 | 58 | #!/usr/bin/bash
MDL_VAR=$1
source ~/.bashrc
cd ~/modelblocks-release/resource-llm-pred/scripts
conda deactivate
# source ~/miniconda3/bin/activate llm-pred
source ~/miniconda3/bin/activate fmri-pred
# for storing intermediate files (will be deleted)
mkdir ~/modelblocks-release/workspace/genmodel/llm_pred_temp
# in... |
4ddb5041fbfacaca747e597ffd9fa0fe5f69a932a5fe46bda0f8715c4891a9db | Shell | 2,559 | 99 | #!/bin/bash
PRECOMPUTE_SCRIPTS_BASEDIR=${PRECOMPUTE_SCRIPTS_BASEDIR:=${SCRIPT_DIR}}
# This allows running this in parallel on different machines
# and use different environment
ENV_FILENAME=${ENV_FILENAME:="${PRECOMPUTE_SCRIPTS_BASEDIR}/../.env"}
echo "ENV file: ${ENV_FILENAME}"
if [[ -f "${ENV_FILENAME}" ]]; then
... |
f548ca4a5066d49a604466632ec857d84a4dcf81ba564df50259df28cc7bfb44 | Shell | 2,559 | 99 | #!/bin/bash
PRECOMPUTE_SCRIPTS_BASEDIR=${PRECOMPUTE_SCRIPTS_BASEDIR:=${SCRIPT_DIR}}
# This allows running this in parallel on different machines
# and use different environment
ENV_FILENAME=${ENV_FILENAME:="${PRECOMPUTE_SCRIPTS_BASEDIR}/../.env"}
echo "ENV file: ${ENV_FILENAME}"
if [[ -f "${ENV_FILENAME}" ]]; then
... |
d239a1c35af8361c80a3fa5baf5f8e5779ff49c7d7ae934d07267d6bb93c5b5c | Shell | 2,603 | 38 | mkdir -p data/008/salmon/ketogenic_diet/raw_fastq
cd data/008/salmon/ketogenic_diet/raw_fastq
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/003/SRR19764203/SRR19764203.fastq.gz -o SRR19764203_GSM6257088_Ketogenic_Diet_Oligodendrocytes_-_R4_Mus_musculus_RNA-Seq.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fast... |
91872045479dcd0bd2e539b9e5560b8aa99545549e1cca40a9491659c45a7690 | Shell | 2,608 | 22 | # parameter exploration settings
# select params
export paramexp_type=" \"iz\""; # choose iz (izhikevich) or tm (tsodyks-markram) parameters exploration
export fdr_prefix="param_explore_iz_" # folder name prefix
export local_run=3 # local run number
export run_on_hopper=1 # run from hopper's system
export use_hopper_... |
576025152af8e241b7424c4b8faf8cd980ebc36b885a175070a5750b7fc37fb5 | Shell | 2,647 | 94 | #!/bin/bash
set -euo pipefail
usage() {
cat <<'USAGE'
Usage: scripts/push_tag_for_release.sh <version> <branch> [options]
Create the release commit and tag for a new pandas version and push them to the
remote, which triggers the wheels/PyPI, docs and GitHub release automation.
Arguments:
<version> R... |
eb3234b659cb810d29253368f4616be570610ea983295fbbfe89523af20e01c1 | Shell | 2,652 | 90 | # Automatically modify simulation parameter settings for parameter explorations
# Use matlab's linspace (e.g., linspace(0,128,5)) to find param ranges.
# This version is for Tsodyks-Markram params
# Note: the target line to be changed with regex must be converted to 1 line not
# multiple lines.
# params
source ./confi... |
61cba6ebe26990d781ce6002fea017b228281bfc5f3fc2207f3ec9e5440e9928 | Shell | 2,663 | 90 | #!/bin/bash
home_dir=$(pwd)
rebuild_poly_links()
{
poly_dir="$1/constant/polyMesh"
if [ -d "$poly_dir" ]; then
rm -r "$poly_dir"
ln -s ../../simpleFoam/constant/polyMesh "$poly_dir"
fi
}
removelink()
{
if [ -L "$1" ]; then
cp "$1" TEMPFILE
rm "$1"
mv TEMPFILE "$... |
1c4aac56c0b937b8f45173b13b37ade88cb2dcff4b7f6489d8034891a450590e | Shell | 2,763 | 63 | #!/bin/bash
# Author:
# Jae Wook Cho
# Input example:
# /home/xli/data/site-newcastle/sub-032104/sub-032104_ses-003_run-1_T1w.nii.gz
# Core parameter for ANTs
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
i=$1
site=`echo ${i} | cut -d '/' -f8`
sub=`echo ${i} | cut -d '/' -f9`
file=`basename ${i}`
filestring=`echo ... |
11f9588c2e417bcc177bea97a13990a469835e1d48dbbaf9146aeee3a50636dd | Shell | 2,776 | 62 | # Process to create, compile, and run new CARLsim6 project
# This version is for use on a supercomputer
# Note: one must already be on the gpu node (salloc -p gpuq -q gpu...)
# to run this script because it exits the script to switch nodes.
# Therefore that step is not automated.
proj_name="$1" #"hello_world_2" # new ... |
3c2b1b48428abb3a064706528c8dce427f7dde626086387d5f11075f73d645db | Shell | 2,801 | 76 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# Function description
# gold standard loops generation
#===============
eqtl=$1
crispr=$2
gencode_v19=$3
candidate=$4
out_dir=$5
# extend genomic loci of variants
awk '{s1=$2-(5000-$3+$2)/2;e1=5000+s... |
63dc67e56db30d8d69b5ff1612b4707728b3e85f881b7bd1c0603c2751b94908 | Shell | 2,832 | 40 | python3 data_preprocessing.py
python3 pretrain_features.py
python3 pretrain_toxicity.py
python3 train_gnns.py --model gatmann --k 25 --blind drugs --pretrained
python3 train_gnns.py --model gamma --k 25 --blind drugs --pretrained
python3 train_gnns.py --model gatmann --k 25 --blind lines --pretrained
python3 train_gnns... |
3f3e58aa37b994d1e96ab59bca30d89420cddc49999d18ed62b272bb95a52162 | Shell | 2,856 | 102 | #!/bin/bash
#SBATCH --job-name=platelet_ml
#SBATCH --output=platelet_ml_%j.log
#SBATCH --error=platelet_ml_%j.err
#SBATCH --time=4:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --partition=godziklab
# ==============================================================================
# Platelet ML Pipeline - HP... |
7f16672de53b4a275e9e8eb3c2ebbf0f3f0a70fb58b9573d0a317be6c239ec78 | Shell | 2,859 | 74 | #!/bin/bash
codedir="../protein_holography"
datadir="../scripts"
download_pdbs=1 # 1 to download pdb files. 0 to skip download
parallelism=4
project=quick_run
subproject=example
csv_file=$datadir/$project/pdbs.csv
verbosity=1
cd $codedir
echo "Making necessary directories"
download_tag=""
if [ $download_pdbs -eq 1 ]... |
b5bba78529319013bdf315b2c3392344576352553c09fb624c885e9d12d95c80 | Shell | 2,873 | 43 | module load bioinfo-tools BEDTools/2.29.2
#first collapse FST outliers in 20 kb windows
bedtools merge -i Outliers_IT_5kb2.5_FST.bed -c 1 -o count -d 20000 > Outliers_IT_5kb2.5_FST_merged_d10kb.bed
wc -l Outliers_IT_5kb2.5_FST_merged_d10kb.bed
bedtools merge -i Outliers_SA_5kb2.5_FST.bed -c 1 -o count -d 20000 > ... |
60ccc8676d3d8c4d730f772c11b0eaddfa1767cea21485880008e3aa4d3d72fa | Shell | 2,885 | 78 | # install majiq folowing their guide:
# https://biociphers.bitbucket.io/majiq-docs-academic/getting-started-guide/installing.html
data=/mnt/d/OneDrive/PhD/projects/agc1_OliNeu/data
raw_reads=$data/delivery_20200428/raw_reads
cd $data
mkdir data/isoforms
# Align reads
mkdir -p isoforms/idx/
curl -L ftp://ftp.... |
19be989ff89a6f45f00961adc965d88b7d7fc33c5c157781ebe6d51be0b5b2d6 | Shell | 2,934 | 99 | #!/bin/bash
# Mac-compatible version of bootstrap.sh
#
# Differences from the Linux version:
# - Uses Homebrew instead of apt-get for system packages
# - Downloads the macOS Elm binary instead of the Linux one
# - Uses environment_mac.yaml (strips Linux-only conda packages)
# - Does not use sudo (Homebrew does... |
72fda1da4ab95453a7bf549bffd16fbab72335c46229224e0e505887984719a0 | Shell | 2,952 | 68 | MASKS_LIBRARY=flyem_hemibrain_1_2_1
TARGETS_LIBRARY=flylight_gen1_mcfo_published
# TOTAL_MASKS is the total number of mask images used for color depth search,
# e.g. for EM is the number of MIPs for the EM neurons plus the number of FL neurons if some neurons require an FL (flip) transformation
export TOTAL_MASKS=4459... |
d6b6e1682d83c89a1ede630ce79c7009a59ee48b0e23a5391c3e0a364f756449 | Shell | 2,978 | 87 | #!/usr/bin/env bash
set -euo pipefail
IN="${1:-us3-icon-1024x1024.png}"
OUTDIR="dist/icons"
ICONSET="dist/us3.iconset"
mkdir -p "$OUTDIR" "$ICONSET"
if [[ ! -f "$IN" ]]; then
echo "ERROR: Input not found: $IN"
exit 1
fi
# Sanity check: master must have transparency
if [[ "$(magick "$IN" -format "%[opaque]" info... |
2f0e3e4ec64d324263b535840a5c441912047b5ae46dc317b39a1901bb16578f | Shell | 3,040 | 26 | #! /usr/bin/env bash
#rm -rf cifti_conn_template_exaversion
#rm -rf cifti_conn_matrix_exaversion
#rm -rf ${FNL_preproc_dir}/filtered_movement_regressors
#rm -rf ${FNL_preproc_dir}/analyses_v2
#rm -rf ${FNL_preproc_dir}/specific_filtered_movement_regressors
/mnt/max/software/MATLAB/R2016b/bin/mcc -v -m -R -singleCo... |
ad04f397a46e0ae829c389154a5d20c11b6b5f5d4c12772f8e8ab002a52e0fad | Shell | 3,068 | 101 | #!/bin/bash
# Data Download Script for PlateletSubpop-ML-ScTranscriptomics
# This script downloads and processes single-cell RNA sequencing datasets
set -e # Exit on error
set -u # Exit on undefined variable
# Create necessary directories
mkdir -p data/{raw,processed}/{covid19,sepsis,sle}
mkdir -p data/tmp
mkdir -... |
83e90c3e391038c9fc18beb6b1df563963ef9d0e5a0b2ac415f1487a0c993d5e | Shell | 3,086 | 79 | #!/usr/bin/env bash
# =============================================================================
# Drive a SOMO CMake/vcpkg build inside the somo-cmake-env container.
#
# us_somo/develop/docker/build.sh [qt5|qt6|root-qt5|root-qt6]
#
# qt5, qt6 SOMO only: us_somo/develop's vcpkg-qt5 / vcpkg-qt6 preset
... |
418e0cdbd0af426e5fc5a276839f0375f94d1cc7fd242891641e2315e9beaf29 | Shell | 3,100 | 61 | #!/bin/bash -e
#from Fair Lab: https://www.ohsu.edu/xd/education/schools/school-of-medicine/departments/basic-science-departments/behn/people/labs/fair-neuroimaging-lab/
if [ $# -ne 4 ]; then
echo -e "\nUsage: `basename $0` <subject_directory> <subject> <atlas_HEAD_prefix> <atlas_BRAIN_prefix>"
echo -e "i.e `basenam... |
3c62af3d3620022d5b8d0517b31050ea2006fbdd835582db829a4446214d8016 | Shell | 3,143 | 76 | #!/usr/bin/env bash
#
# giraffe-speed.sh: evaluate Giraffe mapping speed.
#
# Although CPU instruction counting doesn't work in this configuration for some
# reason, you can run on an AWS r5.4xlarge, with 100 GB disk, the
# "vg-data-user" IAM role and Ubuntu 20.04:
#
# git clone https://github.com/vgteam/vg.git
# cd vg... |
65aa9379d590da1963b4b4fd1360c00493fdd31b8647673fba040157b0c4d0ea | Shell | 3,144 | 52 | #after demultiplexing, RAD-seq data was processed according to the stacks pipeline
module load bioinfo-tools
module load samtools/1.12
module load bwa/0.7.17
#first reads were aligned to the reference genome
#this step was done for all samples; here shown for an example
bwa mem -t 12 /crex/proj/snic2020-6-73/... |
b4ddb948c179fc5beb59da642b4f175a3ee985ad8e3278b22a81f8514f5fc392 | Shell | 3,164 | 48 | #!/bin/sh
# Download data for genotype-based deconvolution methods (popscle tutorial dataset)
outputdir="test_data"
mkdir -p $outputdir && cd $outputdir
wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1xl9g3IPFNISa1Z2Uqj3nia4tDWtMDz5H' -O jurkat_293t_exons_only.vcf.withAF.vcf.gz
wget --no-che... |
336f251deb9424947e71e92e69a996c840d105eaad5d55f28e9652d049a84b37 | Shell | 3,169 | 125 | #!/bin/bash
echo "Upload data"
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
# AREA: brain, vnc, brain+vnc, vnc+brain
if [ "$#" -ge 1 ]; then
AREA=$1
shift
else
echo "Anatomical area must be specified: submit_export.sh <anatomical_area> <export_type>"
echo "Valid values: {brain | vnc | brain+vnc}"
exit... |
a36013da2088f4147d2fe1d7a25565591073efc00a589658c362047a3e5c8af4 | Shell | 3,175 | 96 | #!/bin/bash
Group=GROUPGOESHERE
subgroup=SUBgroupGOESHERE
Histone=HISTONEGOESHERE
cd /work/cascades/bz10/VCU_mouse/data/$Group/$Histone/$subgroup
cd Raw_Data/
gunzip *.gz
trim_galore *.fastq
cd ..
FILES=$PWD/Raw_Data/*.fq
FQ=.fq
SAM=.sam
LOG=.log
BAM=.bam
SORT=_sort.bam
UNI=_unique.bam
PREBED=_pre.bed
BED=.bed
EXT... |
8d766a111e546e00b68e7f0dcd0cad4ab7683276b81b89315c75f2205b31da32 | Shell | 3,184 | 148 | #!/bin/bash
SUDO=
DOCKER=docker
cmd_opts=()
while [[ $# > 0 ]]; do
key="$1"
case $key in
--cmd-opt)
cmd_opts=("${cmd_opts[@]}" "${2}")
shift
shift
;;
*)
break
;;
esac
done
COMMANDS=$1
CMDARR=(${COMMANDS//+/ })
shift ... |
ab75b1b7d0bc156de3e772f6276ed673b2d346424db8418f248e1455a0446555 | Shell | 3,185 | 69 | #!/bin/bash
set -euo pipefail
readlinkf() { perl -MCwd -le 'print Cwd::abs_path shift' "$1"; }
SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
set -x
## This script should get run from the directory that contains `generated-by-pheweb`.
## It needs `generated-by-pheweb/sites/sites.tsv`, so it should get ... |
7909c48b1f300dec54c8f819c5c59461964ed2428c6ca61c1e13b505ccd28354 | Shell | 3,222 | 67 | ### Solo-LTR_identification
# ******************************************
# 1. ltr-harvest
#
# ltr-harvest for paired ltr
# ******************************************
cat short_name.xls | tail -n +2 | awk '{print "mkdir -p '${work}'/"$1"; cd '${work}'/"$1"; ln -s '${data}'/fa/"$1".genomic.fa ./; sh '${bin}'/ltrharvest.s... |
e34b5323051cc8ad78dd78ffc20171c5783d9682bd1d0d6608067db7d5600b09 | Shell | 3,224 | 51 | #!/bin/bash
cd /cis/home/kstouff4/Documents/MeshRegistration/
newV="False" # set to True if using rescaleUnits() function from Younes
# Parameters to use in the setting of rescaleUnits()
sigmaKernel=0.1 # 0.01 orriginall
sigmaIm=1 # 0.2 original
sigmaDist=0.5 # 0.02 original
sigmaError=500 #0.5
if [[ $newV == "Fal... |
0541cc336a18dfba49eb358afb4df5fd163b860f5b68d7ec8ec1badff20860b8 | Shell | 3,244 | 87 | #!/bin/bash
nb_epochs=100
# D2 training
# for training with noise injection 0% to 20% we use the optimal parameters
# found in the grid search using 10% noise injection
seed_values=(42 50 9)
n_in_values=(256)
n_delays_values=(16)
r_mu_values=(500e9)
r_std_values=(0.4)
tau_mem_values=(15e-3)
noise_std_values=(0.0 0.0... |
e8c12b6b01182a6ae65741690fbff4293df93b76a70475caf1ea44b43803d8c8 | Shell | 3,247 | 63 | #This script gathers a number of statistics on LD decay, missing genotyping data and read-coverage and SNP-densities in the candidate region.
module load bioinfo-tools
module load BEDTools/2.29.2
#obtaining the number of SNPs per 10kb-window before and after filtering:
bedtools makewindows -g /crex/proj/snic2... |
42de7066b26ae1c603c591efe73fcfcb2fb4bb5739e184819b6cebc6541aeda1 | Shell | 3,262 | 132 | #!/bin/bash
# somoupd.sh - execute commands to accomplish somo update
##CNVTEXT=us3conv.hydrodyn.txt
CNVTEXT=us3conv.txt
US3BASE=$HOME
US2BASE=${US3BASE}
USDBASE=${US3BASE}
QMAKE="qmake"
SUNAME=`uname -s`
ISMAC=`echo $SUNAME | grep -ci "darwin"`
ISWIN=`echo $SUNAME | grep -ci "cygwin"`
ISUNX=`echo $SUNAME | grep -ci ... |
1be9dc66216b14b966f6197090a0b980c3389250db1540d7f39fec7a4b2353d4 | Shell | 3,276 | 125 | #!/bin/bash
echo "Run VNC aligner with $*"
DIR=$(cd "$(dirname "$0")"; pwd)
nslots=2
reference_channel=Signal_amount
input_filepath=
output_dir=
help_cmd="$0
--nslots <nslots (default = 2)>
--reference-channel <reference channel (default="Signal_amount")>
--templatedir <template config directory>
-... |
f77bf99205aebbfee47934cc1825cd8290dd2d39c00e013aa0f627a51353ac83 | Shell | 3,312 | 100 | #! bin/bash
IFS=
# This linux shell script requires VMD to be installed and is optimized to extract the coordinates of Desmond generated trajectories
base=$(pwd)
MD_simulations=./MD_simulations # Folder of the MD simulations
traj_dir=$(cd "$MD_simulations"; pwd)
frames=1000 ### Set the number of frames ###
if ... |
649ffa58fc02ca0bea1a8f9879d9ed5201373d134f8ac7b949b7118d8860b402 | Shell | 3,328 | 39 | module load bioinfo-tools
module load star/2.7.9a
#Raw reads were trimmed using trimmomatic; here one sample is shown as example
java -jar Trimmomatic-0.39/trimmomatic-0.39.jar PE Sample1_R1.fastq.gz Sample1_R1.fastq.gz Sample1_F Sample1_F_unpaired Sample1_R Sample1_R_unpaired \
ILLUMINACLIP:Trimmomatic-0.39... |
5c39be8d7dd2bc1d3b27b3011ccb25e790b5a7ce85f6d0bedad65ba03e27b639 | Shell | 3,331 | 106 | #!/bin/bash
function run_ga_job {
# job index is 1-based index that should be passed either as the first arg
# or in the LSB_JOBINDEX env var
declare -i ONE_BASED_JOB_INDEX=$1
# convert the 1-based index to 0-based
declare -i JOB_INDEX=$((ONE_BASED_JOB_INDEX - 1))
declare MASK_NEURONS_OFFSET=$... |
0711d36cb68aeab06defc5170dd074337f72086325a58626f4cc93d4ef51a845 | Shell | 3,347 | 104 | #!/bin/bash
SAMPLE=pfc_VEH
cd /work/cascades/bz10/VCU_psychedelics/$SAMPLE
cd Raw_Data/
gunzip *.gz
trim_galore *.fastq
cd ..
FILES=$PWD/Raw_Data/*.fq
FQ=.fq
SAM=.sam
LOG=.log
BAM=.bam
SORT=_sort.bam
UNI=_unique.bam
PREBED=_pre.bed
BED=.bed
EXT=_extend.bed
EXPWIN=_extend_promotor_win.bed
EXG4000=_extend_geno_4000.... |
3a4206329c5f3c0453e5acc260a1bc2a8709cc4414cb6029aad72ccfb63cfe4f | Shell | 3,385 | 90 | #!/bin/bash
# Set up path
Schaefer1000_path='/Volumes/LASA/TBI_OpenNeuro/TBI_openneuro/data/lesions/overlap_Schaefer/Schaefer1000_wotbi09/';
cd $Schaefer1000_path
#Extract parcels from atlas
# for id in `seq -w 1 1000`; do
#
# fslmaths Schaefer2018_1000Parcels_7Networks_order_FSLMNI152_2mm -thr $id -uthr $id -bin ... |
9bfecb2aedf163ed82861fe7c0d8eae624fa16cddb7eb269f1dcde3d110199f1 | Shell | 3,405 | 132 | #!/bin/sh
# us3-update.sh - interactive script to install or update UltraScan3
# Get the directory from which this script was launched
SRCDIR=`dirname $0`
if [ "${SRCDIR}" = "." ]; then
SRCDIR=`pwd`
else
TEMP=${SRCDIR}
SRCDIR=`echo ${SRCDIR}|sed -e 's@^\/@@'`
if [ "${SRCDIR}" != "${TEMP}" ]; then
SRC... |
31404c044d71a8525bb0e5110b55a3262e2fc02b78cd1001df9108f4a0085173 | Shell | 3,532 | 96 | #!/usr/bin/env sh
# UltraScan3: generate build metadata header for the splash/About dialogs.
# - Uses git commit count for BUILDNUM
# - Adds GIT_REVISION (commit hash)
# - Adds REVISION_DATE (commit date, not build date)
# - Adds LOCAL_CHANGES (Δ symbol if uncommitted changes)
# - Writes us_revision.h only if values ch... |
253e07c9a366dc7cc2a989465914f0162e83b733fbbd3c18a2a2e22b311affe5 | Shell | 3,602 | 86 | #this script was run for each of the 149 samples;
#each sample had it's own folder including the raw fastq files
#here is the example of sample AS24
module load bioinfo-tools
module load bwa/0.7.17
module load picard/2.23.4
module load GATK/4.2.0.0
module load FastQC/0.11.9
module load trimmomatic/0.39
modul... |
a3c176c6f95675eb9508c2eefc6fb82cab9a58828f6f46ba6acbfb6e63b5088e | Shell | 3,618 | 87 | #!/bin/bash
#------ The mandatory parameters of MMCT-Loop ------
in_dir=example_workspace
in_valid_bedpe=${in_dir}/example_valid.bedpe # Processed valid pairs in '.bedpe' format.
out_prefix=example # The prefix of the output file name.
cpu=4 # The number of CPU used to run the job, default is 1, set -1 to use al... |
98f4eda01193c0d97a66e57a0a98e36b93b299785015c6768e37d6e3cbf718fc | Shell | 3,648 | 111 | #!/bin/bash
function run_export_job() {
# Supported LM Libraries
declare LM_LIBS=(
${LM_SGAL4_LIB}
${LM_MCFO_LIB}
${LM_ANNOTATOR_MCFO_LIB}
)
# Supported EM Libraries
declare EM_LIBS=(
${EM_HEMIBRAIN_1_2_1_LIB}
${EM_VNC_0_5_LIB}
${EM_MANC_1_0_LIB}
... |
25bcb76493ed89d369ff023eddd3128c948b8a596ffa0336ae52e334af94ffcb | Shell | 3,669 | 143 | #!/bin/bash
MKARGS="$@"
if [ $# -eq 0 ]; then
MKARGS="-j 7"
if [ `uname -s|grep -ci "mingw"` -ne 0 ]; then
MKARGS="-j 2"
fi
fi
export MAKE="make ${MKARGS}"
if [ -z "$ULTRASCAN" ]; then
ULTRASCAN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
echo "Notice: the ULTRASCAN environme... |
45f2b9b68ad8525a90f0e4e9c95fccc790b4d652e95afaef6cdcb391b8f0e37e | Shell | 3,834 | 121 | #!/bin/bash
function run_cds_job {
# job index is 1-based index that should be passed either as the first arg
# or in the LSB_JOBINDEX env var
declare -i ONE_BASED_JOB_INDEX=$1
# convert the 1-based index to 0-based
declare -i JOB_INDEX=$((ONE_BASED_JOB_INDEX - 1))
declare -i MASKS_PARTITION_I... |
e819ddef479bd61d7c6b9eb940fc2c8a01196c79756c5f92dbf1401ac8454ed0 | Shell | 4,041 | 151 | #!/bin/bash
echo "Run brain aligner with $*"
DIR=$(cd "$(dirname "$0")"; pwd)
xyres=1
zres=1
nslots=2
input_filepath=
output_dir=
use_voxel_resolution_args=false
reference_channel=Signal_amount
comparison_alg=Max
help_cmd="$0
--xyres <xy resolution in um>
--zres <z resolution in um>
--reference-channel... |
e661c6f497ea3adc924e9177e385727b0417c2f6e43c620034b41f3705f9362f | Shell | 4,096 | 121 | #!/bin/bash
# Set up some stuff for getopts
OPTIND=1
home_dir=$(pwd)
wind_delta=1
csv_dir="/intel_share/data/cfd_3d_csv"
python_dir="/home/nick/src/intel_wind/openfoam_batch/python"
csv_overwrite=0
unconverged_cases=0
verbose=0
usage() {
echo -e "Usage: $0 [OPTIONS] DIR0 DIR1 ..."
echo -e " DIR0 DIR1 ... Cas... |
f363ebe9a10bcfeb01b44c35322615ac821e33dd23ea9754419b88d450a30c62 | Shell | 4,131 | 208 | #!/bin/sh
# run from the ultrascan root to create unix-based tar.gz
# archive of UltraScan
#
###########################################################
#
# please edit the variables in the following section:
#
###########################################################
VERSION=9.9
TMP=/tmp
# change to QT version:
... |
99759d23e122240faadfd8ad8348f1cbbb9249e1ba21521c668ea047f28cc0d3 | Shell | 4,165 | 80 | #!/bin/bash
cd /work/cascades/bz10/VCU_human/data/HiC/promoter_loops/chr1
mkdir bedfiles_1
mkdir bedfiles_2
cd chr1_group1
ls -d chr1_*/ | cut -d '/' -f 1| while read id;do(cp ./$id/choose_promoter.bed ../bedfiles_1/$id\_promoter.bed);done
ls -d chr1_*/ | cut -d '/' -f 1| while read id;do(cp ./$id/new_choose_promot... |
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