sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c10ccd80f6d1c9ee087b5764709600a66b9d60180aba85019c306652dd921dca | Shell | 1,825 | 1 | phyloFit --tree "((((((((((((((((((((White-throated-sparrow,Yellow-rumped-warbler),(Tawny-bellied-seedeater,Medium-ground-finch)),Common-canary),House-sparrow),(White-rumped-munia,Zebra-finch)),((Collared-flycatcher,Siberian-stonechat),(Javan-myna,Common-starling))),(Silver-eye,(Willow-warbler,(Phylloscopus-plumbeitars... |
c2cd1de81a46c1ff9990949e1f153bcc706ee71fca9b44338e27f1d0744236e6 | Shell | 1,826 | 33 | #!/bin/bash
#SBATCH --job-name=behavior_plot
#SBATCH --output=output/behavior_plot%A_%a.out
#SBATCH --error=output/behavior_plot%A_%a.out
#SBATCH --mem=64000
#SBATCH --cpus-per-task=8
#SBATCH --time=08:00:00
#SBATCH --gres=gpu:A100:1
#SBATCH --array=0-1
#SBATCH --constraint=11GB
#SBATCH --exclude=node088,node114,node10... |
fc148fb9d6f2760a444d60276409ea3500d9814521fa1206628c3283df2eb7db | Shell | 1,828 | 48 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# usage: ./dice_batch.sh $1 $2 $3 $4 $5
# $1: destination atlas folder to be tested (only use label subfolder)
# $2: source atlas folder containing multiple manual labels
# $3: folder containing the parcellated structure... |
248f56483167f1f0aa86d923a458003aa5ee354a64b015571daaedb92431b5ca | Shell | 1,829 | 76 | #!/bin/bash
#$ -cwd
#$ -pe local 8
#$ -l mem_free=8G,h_vmem=10G,h_fsize=300G
# qsub code/spaceranger/filename.sh
############################
# Script to run Space Ranger
############################
# Round 2 LC samples: Linda_2021-05-21
# load spaceranger module (if required)
# module use /jhpce/shared/jhpce/mo... |
78312b6b42983509a126ceaa756f528fc8bbf32a23d95d6be6281b5d5b29c440 | Shell | 1,842 | 52 | #!/bin/bash -x
#SBATCH --time=1-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=48
#SBATCH --job-name=tfep
#SBATCH --output=tfep.%j.out
#SBATCH --partition=batch
# TODO: Load AMBER and Python environment.
# Select molecule ID.
molidx=${molidx:-'6'} # If molidx env variable not defi... |
25f5200c495d240a08b0a2d54e0e0131e53026c91e95268a0a85d2304dd2edaa | Shell | 1,846 | 63 | set -ex
DOWNLOAD_MODEL=${1}
# test code
echo 'test edges2handbags'
if [ ${DOWNLOAD_MODEL} -eq 1 ]
then
bash ./pretrained_models/download_model.sh edges2handbags
fi
bash ./datasets/download_testset.sh edges2handbags
bash ./scripts/test_edges2handbags.sh
echo 'test edges2shoes'
if [ ${DOWNLOAD_MODEL} -eq 1 ]
then
ba... |
2d65ca84d83b303a2f285f1ee45902e09ec0e39086410a3b84c81a3808c6316d | Shell | 1,850 | 67 | #!/bin/bash
## assume script is launched from vsearch/man/
## usage: bash scripts/convert_manpages_to_pdfs.sh
##
## Render every manual page in ./manpages/ as a PDF next to it. This is
## a maintainer convenience, not part of the build: the PDF renderings
## are not tracked, not installed and not distributed.
##
## I... |
f591bdc774e4a6771995b20ea6072e574ab35458ac9083200a3e7700b46365a2 | Shell | 1,851 | 74 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
0af484fc6ba7c17cec21b723fb6ff81d7c90cd282103df19ff22f32402354adc | Shell | 1,855 | 66 | #!$shell
$headers
_galaxy_setup_environment() {
local _use_framework_galaxy="$1"
if [ -z "$_GALAXY_JOB_TMP_DIR" ]; then
_GALAXY_JOB_DIR="$working_directory"
_GALAXY_JOB_HOME_DIR="$home_directory"
_GALAXY_JOB_TMP_DIR=$tmp_dir_creation_statement
fi
$env_setup_commands
if [ ... |
baa2ac01c83a604a112850f405178c6b3dbb30a921b1fdc680f7afae855d05f2 | Shell | 1,857 | 39 | : '
Shell script for job submission to HPC (MOAB compatible)
Task:
Create folders for data and results
Run experiment through 4 phases: growth, stim, post, decay
Parameters:
amplitude (float) : rTMS stimulation strength in pA
whereami (string) : fetch... |
d63517c1ebc88565133c7e5ca6efa880210abe419b53a02caf7ecc2d9a9effac | Shell | 1,861 | 60 | #!/bin/bash
#
#SBATCH --job-name=MLS_ROIest
#SBATCH --array=1 #Only needs 1 job, calculates ROI for all maps within input dir
#SBATCH --time=00:25:00
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=8GB
#SBATCH -p russpold,normal,owners
# Outputs ----------------------------------
#SBATCH --output=../logs/ROI.%A_%a.out... |
9edcc5b13be456590cb86b4708fb6baa9b95f36d82b808576e5e6f321ec56505 | Shell | 1,862 | 52 | #!/bin/bash
# this script will detect doublets in individual snATACseq 10X libraries
# to run locally:
# SCRATCH1=/mnt/g/scratch
# docker run \
# --workdir $HOME \
# -v $HOME:$HOME \
# -v $SCRATCH1:$SCRATCH1 \
# -v /mnt/g/cellranger_atac_counts/version_2.1:$HOME/counts \
# -v /mnt/g/scratch:$HOME/output \
# -e SCRATCH... |
e13a22f0f065a82364ff6b209068df27c3ea44d33d2abf7d599a98e9a64ce942 | Shell | 1,869 | 64 | #!/bin/bash
#$ -pe local 8
#$ -l mem_free=10G,h_vmem=20G,h_fsize=100G
#$ -V
#$ -cwd
# run on JHPCE cluster
# qsub code/scripts/spaceranger/spaceranger_NextSeq.sh
############################
# Script to run Space Ranger
############################
# locations of files:
# -------------------
# spaceranger reference:... |
288d1dc7e13f8ce90c2d6fd6dd8cc83aed358e6c05cf0ac6f1acdeec6f4bc9ae | Shell | 1,870 | 73 | #!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# A POSIX variable
OPTIND=1 # Reset in case getopts has been used previously in the shell.
GPONLY=0 # Whether to run GP only or start notebook server
# Sync with Github repo for latest DAFi... |
0f235d05b354b563b665b3772d863237995e069fdf8e88dfa8c2f3f71df68edf | Shell | 1,876 | 17 | #!/bin/bash
bamtools filter -in F-2-1.sorted.bam -out F-2-1.sorted.bam.filter.bam -isPrimaryAlignment true -isProperPair true -isMapped true -mapQuality '>1'
bamtools filter -in F-2-2.sorted.bam -out F-2-2.sorted.bam.filter.bam -isPrimaryAlignment true -isProperPair true -isMapped true -mapQuality '>1'
bamtools filter ... |
e1e5cc3c44ac49e95f4b179bd1ee68bc54e959986cae56c11680adfa3d6a09e2 | Shell | 1,889 | 55 | #!/usr/bin/env bash
#
# Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# 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
#
# Unle... |
605c50d3127322572fc8f57c9fd995a98d0957288fcaa74f869159950d02dff4 | Shell | 1,896 | 37 | #!/bin/bash
#SBATCH --job-name=behavior_plot
#SBATCH --output=output/behavior_plot%j.out
#SBATCH --error=output/behavior_plot%j.err
#SBATCH --mem=16000
#SBATCH --cpus-per-task=4
#SBATCH --time=01:20:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-30
#SBATCH --constraint=11GB
#SBATCH --exclude=node093,node094,node097,node098,... |
89ca929ebb6e490952cc34636acffe62307db77c581ebfdd3befba294d2f184f | Shell | 1,909 | 47 | #!/bin/bash
proj_dir="/Users/szu/git-recipes/mouseBrainAtlas/CEMBA2"
cicero_dir="${proj_dir}/04.cCREgene/sa2.cicero/out/sa2pdcsum"
meta_col="sa2subclass"
allpeak="${proj_dir}/supple.07.peakcalling.allinone/mba.whole.sa2.final.peak.srt.bed"
pdc_bedpe=${cicero_dir}/mba.whole.${meta_col}.merge.bedpe.all
pdc_pair=${cicero... |
bfc37035b7403276505e5f90683406706ecfb27ec80332fa200f6b5a69496325 | Shell | 1,916 | 24 | #!/bin/bash
source activate kallistobus
cd /data/users/jared/ENS/6mo_LMMP/preprocessing/bus_output/TH
echo TH
mkdir cDNA_capture/ introns_capture/ spliced/ unspliced/ tmp/
bustools correct -w ../../bustools_required_files_10xv2_mm/737K-august-2016.txt -p output.bus | bustools sort -o output.correct.sort.bus -t 4 -
bu... |
e7adb478933c8d88b6f49096f7de0ccd546ed070131c80392b8b9aa4bf9d7911 | Shell | 1,924 | 55 | #!/bin/bash
dir=$(cd -P -- "$(dirname -- "$0")" && pwd -P)
rm -r -f swissprot
mkdir swissprot
cd swissprot
wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/swissprot.tar.gz
gunzip swissprot.tar.gz
tar -xvf swissprot.tar
SWISSPROT_PATH=$PWD
echo "$SWISSPROT_PATH"
cd ..
cd test
echo 'SWISSPROT_DB="'$SWISSPROT_PATH'/swissprot"' ... |
f53962bede98f087d9d08d0b42880f903fb122629643953f4acce9d806096bde | Shell | 1,924 | 58 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pool1,pfen1
#SBATCH --time 1-00:00:00
#SBATCH --job-name=clean_up
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=45G
#SBATCH --error=logs/STARsolo_%A_%a.txt
#SBATCH --output=logs/STARsolo_%A_%a.txt
#SBATCH --array=1-24%4
source ~/.bashrc
##############... |
786a4f6ba613db45ade8bf8fed2829cd33ecf0eed7f2665917712f1f4bb03693 | Shell | 1,928 | 32 | #!/bin/sh
# usage: ./travis_centos.sh [:7|:8|:latest|:stream]
#
## -e : Make sure all errors cause the script to fail
## -x be verbose; write what we are doing, as we do it
set -ex
podman pull registry.access.redhat.com/ubi8/ubi \
&& ... |
98d13e3b43ca8a4188f477a5ed1d270c5325f1d35d49e2203f3169f36db03f5d | Shell | 1,930 | 25 | export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/final/"
wildtype="verified_test_RNA"
shuffled_5_prime="${wildtype}_2-nuc_shuffled_5-prime"
shuffled_3_prime="${wildtype}_2-nuc_shuffled_3-prime"
shuffled_5_prime_1nt="${wildtype}_1-nuc_shuffled_5-prime"
shuffled_3_prime_... |
54a46c61cba9438704021b5d175a5b745b88506585933052404105578ce397f3 | Shell | 1,938 | 47 |
#!/bin/bash
# created by Meng-Yun
# 29-July-2022
# run the preprocessing on mutisubjects with FSL
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional
cd $filepath
# mkdir ./Pre_processing
ls ./Data/Reorganized/All | grep -i sub- > ./Pre_processing/subjList.txt # command grep is trying to filter the inpu... |
39c40bc7d90852ee2d3dfa3c0e9d7421e75962019d74e7dbb6361f3103396f19 | Shell | 1,942 | 25 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject... |
ff52235c9d417d8a2df78091564149be458948bec77c457a35c215c4c07e13da | Shell | 1,943 | 54 | ### align fastq by STAR ###
# create refGene index on hg38
STAR --runThreadN 5 --runMode genomeGenerate \
--genomeDir STAR/index \
--genomeFastaFiles STAR/hg38.fasta \
--sjdbGTFfile STAR/hg38.refGene.gtf \
--sjdbOverhang 49 \
--genomeSAsparseD 2
# align fastq and generate splice junction count... |
6c1a24660f78ceaf5bbde4d31a99ca7003f3fa8d09e6002c9755a9ddccac423f | Shell | 1,952 | 56 | # This scrips add all changes to git updating the version of the changed files by one. And then commits using the message as the second parameter.
# Usage: ./auto-version-commit.sh "My commit message"
if [ "$1" != '' ]; then
IFS="
"
git status -s
for p in `git status -s` # For each file in git status
do
file=`echo "$... |
4b8902dce0c2554a79a7a81bafa837dc379129b246a01cd078ff542d06b22c0c | Shell | 1,956 | 74 | #!/usr/bin/env bash
############################################################
# run-rscript-pkgs.sh
# Run an 'Rscript' module, installing R packages if necessary
# Usage:
# ./run-rscript-pkgs.sh \
# [--dry-run] \
# -v r-version \
# -c env-custom \
# -e GP_R_LIBS_SITE=gp-r-libs-site \
# -e GP... |
d06627f7bb48662a9ea818a1b7aa6081b99da27bf1109b0a69a74747dd48e339 | Shell | 1,956 | 37 | #!/bin/bash
#SBATCH --job-name=behavior_plot
#SBATCH --output=output/behavior_plot%j.out
#SBATCH --error=output/behavior_plot%j.err
#SBATCH --mem=16000
#SBATCH --cpus-per-task=4
#SBATCH --time=24:00:00
#SBATCH --gres=gres:gpu:tesla-v100:4
#SBATCH --array=0-17%9
#SBATCH --constraint=11GB
#SBATCH --partition=mcdermott
#... |
1491b64eaaa05c386fb8cc4cf5bef4efb953e223c8c6c0c71776edc9e3199771 | Shell | 1,957 | 81 | #!/bin/bash
# convenience logging function
log() {
echo "pnet_robustness [$(date -Is)]:" "$@"
}
# parse arguments
while getopts e:l:u: opt
do
case $opt in
e) experiment=$OPTARG;; # experiment, required
l) lower_seed=$OPTARG;; # lower seed, optional (default: -1)
u) upper_seed=$OPTARG;; # upper seed, o... |
0a0e802bfa5e25ab249148aead802e2e5b1e94375f3d0ef85e274e8f91d91d43 | Shell | 1,959 | 65 | #!/usr/bin/env bash
# A simple set of tests checking if a wheel is working correctly
set -eux
# taken from:
# https://stackoverflow.com/q/3572030
this_dir="$( cd "$(dirname "$0")" ; pwd -P )"
if [ "$#" -lt 2 ]; then
echo "Usage: $(basename "$0") python_exe python_wheel [use_virtual_env]"
exit 1
fi
# cli para... |
b778d21ea1da2f3e8e29fdaa7abef55a74228cf9d10e1d916a7b49c12c22dedb | Shell | 1,963 | 56 | #! /bin/bash
# this script will count a 10x genomics multiome gex and atac library
# to run LSF detached
# library_id=2-15Nx
# export LSF_DOCKER_VOLUMES="$HOME:$HOME \
# $STORAGE1/reference:$HOME/reference \
# $STORAGE1/cellranger_multi_counts:$HOME/cellranger_multi_counts \
# $STORAGE1/multiFastq:$HOME/multiFastq \
... |
2f88d452591f8486a35fa9846cae8566fd72316afad38dca9540e52e2f641369 | Shell | 1,973 | 63 | #!/bin/bash
if [[ -z $1 ]] || [[ -z $2 ]]; then
echo "Usage: ./count.sh <k> <input.fofn> [offset line_num]"
echo -e "\t<k>: k-size mers will be collected. REQUIRED."
echo -e "\t<input.fofn>: list of fastq.gz file. Read pair 1 from 10X reads. REQUIRED."
echo -e "\t[offset]: OPTIONAL. DEFAULT=0. For arr... |
9451c5a712639b571e57462806ad942f02bfd3979ca23ebcd69e9e04863cfe3c | Shell | 1,984 | 66 | #!/bin/bash
#
#SBATCH --job-name=AHRB_seclvl
#SBATCH --array=01# run job array
#SBATCH --time=00:20:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=6GB
#SBATCH -p ${PROFILE}
# Outputs ----------------------------------
#SBATCH --output=../logs/Grp.%A_%a.out
#SBATCH --error=../logs/Grp.%A_%a.err
#SBATCH --mail-user=$... |
cc95487d7534a410b2d3c6145f66d4162f1f9937d1b874eb4411a1f184e2aae3 | Shell | 1,984 | 50 | #!/bin/sh
## -e : Make sure all errors cause the script to fail
## -x be verbose; write what we are doing, as we do it
set -ex
## Should we init a container?
if [ ".$1" = .setup ]
then
# fedora
# note: when you PR, docker-cp provides, in the container, the branch associated with the PR (not master where there's n... |
9e0679272a5c75f5b63d8e4f1243a2b5700a7bc2de7f50433dcd9134fbd1bc56 | Shell | 1,992 | 52 | #!/bin/bash
# Created by M.Y. WANG
# 31-03-2022
# Organize the data into BIDS format
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/Data
cd $filepath
mkdir ./Reorganized/All
ls ./Raw_data | grep -i sub- > ./Raw_data/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the ... |
d45818f3275ec6cebdbc3476138c6b1ef368c35f0a5da323ee0b7e9b6c1b5cd5 | Shell | 1,992 | 63 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- DAFi gating on single txt format FCM sample. Please use FCSTrans to first preprocess and convert the sample FCS format to txt format.
where:
--help show this help text
--nclusters specify number of initial clusters to use for the k-means clusteri... |
0d432c5f6255e3134e1d9989c1fca6fa4cb7d9f39da8b7fe3ff78ca487bc1d26 | Shell | 1,996 | 50 | #!/bin/bash
# Sparse Grouping Example
# Use case: Sample a diverse candidate pool, use fewer exact groups for faster training
# This example shows how to load more data for diversity but train on fewer groups
echo "=================================================="
echo "Sparse Grouping Example"
echo "Goal: Load a di... |
2fc812d3d3f00a50c769d460999bd060a8577f2268426a5c74ac7dd97b1f7dd1 | Shell | 1,996 | 84 | #!/bin/bash
if [ "*${1}*" == "**" ]; then
EXTRA=""
else
EXTRA="-m"
fi
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
BDIST=${BDIR}/dist
echo "_______________________________________________________________________"
echo "__... |
337befaae974bcb7d1b88f7d7ee267c8b343a352bc9c7b200acd08cbd8831a8d | Shell | 2,002 | 59 | #!/bin/bash
# This script must be run with sudo.
set -e
MAKE="make --jobs=$NUM_THREADS"
# Install apt packages where the Ubuntu 12.04 default and ppa works for Caffe
# This ppa is for gflags and glog
add-apt-repository -y ppa:tuleu/precise-backports
apt-get -y update
apt-get install \
wget git curl \
python... |
92c0f958e7650503090c637e277b2c99a1cbcf14371fb67b820abec8e7f1bff0 | Shell | 2,005 | 36 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pool1
#SBATCH --time 3-00:00:00
#SBATCH --job-name=ldsc_ifn_tau
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10G
#SBATCH --error=logs/ldsc_ifn_tau_%A_%a.txt
#SBATCH --output=logs/ldsc_ifn_tau_%A_%a.txt
#SBATCH --array=1-78
# get the GWAS for this arra... |
36b0f50c12c55a7ceeaa5f2356392b1ad80b284966d868605d3f5ddeaad69323 | Shell | 2,007 | 35 | : '
Shell script for job submission to HPC (MOAB compatible)
Task:
Analyse data obtained via jobcall.sh through 4 phases: growth, stim, decay, post
Parameters:
amplitude (float) : rTMS stimulation strength in pA
whereami (string) : fetch current location (all... |
e43dd224a32eeedd304929a4b737f30582c73f0b35697836dadd82b234be5423 | Shell | 2,019 | 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... |
2328b293e15881230fee1d4a3b5d9186a1d44105e4ecaa5f2e341612a4617323 | Shell | 2,023 | 69 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.09.11
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# $1: enquiry image
# $2: atlas folder "in_vivo" or "ex_vivo"
# $3: STEPS parameter k (kernel size in terms of voxel number)
# $4: STEPS parameter n (number of ... |
f29d28e6cf682190a39761dde9a86c89d3ff14000040871a6b513fe12ef0c4e8 | Shell | 2,031 | 85 | #!/bin/bash
# Run denoise.m and unring.m as a step 1 in the pipeline
# Ivan I. Maximov, Ullevål
# 22.11.2018, ver 1.0
# 11.12.2018, ver. 1.1
#SBATCH --account=p33_norment
#SBATCH --time=12:00:00
#SBATCH --job-name=UKstep1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=8G
#source /cluster/software/fsl/6.0.1/setup.sou... |
1fed3a6a22a1188dcdc44d3f55c4cc2a712bcb88fc80934931bca2bfec4a0669 | Shell | 2,033 | 72 | # Copyright 2023 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 applicable law or agree... |
e6ba21bfa242a8899a8d0533cdb6373491b1983911362cf7498eadb9bae8a88d | Shell | 2,038 | 61 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1,pfen_bigmem,pfen3
#SBATCH --job-name=STARsolo
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=60G
#SBATCH --error=logs/align_STARsolo_%A_%a.txt
#SBATCH --output=logs/align_STARsolo_%A_%a.txt
#SBATCH --array=1-16
###################
## 1) set up pat... |
f845d9ad5116ea2d3e755259d702f36384faf7aca77b1230b4496048724a799e | Shell | 2,040 | 61 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
0273c8408d84ad7fa4a44628aa95493bff812d09d5bdf8281e58b33bcaf0ec80 | Shell | 2,044 | 38 | #!/bin/bash
#SBATCH --job-name=behavior_plot
#SBATCH --output=output/behavior_plot%j.out
#SBATCH --error=output/behavior_plot%j.err
#SBATCH --mem=16000
#SBATCH --cpus-per-task=4
#SBATCH --time=36:00:00
#SBATCH --gres=gpu:tesla-v100:1
#SBATCH --array=0-17
#SBATCH --constraint=high-capacity&12GB
#SBATCH --partition=mcder... |
3d01b7b2fce438ef385f89ffd7db9da1bd0386e4eb7bd1e82843ede9284a2a6b | Shell | 2,044 | 66 | #!/bin/bash
#
#SBATCH --job-name=MLS_seclvl
#SBATCH --array=01# run job array
#SBATCH --time=00:20:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=4GB
#SBATCH -p russpold,normal,owners
# Outputs ----------------------------------
#SBATCH --output=../logs/Grp.%A_%a.out
#SBATCH --error=../logs/Grp.%A_%a.err
#SBATCH --... |
ab04909faf988e83b12d4d1d89fb0fa32409d74b9c492a8babb996617df7d070 | Shell | 2,055 | 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... |
825b028e9abaec3ca9f85ea1281382cf292e334401dba18d68282b9441aaf9e3 | Shell | 2,058 | 97 | #!/usr/bin/env bash
ID=$(cat /etc/machine-id)
start="http://localhost:9000/controls/$ID/start"
stop="http://localhost:9000/controls/$ID/stop"
close="http://localhost:9000/controls/$ID/close"
JSON_FILE=./test_generic_config.json
SERVER_SCRIPT="../../../scripts/device_server.py"
tmp=$(mktemp)
failed(){
echo "ER... |
3e8e1b44de4c6f23c14e259d6f9e89f44e8b312a56a2bef60d1d507051b2a2cb | Shell | 2,063 | 21 | #cafetutorial_prep_r8s.py was downloaded from cafe turorial website
python cafetutorial_prep_r8s.py -i SpeciesTree_rooted.txt -o r8s_species11_file.txt -s 1000000 -p 'elegans_longest_transcript,briggsae_longest_transcript' -c '18.6'
r8s -b -f r8s_species11_file.txt > r8s_tmp.txt
tail -n 1 r8s_tmp.txt | cut -c 16- > ... |
fd007da2203d17f1db33ad3f8264df7ef275ac9788b3b08d7c32b79fef121f9f | Shell | 2,070 | 35 | #!/usr/bin/env bash
# Fast two-pass testing: compile every kernel of a test selection in parallel under
# FakeTensorMode (no GPU work), then execute with the persistent compile cache, failing any
# test that still compiles (fake / real compile-key drift, or a test that skips a variant in
# fake mode). See CLAUDE.md "Fa... |
f1056134d788d3f311ceaf90d6e21be7276271fad142f053480ce0c90c1468c0 | Shell | 2,072 | 25 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject... |
895d2e937ec98755ea527369f4951102553d92cc1be0fd5946bce0f2f8e14a81 | Shell | 2,076 | 27 | #!/bin/bash
#dsource=grf
#prefix=grf2
dsource=$1
prefix=$2
nepochs=$3
outer_offset_train=8
outer_offset_test=20
# Invocation 1
python ptycho/train.py --data_source $dsource --nepochs $nepochs --offset 4 --output_prefix $prefix --model_type pinn --gridsize 2 --n_filters_scale 2 --object_big True --intensity_scale_tr... |
fdb8d2f58944942a14325870f142e1de96462a73993259adad341c45c890e5db | Shell | 2,077 | 72 | #!/bin/bash
set -eux
CURR_FILEPATH=`realpath $0`
CURR_DIR=`dirname ${CURR_FILEPATH}`;
HOME_DIR=`realpath ${CURR_DIR}/../..`;
DATAEXTRACTOR_DIR="${HOME_DIR}/data_extractor"
LOCALSTORE_DIR="${HOME_DIR}/localstore"
TABNET_DIR="${HOME_DIR}/tabnet_model"
conda activate covid
which pip3
which python3
# Install dropbox l... |
7ebe46e0330f8c91c143b1e854fd6879b51184750ad15be4862ed1f8bdfdf6f6 | Shell | 2,080 | 59 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
leftout=B0702
DePTH train --hla_class HLA_I \
--data_dir data/HLA_I_leave1out_match/HLA_I_leave1ou... |
c9d573b93181288d0237cf060dc2cb703e7cfd888d557943b9a2e37118ea90df | Shell | 2,091 | 72 | #!/bin/bash
# called by main routing function (see 01_qbatch_subcall.sh)
# Calls individual functions in micapipe ($MICAPIPE/functions)
#
# Inputs:
# $1 : subject tag {01, 02, ..., 50}
# $2 : FUNC_ID indicating which function from micapipe to call
#
# NOTES:
# 1. nocleanup flag may not be desireable in some cases
# ... |
b8b92442e5f8b1aeffa68f45f6b0223d3a8b10108c0a9c8e062d90b348e11c01 | Shell | 2,093 | 69 | #!/bin/bash -l
#SBATCH -J grp_runs
#SBATCH --array=1 # jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=10G
#SBATCH -t 02:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=${USER}.edu
#SBATCH -p msismall,amdsmall
#SBATCH -o batch_logs/%x_%A_%a.out
#SBATCH -e batch_logs/... |
6c381fbc6064fb1044c5d41ef59cd0aec012a739416c75bb39914b8c228816cf | Shell | 2,110 | 74 | #! /bin/bash
# to run LSF detached
# bgadd -L 10 /parkerw/cellranger_atac
# export LSF_DOCKER_VOLUMES="$HOME:$HOME \
# $STORAGE1/cellranger_atac_counts/version_2.1:$HOME/counts \
# $STORAGE1/atacFastq:$HOME/fastq \
# $STORAGE1/reference:$HOME/reference \
# $SCRATCH1:$SCRATCH1"
# library_ids=(Control_1 Control_2 Contro... |
58b8a14c576a1e8e06603e5fe75d6e61f2c15af2f2a3e704e56768e5f67bbd06 | Shell | 2,111 | 49 | #!/usr/bin/env bash
export dir="experiments/analysis/"
# Table 1 (Classification)
python $dir/eval_classification.py --config $CONFIG
python $dir/eval_tools_homology.py experiments/competitor_results
# Table 2 (Micropeptides)
python $dir/eval_lncPEP_translation.py --config $CONFIG align > lncPEP_needle_cmds.txt
SGE_... |
5e06fe39835ffb113f690cef1d9e3c5052af8c00db129afa979ce3dafb01b1a8 | Shell | 2,112 | 73 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
decoder_src=$3
if [ "$decoder_src" = "--pypi" ]; then
# Disable automatically picking up decoder package built in this CI group
export DECODER_ARTIF... |
b296b0fd6221a2e43dd716d5de160df48b763fa273547f0bd8e42df4b7c00ea9 | Shell | 2,117 | 28 | #!/bin/bash
set -u
set -e
# script to determine density of contacts at OR alleles relative to the surounding regions
# for each cell calculates ratio of 1) mean interchromosomal contact density within 200 kb of all OR pairs and 2) the mean density in surrounding regions (within 10 Mb)
# all ORs vs all ORs
python ma... |
6e3c0b1bce9c95e6e08cdf01628e222b9ef579a5071a480ef955e674127c348e | Shell | 2,122 | 68 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
7cc115efb40efb96be15c47fc0e20752a28391775c99d3c6861e91076603714d | Shell | 2,130 | 63 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_charges_eps_4
train_path=../data/charges_eps_4/train.csv
val_path=../data/charges_eps_4/val.csv
test_path=../data/charges_eps_4/test.csv
train_constraints_path=../data/charges_eps_4/train_constraints.csv
val_co... |
ffd8339048f675a51eb9ab0c11ad7cb73db5eb3cf0a219166a4026723fb02932 | Shell | 2,133 | 50 | #!/bin/bash
# Dense Grouping Example
# Use case: Maximum data utilization with centered-nearest grouping
# This example shows how to use every candidate row as a group center
echo "=================================================="
echo "Dense Grouping Example"
echo "Goal: Use as much of the loaded candidate pool as ... |
98020cb8b3d3538e68d342a5698a6801c1ed5af667933ff4e1d2683d5358041d | Shell | 2,137 | 59 | #!/bin/sh -e
if test -x /usr/bin/dnf; then
echo Installing prerequisites via dnf...
dnf -y install epel-release
dnf -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools
elif test -x /usr/bin/yum; then
if yum -y install epel-release; then
echo Insta... |
e301851e0d04d72fa06f4633ef4841790e9d5a8351111ee96fa6ad8fadc38463 | Shell | 2,139 | 63 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_charges_eps_78
train_path=../data/charges_eps_78/train.csv
val_path=../data/charges_eps_78/val.csv
test_path=../data/charges_eps_78/test.csv
train_constraints_path=../data/charges_eps_78/train_constraints.csv
v... |
933a3cc9806d8ab25cfc43c068f1504f4b85d0d7ecf13a0d03d12c74263f2cc1 | Shell | 2,143 | 47 | #! /bin/bash
export FREESURFER_HOME=/Applications/freesurfer/7.2.0
export SUBJECTS_DIR=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/sub-1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cd SUBJECTS_DIR
recon-all -base sub-1_base -tp sub-1_ses-1_T1w \
-tp sub-1_ses-2_T1w \
... |
1a9a99336f23c86ee8968e46b2631c8bfe81085fcc80bb908d0599d1fe393b35 | Shell | 2,145 | 71 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
e9be22a968911412cef17b54e68029ee9e32c79c82aa2706694caee78cf39ad0 | Shell | 2,153 | 68 | #!/bin/bash -l
#SBATCH -J grp
#SBATCH --array=1 # jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=10G
#SBATCH -t 02:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=${USER}.edu
#SBATCH -p msismall,amdsmall
#SBATCH -o batch_logs/%x_%A_%a.out
#SBATCH -e batch_logs/%x_%A... |
fb71ed6bc3fefff9e5e6a7356c753eb37aafad738622219ff58aae2dc11dc1aa | Shell | 2,156 | 41 | #!/bin/bash
set -u
set -x
##sample with the most reads: z5OMP.25 (~4 million reads)
##sample with fewer reads (use to test pipeline): z5OMP.15 (only ~1 million reads)
#run from /media/storageA/lisa/dipc/
name=$1 #example: for files dipc.z5OMP.25.R1.fastq.gz and dipc.z5OMP.25.R2.fastq.gz the name is "z5OMP.25"
SNP_fi... |
5054ac7999c26f40eb9279c3feb8b295c9e6ce548800f88968485d7bcfb6ca4e | Shell | 2,160 | 74 | #!/bin/bash
#
#SBATCH --job-name=AHRB_seclvl_rn
#SBATCH --array=01# run job array
#SBATCH --time=00:20:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=6GB
#SBATCH -p ${PROFILE}
# Outputs ----------------------------------
#SBATCH --output=../logs/Grp_rn.%A_%a.out
#SBATCH --error=../logs/Grp_rn.%A_%a.err
#SBATCH --ma... |
ea949536d32208ccebd199af832189cfa7c1ba47faacbbd12186f2b1d58e71b4 | Shell | 2,160 | 69 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.09.11
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# $1: enquiry image
# $2: atlas folder "in_vivo" or "ex_vivo"
# $3: if exist, read user defined parameters
# echo "********************************************... |
9a62993d0d6f4d60477f8badab8ec2eeecb041edd00e6735d483ef88889edaa0 | Shell | 2,164 | 59 | set -euo pipefail
export PATH=/scratch/ucgd/lustre/work/u6000771/Projects/src/samtools/:/scratch/ucgd/lustre/work/u6000771/Projects/src/bedtools2/bin/:$PATH
export LD_LIBRARY_PATH=/scratch/ucgd/lustre/work/u6000771/Projects/src/htslib/
export bam=/scratch/ucgd/lustre/work/u6000771/Data/NA12878.mem.bam
export bam=/scra... |
4dafec4ead1956ab5974d25537604d7c17de15736db11ff96c8f90a7b75200b5 | Shell | 2,167 | 42 | #!/bin/zsh
# Автономная цепочка после A.5. Порядок строго по блокам: доделать блок A
# (A.1, A.4) -> блок B -> блок C (C.1..C.4). Ждёт завершения compare.jsonl
# (48 строк). Всё однопоточным BLAS, логи по шагам в runs/*.log.
cd "$(dirname "$0")/.."
export OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 VECLI... |
28bb129b7fee34a726f11a5beea1d91bb0fb10d0f9cd8ce1257578d4a55f33c2 | Shell | 2,176 | 81 | #!/usr/bin/env bash
# Deploy docs to gh-pages with versioning.
# Merges new version into existing gh-pages content.
# Usage: deploy-docs.sh VERSION_FULL [SITE_DIR] [DEPLOY_DIR]
set -euo pipefail
VERSION_FULL="${1:?Usage: deploy-docs.sh VERSION_FULL}"
VERSION_MINOR="${VERSION_FULL%.*}"
REPO_ROOT="$(cd "$(dirname "${BA... |
51378e736afbfe0da5b157aedb93f6b34d6529ba8fd93276dc25c0a3c43d287b | Shell | 2,176 | 86 | #!/bin/bash
#set -eu
#1.python环境设置
allhost=$1
if [[ -n "${allhost}" ]]; then
module rm compiler/rocm/2.9
module load compiler/rocm/4.0.1
module load apps/anaconda3/5.2.0
source activate ~/conda-envs/paddle_dcu
#2.机卡信息显示
echo "-------------input params ${SLURM_NODEID}--------------"
echo "... |
5d9d343e4a23cebe94c8fcd954e42416e12e3bad477a3017bd8fe63bc2647fa0 | Shell | 2,193 | 60 | #!/bin/bash
CURR_DIR="$( cd -- "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"
HOME_DIR="$( cd "${CURR_DIR}/.." > /dev/null 2>&1 ; pwd -P )"
DATAEXTRACTOR_DIR="${HOME_DIR}/data_extractor"
TABNET_DIR="${HOME_DIR}/tabnet_model"
echo `which pip3`
echo `which python3`
# Install dependencies of python packages
echo "Inst... |
96d8a2ad079edc87c9e9b5cb0d11d235838e81d554f72d5e4bcb941006519ab6 | Shell | 2,197 | 30 | #!/bin/bash
#dsource=grf
#prefix=grf2
dsource=$1
prefix=$2
nepochs=$3
outer_offset_train=$4 # 8
outer_offset_test=$5 # 20
#outer_offset_train=8
#outer_offset_test=20
# Invocation 1
python ptycho/train.py --data_source $dsource --nepochs $nepochs --offset 4 --output_prefix $prefix --model_type pinn --gridsize 2 --n... |
4b3c35a3815a43975d7a220d6ff0924c956047c1b2ad6eddbbe46cc0292a78b7 | Shell | 2,205 | 85 | #!/usr/bin/env bash
#
# Build opencc.node with Bazel and copy it to the npm prebuilds directory.
# Usage: ./scripts/build-node-prebuild-bazel.sh [<target>]
# With no argument, builds for the host platform.
set -euo pipefail
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$ROOT_DIR"
# Git Bash/MSYS re... |
7d2f63b801098f48d8f07a407437b45f3080a31c0f000a2d671ab0a673cc217e | Shell | 2,207 | 75 | #!/bin/bash
#SBATCH -J roi_est
#SBATCH --array=1 # jobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=8G
#SBATCH -t 03:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=${USER}@umn.edu
#SBATCH -p msismall,amdsmall
#SBATCH -o batch_logs/%x_%A_%a.out
#SBATCH -e batch_logs/... |
8c2ba4f682995d28f33a94c6c2c24de88f5efb2c266d56b4f0202ff3d4b25a6f | Shell | 2,208 | 60 | #!/bin/sh
set -xe
ldc93s1_dir=`cd data/smoke_test; pwd`
ldc93s1_csv="${ldc93s1_dir}/LDC93S1.csv"
ldc93s1_wav="${ldc93s1_dir}/LDC93S1.wav"
ldc93s1_overlay_csv="${ldc93s1_dir}/LDC93S1_overlay.csv"
ldc93s1_overlay_wav="${ldc93s1_dir}/LDC93S1_reversed.wav"
play="python bin/play.py --number 1 --quiet"
compare="python bin... |
3846ecdabaef1317b2b469b3ab7e1eea38bf7222f1ac60cb8bdb8875c897a2b3 | Shell | 2,222 | 59 | #!/bin/sh
# version.sh -- Script to build the htslib version string
#
# Author : James Bonfield <jkb@sanger.ac.uk>
#
# Copyright (C) 2017-2018, 2021 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
f1285ea5c711101a7a1c101bccd575408b19fc3094cbd4aa8a553faa5b4990d5 | Shell | 2,232 | 62 | #!/bin/bash
CURR_FILEPATH=`realpath $0`
CURR_DIR=`dirname ${CURR_FILEPATH}`;
HOME_DIR=`realpath ${CURR_DIR}/..`;
DATAEXTRACTOR_DIR="${HOME_DIR}/data_extractor"
TABNET_DIR="${HOME_DIR}/tabnet_model"
echo `which pip3`
echo `which python3`
# Install dependencies of python packages
echo "Installing 'ghostscript' and '... |
042644124abc17371ed240449d26e42edcc2fb5319149b9402e5ab63fa9c5649 | Shell | 2,235 | 74 | #!/bin/bash
#
#SBATCH --job-name=MLS_seclvl_rn
#SBATCH --array=01# run job array
#SBATCH --time=00:20:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=6GB
#SBATCH -p russpold,normal,owners
# Outputs ----------------------------------
#SBATCH --output=../logs/Grp_rn.%A_%a.out
#SBATCH --error=../logs/Grp_rn.%A_%a.err
#... |
60e3a7261b57994d7dbf8fd735c39f46f4fa7c54760735aaea9cf0b22a0d8535 | Shell | 2,237 | 91 |
grep -v Intergenic 20227.uniq.sites.bed.ann|grep protein-coding|cut -f 2,16|sort -k2|uniq -c |sort -k1nr|head -100 |awk '{print $3}' > top100.new.gene
cat 20227.uniq.sites.bed.ann |grep -f top100.new.gene > new.site.primer.sites
awk '{print $2"\t"$3-3"\t"$3-1}' ../../random_sites/new.site.primer.sites > new.s... |
f9f573fc9bdfe698fe9bf649f2101ce580220ddbb851a7946dd22aef00988323 | Shell | 2,243 | 49 | #! /bin/bash
export FREESURFER_HOME=/Applications/freesurfer/7.2.0
export SUBJECTS_DIR=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/sub-2
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cd SUBJECTS_DIR
recon-all -base sub-2_base -tp sub-2_ses-1_T1w \
-tp sub-2_ses-2_T1w \
... |
25b2c11e6ab70a5d42889fab17b2c38749fe061c2037c4ef2691587c25cac0e8 | Shell | 2,270 | 75 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
4b878aeb4f0de86ee614b7fe3be16c4d7a225072ef5459823f20009883816019 | Shell | 2,274 | 91 | #!/bin/bash
#$ -cwd
#$ -pe local 8
#$ -l mem_free=8G,h_vmem=10G,h_fsize=300G
# qsub code/spaceranger/filename.sh
############################
# Script to run Space Ranger
############################
# Round 3 LC samples: KMay_2021-07-09
# load spaceranger module (if required)
# module use /jhpce/shared/jhpce/mod... |
9d8c2f8b90be680ccb15a58e9f92534b30482390b11e7696dd2fc35a6dc5c473 | Shell | 2,282 | 44 | #!/bin/bash
#####################################################################
# #
# start biomedisa workers #
# #
############################... |
160d15303888355d6710a634ff3fc9d0ca94f9bfd35aa5d726bab2eae430d154 | Shell | 2,285 | 63 | #!/bin/bash
set -e
if [ $# -lt 1 ]; then
echo "Usage: ./run_mysql_server_docker.sh [DB_DIR] [PORT] [CONTAINER_NAME] \
[MYSQL_USER] [MYSQL_PASSWORD] [MYSQL_DB_NAME]"
echo
echo "Example: run_mysql_server_docker.sh ~/cromwell_data_dir 3307 mysql_cromwell2"
echo
echo "[DB_DIR]: This directory will be mapped to '... |
ef86f6a4883131c6475ef3427036f18839860cef4e20954688b6ba641101cf60 | Shell | 2,297 | 96 | #!/usr/bin/env bash
set -euo pipefail
if [[ $# -ne 4 ]]; then
echo "Usage: $0 <output.node> <node_api.h> <napi.h> <node.lib>" >&2
exit 2
fi
output="$1"
node_api_header="$2"
napi_header="$3"
node_lib="$4"
zig="${ZIG:-zig}"
node_include_dir="$(dirname "$node_api_header")"
napi_include_dir="$(dirname "$napi_header... |
83b75c7d23db446c3089a9f970abc92d18d631ba0a550b25a333498b78688dc8 | Shell | 2,298 | 27 | #!/bin/bash
# HOMER script to quantify histone ChIP reads over OR gene bodies
# takes as input ChIP bigwig files and bed files with regions to compute tag count for
# used bigwigs from two merged replicates of H3K9me3 and H3K79me3 native ChIPs (Figure 2B)
bed_dir="zonal_paper/annotation"
tk79_homer="homer.mergedReps.... |
a89af39e6537b6041b288f7e9e108fb8ca31259a167049694d34ecc19a899ed7 | Shell | 2,298 | 74 | #!/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... |
5197cc9c512bf02b2a5320e9908c9f3c19ac8ff5487fc250afa3048b847bead0 | Shell | 2,301 | 24 | export BIOHOME=/home/bb/valejose/valejose
export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/coding_noncoding/"
rna=${1}_RNA.fa
prot=${1}_PROTEIN.fa
#python $PYTHONPATH/bioseq2seq/interpret/run_attribution.py --input $rna --tgt_input $prot --inference_mode EDC --num_gpus... |
af2005c7703dda305024ea4670a8ceafa8423e22d26fd7a1d037780465eb7690 | Shell | 2,317 | 75 | #!/bin/bash
# this script will aggregate snAtacseq output using cellranger-atac
# to run LSF detached
# export LSF_DOCKER_VOLUMES="$HOME:$HOME \
# $STORAGE1/cellranger_atac_counts/version_2.1:$HOME/counts \
# $STORAGE1/ckd:$HOME/project \
# $SCRATCH1/ckd/:$HOME/github_repository \
# $STORAGE1/reference:$HOME/referenc... |
a1e45e3ef57cd0a171d935033df88ceadb6e62c822fd1b9e760376707a0d8885 | Shell | 2,351 | 80 | #!/usr/bin/env bash
set -euo pipefail
export BUILDDIR=$1
echo $0
if [[ "$OSTYPE" == "darwin"* ]]; then
findarg="-perm +111"
else
findarg=-executable
fi
## note you must run this from the regression dir.
## first arg is build dir second is either test or regen
fastqr1=./test_r1.fastq.gz
fastqr2=./test_r2.fast... |
9ae0c506e965a127463f74f09df5a02ad12901456bdf34e3bc70dfcc936159ea | Shell | 2,352 | 77 | #!/usr/bin/env bash
set -euo pipefail
endpoint=""
input=""
output=""
add_paragraph_context="0"
while [[ $# -gt 0 ]]; do
case "$1" in
--endpoint) endpoint="$2"; shift 2 ;;
--input) input="$2"; shift 2 ;;
--output) output="$2"; shift 2 ;;
--add-paragraph-context) add_paragraph_contex... |
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