sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
c753f60877832c0f3218a2d948e3587670ccb92b51759cc699a33ddff6c693d5 | Shell | 3,137 | 55 | # download chain files to liftover
mkdir -p chainFiles
cd chainFiles
wget -nc https://github.com/broadgsa/gatk/raw/refs/heads/master/public/chainFiles/b37tohg19.chain
wget -nc https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
cd ..
#download and liftover Positive mask where we have power... |
01ce918aa90094bf3fdab308d07a8a81aab56595866c711d1d82d4dea3a8757d | Shell | 3,144 | 21 | # first, grant KMS permissions to the google cloud project/user to be able to run without CC
DATA_CONFIG='{"project_id": "data-owner-cc", "project_number": "470901555042", "account": "hasankassim8@gmail.com", "bucket": "data-owner-bucket-medperf", "encrypted_asset_bucket_file": "data.enc", "encrypted_key_bucket_file": ... |
83b381d4dc7f787347bf5d5c62eff5edd071988e94f4f9145d1298afa4ee3ce4 | Shell | 3,162 | 102 | #!/usr/bin/env bash
#SBATCH --job-name=generate_no_tp # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=1 # total number of tasks across all nodes
#SBATCH --cpus-per-task=4 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=20G # memory per cpu-core (4G is ... |
ea13a0099595659d0f205c1a2b359e1b330e0b09469b354ac7347075e5bb0dac | Shell | 3,164 | 60 | #!/bin/bash
###
# @Date: 2022-11-29 13:42:46
# @LastEditors: yuhhong
# @LastEditTime: 2022-11-29 13:43:51
###
start=$(date +%s)
for VARIABLE in {0..17}
do
if [[ "$VARIABLE" =~ ^(4|16|7|10)$ ]]; then
echo "python main_chir.py --config ./configs/molnet_train_l.yaml --csp_no $VARIABLE \
... |
7c75fb31c3916ef68ef21395cacd8a0cf1f7bd4c84cd1ce54fb3fc3d158a2893 | Shell | 3,174 | 107 | #!/bin/bash
set -e
set -x
export LC_ALL=C
package=cwltool
module=cwltool
extras="[deps]"
if [ "$GITHUB_ACTIONS" = "true" ]; then
# We are running as a GH Action
repo=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}.git
HEAD=${GITHUB_REF}
else
repo=https://github.com/common-workflow-language/cwltool.git
... |
fcd626470047368405aca0d1fd59ab97d4009a4c9fd23af97210dbe450dc71c5 | Shell | 3,219 | 126 | #!/bin/bash
#SBATCH --job-name=finetune_wenzhong
#SBATCH --cpus-per-task=50
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1 # number of gpus
#SBATCH -o %x-%j.log
#SBATCH -e %x-%j.err
set -x -e
export MASTER_PORT=$[RANDOM%10000+50000]
export TORCH_EXTENSIONS_DIR=/cognitive_comp/gaoxiny... |
eaaffa9ae914efa035e17e03f69314c8a1cda9c6e01db3f8e2df3d63d4a20420 | Shell | 3,224 | 100 | # sh/bash/zsh configuration file for Gromacs
# First we remove old gromacs stuff from the paths
# by selecting everything else.
# This is not 100% necessary, but very useful when we
# repeatedly switch between gmx versions in a shell.
#we make use of IFS, which needs shwordsplit in zsh
test -n "${ZSH_VERSION+set}" && ... |
681d0ffa85325a2b689974c9dbe3cc776bf4f48822fd0a6faa799d0f7b8acb84 | Shell | 3,235 | 37 | #!/bin/bash
## Apply randomise on the posterior segment of the left arcuate fasciculus ##
# Path of all xtract files
cd /path
# List of fasciculi
tracts=("contrast_aflp")
for fsx in "${tracts[@]}"; do
# Concatenate the pAF tractogram of all the participants (controls & tts)
fslmerge -t ${fsx}_all_density... |
923b8e1993c428f1ceb5800c7da38f887ed16870a623d83e19971a6e2276180f | Shell | 3,262 | 107 | #!/bin/bash
#SBATCH --partition=imghmemq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=5g
# This specifies maximum memory use will be 5 gigabytes
#SBATCH... |
679f05e1660f3df376a9690e3bf6935660e7bc401a0ceb4c4219ab6a693b0057 | Shell | 3,275 | 39 | #!/bin/bash
## Apply randomise on the posterior segment of the left arcuate fasciculus ##
# Path of all xtract files
cd /path
# List of fasciculi
tracts=("af_l_post") # "contrast_aflp"
for fsx in "${tracts[@]}"; do
# Concatenate the pAF tractogram of all the participants (controls & tts)
fslmerge -t ${fs... |
1669f0e8548139836a6bb82155ddb06628fd57a4c32e7dfbc16fe55708370d61 | Shell | 3,282 | 70 | # Complete demo of CHISEL in nonormal mode
: ex: set ft=markdown ;:<<'```shell' #
The following CHISEL demo represents a guided example of the complete CHISEL pipeline in nonormal mode starting from an exemplary barcoded [BAM file](https://doi.org/10.5281/zenodo.3950299) publicly available. From this directory, simply... |
cb797f41577651852b74408e3240986c46ed1f506d26a246f8b2c01a175a754d | Shell | 3,283 | 91 | #!/bin/bash
## Usage: sh 0.0_ps_Pipeline_v3.sh SRR3304509 c.0_RNAseq_QuantTERRA.cfg
expID=$1
cfgFile=$2
isDump=$3
fqPath=$4
if [ -z "$expID" ] || [ -z "$cfgFile" ]; then
echo "Usage: sh 0.0_ps_Pipeline_v3.sh SRR_ID config.cfg [is-dump] [fqPath]"
exit 1
fi
source $cfgFile
fastqDIR="$workdir/... |
61b57ee3307c2afcd51f10c9f58a50787c11fa5cd48ce9f477faae4fe45ef441 | Shell | 3,295 | 128 | #!/bin/bash
#SBATCH --job-name=randeng_t5_77M_summary
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --gres=gpu:2 # number of gpus
#SBATCH --cpus-per-task=30
#SBATCH -o %x-%j.log
set -x -e
echo "START TIME: $(date)"
MODEL_NAME=randeng_t5_77M_summary_test2
MICRO_BATCH_SIZE=64
ROOT_DIR=/cognitive_c... |
2511105db85642fde97beffb1c79ee85949a8034efbe30a1109f60032a3677f8 | Shell | 3,302 | 95 | #!/bin/sh -e
# Iterative sequence search workflow script
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
# pre-processing
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
# check number of input variables
[ "$#" -lt 4 ] && echo "Please pr... |
b99887d3fc35d3d228304f6332834e8a4a0c2572d68484b5be3700abb0d484fe | Shell | 3,321 | 64 | ###
# @Date: 2022-11-29 13:42:46
# @LastEditors: yuhhong
# @LastEditTime: 2022-11-29 13:43:51
###
for VARIABLE in {0..17}
do
if [[ "$VARIABLE" =~ ^(4|16|7|10)$ ]]; then
echo "python main_chir_kfold.py --config ./configs/molnet_train_l.yaml --k_fold 5 --csp_no $VARIABLE \
--log_dir ./logs/molnet_chirali... |
138e3d11453322ffa0820b0637bdfddf8892931efd43dd93eb8db7318bb17a48 | Shell | 3,337 | 123 | #!/bin/bash
#SBATCH --job-name=medical_qa_finetune
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH -o /cognitive_comp/wuziwei/task/fs_medical_qa_finetune/%x-%j.log
#SBATCH -e /cognitive_comp/wuziwei/task/fs_medical_qa_finetune/%x-%j.err
#SBATCH -x dgx[050,049]
... |
5d3018f6ebc6eea8546a7624604a753b0d7248733fa50447d82a7847b2da4c76 | Shell | 3,341 | 137 | #!/bin/bash
#SBATCH --job-name=deep_vae_pretrain
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=32 #
#SBATCH --gres=gpu:1 # number of gpus
#SBATCH -o xxx/outputs/deep_vae/logs/slurm/%x-%j.log
#SBATCH -e xxx/outputs/deep_vae/logs/slurm/%x-%j.err
# SBATCH --requeue
# SBATCH --qos=p... |
ebde1c4526a2bf20609c0bba9adc21c85a3765e2ea9187b59b76f310ce56d7c8 | Shell | 3,347 | 86 | #!/bin/sh -e
# shellcheck disable=SC2086
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
[ "$#" -ne 2 ] && echo "Please provide <inputTSV> <outDB>" && exit 1
notExists() {
[ ! -f "$1" ]
}
IN="$1"
OUT="$2"
[ ! -f "${IN}.tsv" ] && echo "${IN}.tsv not found!" &... |
31c1775b1bf12dae9bd6b3172388306d65ebb2e7ec4fdbe08b4a81e00996df6a | Shell | 3,351 | 74 | # Demo for WGS data from a cancer patient
: ex: set ft=markdown ;:<<'```shell' #
The following CHISEL demo represents a guided example of the complete CHISEL pipeline starting from the barcoded [BAM file](https://support.10xgenomics.com/single-cell-dna/datasets/1.0.0/breast_tissue_E_2k) publicly available from 10X Gen... |
9381b1143c6587845dc58c5581ef1f2b65a9483d2040cd8acbfca611458b0ea3 | Shell | 3,369 | 82 | #!/bin/bash
set -x
# script to print message and cancel if jobs never satisfied or cancelled
# change : to ;
jids=${jid_to_check//:/,}
# states of jobs that's not completed in sacct
state_jids=($(sacct -j $jids --format=JobID,State --noheader | grep -v "COMPLETED"))
# while jobs is not completed yet keep monitoring
... |
62a681748db90da8d469f29071cabfc147de6801e404ced3a49724c46080ef4e | Shell | 3,393 | 93 | #!/bin/bash -l
#SBATCH --job-name=spctp_fmriprp
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=1-00:00:00
#SBATCH -o ./log/FMRIPREP_%A_%a.o
#SBATCH -e ./log/FMRIPREP_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=preemptible
#SBATCH --array=7
## --array=1-17%5
#source /optnfs/commo... |
3810c828540a879e260280904d1aed269b8d62511358c6afcdead95bc1f54aa8 | Shell | 3,413 | 67 | #!/bin/bash
#a demo for generate splicing events and sequence features
################################################################
# #
# Part II. Define splicing events and fetch features #
# ... |
08a342bb8bfaeccd74d6482fa4545eea0c2d3a5113493218dd1560f6bb79245a | Shell | 3,418 | 93 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
if notExists "${OUTDB}"; then
# shellcheck disable=SC2086
"${MMSEQS}" createdb "$@" "${OUTDB}" ${CREATEDB_PAR} \
... |
cc216f13ad79d31d5579a0366fdbb860c7f1b0ca839955299d1e523bbae70433 | Shell | 3,422 | 30 | python -u train.py ERing UEA --loader UEA --batch-size 8 --repr-dims 320 --max-threads 8 --seed 42 --eval
python -u train.py Libras UEA --loader UEA --batch-size 8 --repr-dims 320 --max-threads 8 --seed 42 --eval
python -u train.py AtrialFibrillation UEA --loader UEA --batch-size 8 --repr-dims 320 --max-threads 8 --see... |
e0ffba82ea7e7ad06341bdf1f12b1feeac6f1aee9bad99cc2e575afcca7b4991 | Shell | 3,431 | 103 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
#pre processing
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
# check number of input variables
[ "$#" -ne 4 ] && echo "Please provide <queryDB> <targetDB> <outDB> <tmp>"... |
07dcf9800dbe58cf70d15914991975dfc6ba813f586a7db13aa77192553f812d | Shell | 3,440 | 107 | #!/bin/sh
#
# Downloads sequence for the GRCm38 release 81 version of M. Musculus (mouse) from
# Ensembl.
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful. To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# var... |
a6768df48bcbfd0e1d9a5f59b068572acd3cf8a2bff444fbce3517700bb4f64f | Shell | 3,440 | 128 | #!/bin/bash
#SBATCH --job-name=pretrain_randeng_t5_char_57M
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=32 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o /cognitive_comp/ganruyi/experiments/randeng_t5_char_57M/%x-%j.log
#SBATCH ... |
ed63c41e32d08e97b2ac649f34626e21cde4bf1d3e6cc78114150b3ec92531e5 | Shell | 3,440 | 110 | #!/bin/sh
#
# Downloads sequence for Zea mays AGPv3.31 from
# Ensembl.
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful. To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# var... |
f086f18d3e9dd052898b25e2cbdda076cc4fb9784ffedec3c07bd3da0578292e | Shell | 3,447 | 116 | #!/bin/bash
#SBATCH --job-name=pretrain_bart # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.... |
bf76626b76e2f20fa28320da389f6d47b2aea4d7499526b41438192cd17f04d8 | Shell | 3,449 | 95 | #!/bin/sh -e
# reciprocal best hit workflow
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
# check number of input variables
[ "$#" -ne 4 ] && echo "Please provide <sequenceDB> <sequenceDB> <outDB> <tmp>" && exit 1;
# check if files exist
[ ! -f "$1.dbtype" ] && echo "$1.dbtype not found!" ... |
f95298d34d8798858dff5d6a757f03338514cda1f76b53080d49eed8c7132bd3 | Shell | 3,462 | 126 | #!/bin/bash
#SBATCH --job-name=t5_cn_small_pretrain
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o /cognitive_comp/ganruyi/fengshen/t5_cn_small_pretrain/%x-%j.log
#SBATCH -e /cognit... |
3e21a066cdb4b40f6a3e049fde4e4e1d3a10b99fdb4f860fb8242f7a84cc34ff | Shell | 3,470 | 83 | #!/bin/bash
## TODO: change the file so that the dup is the earlier scan
## the latter scan should be better. always.
# Define a file to log errors
# error_log="error_log_funcanat.txt"
LOG_FILE="anat_error_log.txt"
if [ -f "$LOG_FILE" ]; then
rm "$LOG_FILE"
fi
SUMMARYLOG_FILE="anat_summary_log.txt"
if [ -f "$S... |
39b03c647344dfb65c24a01f6c11391b481c2aeb0b8b57021483b7fe07b6b0cb | Shell | 3,478 | 129 | #!/bin/bash
#SBATCH --job-name=pretrain_randeng_t5_char_700M
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o /cognitive_comp/ganruyi/experiments/randeng_t5_char_700M/%x-%j.log
#SBATC... |
e1e6e58628ffa7deccf1c655d3dcee6c7858e74a6ef4f3b3fdae68f3e92f2dbe | Shell | 3,479 | 129 | #!/bin/bash
#SBATCH --job-name=pretrain_randeng_t5_char_10B
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=32 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o /cognitive_comp/ganruyi/experiments/randeng_t5_char_10B/%x-%j.log
#SBATCH ... |
30dd4270b866287571e21ae441f5a889437edd0ba5e8e4cd93fe6465abc65b44 | Shell | 3,488 | 119 | #!/bin/bash
#SBATCH --job-name=pegasus-base_last # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.lo... |
32076294d24140ce891505ee2a1da19604e9c59c16a6cd161e5a4053421b4b50 | Shell | 3,496 | 120 | #!/bin/bash
#SBATCH --job-name=pretrain_bart # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks-per-node=8 # number of tasks to run per node
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:8 # number of gpus per node
#SBATCH -o %x-%j.log # ... |
5e679534bb6bbb8ccec0b556184a133737b1e1a6e0b8276c45603f25d3846da9 | Shell | 3,521 | 75 | # Complete demo of CHISEL
: ex: set ft=markdown ;:<<'```shell' #
The following CHISEL demo represents a guided example of the complete CHISEL pipeline starting from an exemplary barcoded [BAM file](https://doi.org/10.5281/zenodo.3950299) publicly available. From this directory, simply run this file through BASH as a s... |
a208efdd117b40e7c2e6296120e54e6a383f081900abce29db34d1aae13ba914 | Shell | 3,535 | 120 | #!/bin/bash
#SBATCH --job-name=t5_cn_small_pretrain_v2
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o %x-%j.log
#SBATCH -e %x-%j.err
#SBATCH -x dgx050
set -x -e
source activate bas... |
3977dbb4b1c04e013920dafe9a9b654ecf6feb15f3025ed22a0dcfcf9c863898 | Shell | 3,549 | 127 | #!/bin/bash
# ============================================================================
# Rica - Environment Initialization Script
# ============================================================================
#
# Purpose:
# Sets up the Node.js development environment for rica, installs dependencies,
# and verif... |
71b1cff20ca896a2b07e4f65c55aeb62e612e2043cedd8926f006b9d2d50bbd6 | Shell | 3,549 | 85 | #!/usr/bin/env bash
# Prove a release-branch split lost no content: every moved commit's patch-id
# must appear in exactly one theme branch, and every stay-behind commit
# (bucket STAY or FORMAT) must appear in none.
#
# This is the final verification of the split workflow in docs/RunningBabel.md
# ("Releasing a new Ba... |
8d476573b65a2c733afdfea1c567ce9b3e011289b4e202ddb591528416caae32 | Shell | 3,561 | 112 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
f40b003cd556865557000a4f6fc489f97099fc7daeeaa57b9ce3e2e2da62e5e2 | Shell | 3,576 | 86 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# ======================================================================
# SCRIPT INFORMATION:
# ======================================================================
# SCRIPT: CREATE EVENTS FILES ON THE MPIB CLUSTER
# PROJECT: ZOO
# WRITTEN BY LENNART WITTKUHN, 2020 - 20... |
f9f309173237873d9916bc3a86749abac36fa611f5a2f1bb5851005db0d57dd3 | Shell | 3,580 | 112 | #!/bin/sh
#
# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh37 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
d10bc56884794a5c4bca9b795e54a118ebe92dbb9ce050c45a52eb2c91a73430 | Shell | 3,591 | 138 | #!/bin/bash
#SBATCH --job-name=randeng_t5_77M_summary_predict
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --gres=gpu:2 # number of gpus
#SBATCH --cpus-per-task=30
#SBATCH -o %x-%j.log
set -x -e
echo "START TIME: $(date)"
MODEL_NAME=randeng_t5_77M_summary_predict
MICRO_BATCH_SIZE=16
ROOT_DIR=/c... |
10795f47e9f5338a372f6e485f2fa1027d4daf579651b6ef36c93810fe95c113 | Shell | 3,614 | 56 | # EDSR baseline model (x2) + JPEG augmentation
python main.py --model EDSR --scale 2 --patch_size 96 --save edsr_baseline_x2 --reset
#python main.py --model EDSR --scale 2 --patch_size 96 --save edsr_baseline_x2 --reset --data_train DIV2K+DIV2K-Q75 --data_test DIV2K+DIV2K-Q75
# EDSR baseline model (x3) - from EDSR bas... |
6a54d941d9671f493ca5bf9cc6eca5e566b2334065cecb622a9ca91a6f597b81 | Shell | 3,642 | 132 | #!/bin/bash
# Deploy MagellanMapper to AWS
# Author: David Young 2017, 2020
HELP="
Deploy MagellanMapper and related files to AWS.
Arguments:
-h: Show help and exit.
-d [file]: Deploy file or folder recursively. Can be used
multiple times to add additional files for upload.
-i [IP]: IP address of the AWS... |
c8ed624934a3ec36310855721b4b39f27f90b208268882917bbfc136e68d792b | Shell | 3,662 | 129 | #!/bin/bash
#SBATCH --job-name=finetune_unimc_randeng_t5_char_57M
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=32 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o /cognitive_comp/ganruyi/experiments/randeng_t5_char_57M/%x-%j.log
#S... |
6e1b33fed17aa5ba3ccb79cf16b2d3b795413941df1874b60f913641dcd0bf21 | Shell | 3,668 | 130 | #!/bin/bash
#SBATCH --job-name=randeng_t5_77M_summary
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --gres=gpu:2 # number of gpus
#SBATCH --cpus-per-task=30
#SBATCH -o %x-%j.log
set -x -e
echo "START TIME: $(date)"
MODEL_NAME=randeng_t5_784M_summary
MICRO_BATCH_SIZE=8
ROOT_DIR=/cognitive_comp/do... |
632aa9d35446aac7ce9128063c30e7cd28f5a75b3249bc199125994791b5c7e3 | Shell | 3,689 | 79 | #!/bin/bash
#update these to the path of the bert model and the path to the NER data
BERT_DIR=/PATH/TO/BERT/MODEL #clinical bert, biobert, or bert
#path to NER data. Make sure to preprocess data according to BIO format first.
#You could use the scripts in the i2b2_preprocessing folder to preprocess the i2b2 data
NER_... |
84a532293460d7107e7c9bc90a06fb2fb5ac8190a8d2be22880b2e585acf953b | Shell | 3,694 | 93 | # Declare an associative array
declare -A myArray=(
["task-narratives_acq-mb8_run-01"]=967
["task-narratives_acq-mb8_run-02"]=1098
["task-narratives_acq-mb8_run-03"]=1298
["task-narratives_acq-mb8_run-04"]=1156
["task-social"]=872
["task-fractional_acq-mb8_run-01"]=1323
["task-fractional_acq-mb8_run-02"]=1322
["task-sh... |
d0cd7e0a467c3d2c11e9d67d602210e3b2ed37f6f71a283175023a946834cd33 | Shell | 3,706 | 99 | COL1_DATA=""
COL1_LABELS=""
COL2_DATA=""
COL2_LABELS=""
COL3_DATA=""
COL3_LABELS=""
while [[ "$#" -gt 0 ]]; do
case $1 in
--d1)
COL1_DATA="$2"
shift
;;
--d2)
COL2_DATA="$2"
shift
;;
--d3)
COL3_DATA="$2"
shift
;;
--l1)
CO... |
3f7ebc6d6b50b28084e05483d22b2a6d81d611ef32212c68d6e5db331c14b9ab | Shell | 3,731 | 143 | #!/bin/bash
#SBATCH --job-name=randeng_pegasus_523M_summary
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30
#SBATCH -o %x-%j.log
set -x -e
echo "START TIME: $(date)"
MODEL_NAME=randeng_pegasus_523M_summary_last
MICRO_BATCH_SIZE=128
ROOT_DIR=... |
63e5279f254077fcc03363ac8a9b5eb9baa8c26b0a8e9e25dd570d6175450d36 | Shell | 3,731 | 138 | #!/bin/bash
# Function to display help
function show_help {
echo "Usage: $0 [OPTIONS]"
echo ""
echo "Options:"
echo " --age AGE Age of the subject (required, between 3 and 19)"
echo " --threads THREAD Number of threads to use (default: 4)"
echo " --help Show this help messa... |
ee9edc72cd65a474f52037cc4d6c866386020b3f7c38cc7fe558ee82f3af7cd6 | Shell | 3,750 | 108 | #!/bin/bash -e
############################################################################
# @ Filename : run.sh
# @ Description : Loads from config file "config/config_setup.conf"
# @ Arguments : --exp=stiffness|mass
# @ Date :
#####################################################################... |
a04c07c5a3c3918430a77a60978ad7873405fb7c18fd66ee5f820f448a79f4d9 | Shell | 3,757 | 91 | #!/usr/bin/bash
### Merge
ln -s ../annot_reduced.gtf ref.gtf
raw_gtf_files=(\
../bambu/filter/out_transcript.gtf \
../espresso/filter/out_transcript.gtf \
../isoquant/filter/out_transcript.gtf \
../rnabloom/filter/out_transcript.gtf \
../stringtie/filter/out_transcript.gtf \
)
for i in $(seq 0 $(... |
85fc90a733f2a9ffb8dc1b8e06f2521f3ec4536ef46cf73f58bf51ecebc1f003 | Shell | 3,793 | 124 | #!/bin/bash
#SBATCH --job-name=randeng_t5_77M
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o %x-%j.log
#SBATCH -e %x-%j.err
set -x -e
echo "START TIME: $(date)"
MICRO_BATCH_SIZE=6... |
18af5a560e8fa3587df828b60204cc5670f5d28f5525071464537a9b3e285df3 | Shell | 3,830 | 117 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
e92338aa9a93ea3a1d555babf8f88b25483f7450b9f56e2fdcf94d206c842f78 | Shell | 3,830 | 141 | #!/bin/sh
#
# Copyright (C) 2019 Matthias Klumpp <matthias@tenstral.net>
#
# Licensed under the GNU Lesser General Public License Version 3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundatio... |
72811db58d82efe9c804881d85ae48be32bbeaafdd098b000d6d169409cb40fb | Shell | 3,849 | 117 | #!/bin/sh
#
# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh37 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
14a3db5c354eef39fe384683b80d7ca19b23689b282f9ab1804cf73c37ff852a | Shell | 3,850 | 119 | while getopts n: flag; do
case "${flag}" in
n) NUM_COLS=${OPTARG} ;;
esac
done
NUM_COLS="${NUM_COLS:-3}"
setupCA() {
mkdir ./ca
openssl genpkey -algorithm RSA -out ca/root.key -pkeyopt rsa_keygen_bits:3072
openssl req -x509 -new -nodes -key ca/root.key -sha384 -days 36500 -out ca/root.crt \
... |
862683a0f63d03e9e546a9304e3059a401071de234ab5ed6207ce5c3868d1f31 | Shell | 3,850 | 98 | #!/bin/bash -l
#SBATCH --job-name=fmriprep
#SBATCH --nodes=1
#SBATCH --cpus-per-task=10
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=12:00:00
#SBATCH -o ./log/FMRIPREP_%A_%a.o
#SBATCH -e ./log/FMRIPREP_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=11-34%15
## --array=1-17%5
#source /optnfs/co... |
1dea7a365c723c11ee3927ac65946ab707b51056262e2d0a773227f8937f8603 | Shell | 3,867 | 109 | #!/bin/sh -e
# Translated search workflow
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
# check number of input variables
[ "$#" -ne 4 ] && echo "Please provide <sequenceDB> <sequenceDB> <outDB> <tmp>" && exit 1;
# check if files exist
[ ! -f "$1.dbtype" ] && echo "$1 not found!" && exit 1... |
327c254f2e09d2132516f5d5994f450dfe2a9f72d2431ab44c6aca50ff8c64b4 | Shell | 3,933 | 109 | #!/bin/bash
# Install the micromamba to be able to fast deploy the python environment
# The default base directory is the current working directory
# Usage: bash install_mamba.sh <base directory>
if [ ${#1} -eq 0 ]; then
echo "Usage: bash install_mamba.sh <base directory>" 1>&2
exit 0
fi
set -eu
basedir=${1:-./mi... |
a9d04f882bc8ebac6a5c49a56d9f5be363be4a24a1b41c4a52ac260f5a1789a0 | Shell | 3,944 | 143 | #!/bin/bash
#SBATCH --job-name=afqmc-bart-base # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH --mail-type=ALL... |
49e0853f320441834c5ec91f61af62748d7bb0ec9506f1dc4954847bdb945ffc | Shell | 3,945 | 143 | #!/bin/bash
#SBATCH --job-name=ocnli-bart-base # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH --mail-type=ALL... |
3bd2a00d141090bbf5e6b98f46c4af2d184ea4d82cd31500ff09992652ca4290 | Shell | 3,980 | 102 | # Checks
: ex: set ft=markdown ;:<<'```shell' #
This script runs all the tests to check that the current CHISEL implementation is correct and behaves as expected.
## Set up
```shell
set -e
set -o xtrace
PS4='[\t]'
cd $( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )
rm -rf X/ complete/ callingE/ cloningE/ plottingE... |
5a78416b0d81eeaf5146484247ef33e7bdb531d1d1056b26ed1ad211aa2132ab | Shell | 3,988 | 109 | #!/usr/bin/env bash
# Build the eggnog-mapper Apptainer image.
#
# Usage:
# ./build.sh [--local] [EMAPPER_VERSION] [DIAMOND_VERSION] [MMSEQS_VERSION] [HMMER_VERSION] [PRODIGAL_VERSION]
#
# --local Bundle the working directory as-is (includes uncommitted changes).
# Useful for testing dev builds before... |
1ff91879cc2382d969d1b668b72e36b93523c51c279117d67f6fe38e3ac1a9c6 | Shell | 4,050 | 125 | #!/bin/bash
set -e -x
PROJECT_ROOT="$(pwd)"
if [ -z ${HDF5_DIR+x} ]; then
echo "Using OS HDF5"
else
echo "Using downloaded HDF5"
if [[ ${HDF5_MPI} != "ON" ]]; then
echo "Building serial"
else
echo "Building with MPI"
EXTRA_MPI_FLAGS=(-D "HDF5_ENABLE_PARALLEL=ON")
fi
... |
5e661b42423c4a5499dc4bc69c61aaf1b8e4fcc35c70404eb9f4f3057feb224a | Shell | 4,059 | 132 | #!/bin/bash
#SBATCH --job-name=randeng_t5_large
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:8 # number of gpus
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH -o %x-%j.log
#SBATCH -e %x-%j.err
set -x -e
echo "START TIME: $(date)"
MICRO_BATCH_SIZE... |
56e68816c2b8f7e5a64c094aee342e1ded0a68d486ae3e98bd1f4818ebaed464 | Shell | 4,075 | 146 | #!/bin/bash
#SBATCH --job-name=afqmc # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=4 # total number of tasks across all nodes
#SBATCH --cpus-per-task=20 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:4 # number of gpus per node
#SBATCH --mail-type=ALL # send em... |
9b2b24bbc977f7cd0826a081c2c00a103a99e428f8b4dbdad9a575062b471f8b | Shell | 4,102 | 151 | #!/bin/bash
#SBATCH --job-name=afqmc-bart-base # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH --mail-type=ALL... |
cbe31ced596bccb6f4ea57b36a645c70258fcfb1c058b6a92197b012fa86fab8 | Shell | 4,109 | 150 | #!/bin/bash
#SBATCH --job-name=afqmc-bart-base # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=30 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --gres=gpu:2 # number of gpus per node
#SBATCH --mail-type=ALL... |
e1458de1b49ed8a3da8d43ac51f2f33bdbd7c7cc2bce8a08c88a75e621d2ebc7 | Shell | 4,122 | 147 | #!/usr/bin/env bash
# Build wheels for MagellanMapper dependencies
venv_dir="../venvs"
output_dir="../build_deps"
HELP="
Build dependencies in Venv environments for multiple Python versions.
Assumes that environments for each Python version have been set up using
\"setup_multi_venvs.sh\".
Arguments:
-h: Show help ... |
3e2aff322602a3b669135895b365539289c40c15b3345dfa8bed571a262edeea | Shell | 4,155 | 103 | #!/bin/bash
#SBATCH --partition=imgcomputeq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=1g
# This specifies maximum memory use will be 4 gigabytes
#SBA... |
d90dd9dd59bbbcbbfcdfd812f667c80867ce6d8bc616dbc758a4a57aee9bc207 | Shell | 4,186 | 116 | #!/bin/bash
set -e
set -x
DB_NAME=${DB_NAME:-"catmaid"}
DB_USER=${DB_USER:-"catmaid_user"}
DB_PASSWORD=${DB_PASSWORD:-"p4ssw0rd"}
if [ -f "$HOME/timezone" ]; then
DEFAULT_TZ=$(cat $HOME/timezone)
else
DEFAULT_TZ="America/New_York"
fi
TIMEZONE=${TIMEZONE:-$DEFAULT_TZ}
POSTGRES_VERSION=$(psql --version | awk '{... |
a1a09722afe6d40412e82760144d7e98a6988f64d20f6f3360303fea34d99b05 | Shell | 4,248 | 103 | #! /bin/bash
# Created/Written by Cesar Caballero Gaudes @ BCBL.
# Amended and adapted by Hilmar P Sigurdsson - email: hpsig86@gmail.com
# @ Nottingham 2018
# Amended and adapted by Eneko Uruñuela and Mairi Houlgreave December 2021
PRJDIR=/mnt/h/Experiments/Experiment2-Blink_Tic/SPFM
MINBETA=0.01
CLUSTERSIZE=5
MYMASK... |
9840ab5557caf89750f6f265e68afaef4daa9b5776fff786711066c5f1af9102 | Shell | 4,278 | 103 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALLELIZE BIDS CONVERSION USING HEUDICONV ON THE MPIB CLUSTER
# PROJECT NAME: HIGHSPEED
# WRITTEN BY LENNART... |
2aa40863850c2436601900e445cc0451e5242ce2c3a5949e62d9decf51b22841 | Shell | 4,284 | 101 | #! /bin/bash
# Created/Written by Cesar Caballero Gaudes @ BCBL.
# Amended and adapted by Hilmar P Sigurdsson - email: hpsig86@gmail.com
# @ Nottingham 2018
# Amended and adapted by Eneko Uruñuela and Mairi Houlgreave December 2021
PRJDIR=/mnt/h/Experiments/Experiment2-Blink_Tic/SPFM
MINBETA=0.01
CLUSTERSIZE=5
MYMASK... |
587a8b57174210e90789b8e59092248730cb5aec934dfbbe6bc19fc36fd772bb | Shell | 4,352 | 82 | PRJDIR=/gpfs01/share/TS-SPFM
echo "Working directory: ${PRJDIR}"
# subject ID
# LIST_SBJID=$(cat list_subject_runs.txt)
LIST_SBJID="Sub01_run01"
set -e
# ==================================================
# PREPARING FOR ME-SPFM (Detrending and Signal Percentage Change)
# ==============================================... |
f86f112362997c29ee2e819c74f0cd5f513b07fa76804a02ad1ee29665970655 | Shell | 4,355 | 158 | #!/bin/bash
#SBATCH --job-name=slurm-test # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=16 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=8G # memory per cpu-core (4G is default)
#SBATCH --gr... |
8a5c8c8000f7dcbbb8f5471fd269f3a0ec8d624ac15225c4d04febb5b826b450 | Shell | 4,375 | 158 | #!/bin/bash
#SBATCH --job-name=slurm-test # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=16 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=8G # memory per cpu-core (4G is default)
#SBATCH --gr... |
b213de819b3a76ebfe379ab8685f830ec56eb0c3efce0ada684895b6d577c989 | Shell | 4,419 | 125 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
# check number of input variables
[ "$#" -ne 3 ] && echo "Please provide <sequenceDB> <outDB> <tmp>" && exit 1;
# check if files exist
[ ! -f "$1.dbtype" ] && echo "$1.dbtype not found!" && exit 1;
[ -f "$2.dbtype" ] && echo "$2.... |
8b500651ecc7c11b58107c4ddbeb626dd5c39384295e1d8d376a0a1f90820d1f | Shell | 4,436 | 161 | #!/bin/bash
#SBATCH --job-name=slurm-test # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=16 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=8G # memory per cpu-core (4G is default)
#SBATCH --gr... |
d582dbca9502c9337739a32211e580045c63f8a85dcbadb0112b9b3094daed02 | Shell | 4,439 | 30 | python3.8 ./scripts/runNetFromFile.py -w1 PEG_lr8_t0_w1_init -w2 PEG_lr8_t0_w2_init -o ./PEG_lr8/PEG_lr8 -t PEG_lr8_t0_init -p ./voltagePlots
python3.8 ./scripts/runNetFromFile.py -w1 PEG_lr8_t0_w1_e14_b45 -w2 PEG_lr8_t0_w2_e14_b45 -o ./PEG_lr8/PEG_lr8 -t PEG_lr8_t0_e14_b45 -p ./voltagePlots
python3.8 ./scripts/runNetF... |
ac3fad9709a2a5a972a2e7f32dd937e52f9a6df202902d733f26938d80b2eaf0 | Shell | 4,459 | 161 | #!/bin/bash
#SBATCH --job-name=slurm-test # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=4 # total number of tasks across all nodes
#SBATCH --cpus-per-task=16 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=8G # memory per cpu-core (4G is default)
#SBATCH --gr... |
a061fe2737621d1925e0ab91a65b0db8156b2915a44bb5b8ac6bdb705d42dadc | Shell | 4,494 | 120 | #!/bin/sh -e
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}" ]; then
echo "$(cd "${1%/*}"; pwd)/${1##*/}"
else
echo "$(pwd)/$1"
fi
elif [ -d "$(dirname "$1")" ]; then
echo "$(cd "$(dirname "$1")"; pwd)... |
21414d0f42fc0f4bfa55bdc1f525c60b5fee3451c5b13c275022d73a0ade5452 | Shell | 4,497 | 131 | #!/bin/bash
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
# Download specific genomic libraries for use with Kraken 2.
# Supported libraries were chosen based on support from NCBI's FTP site
# in easily obtaining a good collect... |
aa107cda8b8f64c48f10d0acbe44b13259c578b47a3f5da54bc15a2b8c23b77f | Shell | 4,510 | 163 | #!/bin/bash
#SBATCH --job-name=slurm-test # create a short name for your job
#SBATCH --nodes=1 # node count
#SBATCH --ntasks=2 # total number of tasks across all nodes
#SBATCH --cpus-per-task=16 # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=8G # memory per cpu-core (4G is default)
#SBATCH --gr... |
b246e2f5cb2192e96a7233a2b229a1fd217903d9b01d7301e92209c3d67ed44d | Shell | 4,512 | 122 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -e "$1" ]
}
hasCommand () {
command -v "$1" >/dev/null 2>&1
}
notExists "$1" && echo "$1 not found!" && exit 1;
hasCommand awk
hasCommand gunzip
hasCommand touch
hasCommand tar
TAXDBNAME="$1"
TMP_PATH="$2"
STRATEGY=""
if hasCommand ... |
93ae7f277c658c15546f11cafd70aa7cbfe11f90bdb647ee9556b23297e3a93a | Shell | 4,517 | 119 | #!/usr/bin/env sh
set -e
# The following example allows for the MNIST example (using LeNet) to be
# trained using the caffe docker image instead of building from source.
#
# The GPU-enabled version of Caffe can be used, assuming that nvidia-docker
# is installed, and the GPU-enabled Caffe image has been built.
# Settin... |
0e7579ed4c4201691b05f8456d7e9b937145050f3676abab3e22c9d909a6fd3b | Shell | 4,530 | 76 | python3 /private/groups/brookslab/gabai/tools/NEMO/src/predict.py \
--bam /private/groups/brookslab/gabai/projects/Add-seq/data/ctrl/pod5/220308_ang_0.sorted.bam \
--parquet /private/groups/brookslab/gabai/projects/Add-seq/data/ctrl/pod5/220308_ang_0-sigalign.parquet \
--ref /private/groups/brookslab/gabai... |
f9773aa90469bff5bf6a5acaf483b93da354ff4da9abc70d3d4011f5672033aa | Shell | 4,650 | 191 | #!/bin/bash
#
# Library for file system actions
# shellcheck disable=SC1091
# Load Generic Libraries
. /scripts/liblog.sh
# Functions
########################
# Ensure a file/directory is owned (user and group) but the given user
# Arguments:
# $1 - filepath
# $2 - owner
# Returns:
# None
####################... |
8d10163a6baae9dd7e20266d88e051432a430afa9fd0f9b4add8de0df1c85a62 | Shell | 4,654 | 145 | #!/bin/bash
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
# Build a Kraken 2 database
# Designed to be called by kraken2-build
set -u # Protect against uninitialized vars.
set -e # Stop on error
set -o pipefail # Stop on fail... |
25b0ab6ce95413582cea0060af4dfbacab7168960fa54a56639ef27187b4116c | Shell | 4,664 | 150 | #! /bin/sh
# test-driver - basic testsuite driver script.
scriptversion=2016-01-11.22; # UTC
# Copyright (C) 2011-2015 Free Software Foundation, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foun... |
3c0cc0a5e51c4320a1fadb978ffc445381abb75523e01d78b334830f27aca1e4 | Shell | 4,684 | 92 | PRJDIR=/gpfs01/share/TS-SPFM
echo "Working directory: ${PRJDIR}"
# subject ID
# LIST_SBJID=$(cat list_subject_runs.txt)
LIST_SBJID="Sub01_run01"
set -e
# ==================================================
# PREPARING FOR ME-SPFM (Detrending and Signal Percentage Change)
# ==============================================... |
7cab6878ef94b743e7afa4c4c6eedaa74d19a529923c32047c67b9be3061af92 | Shell | 4,785 | 112 | #!/bin/bash
## TODO: change the file so that the dup is the earlier scan
## the latter scan should be better. always.
# Define a file to log errors
# error_log="error_log_funcanat.txt"
LOG_FILE="fmap_error_log.txt"
if [ -f "$LOG_FILE" ]; then
rm "$LOG_FILE"
fi
SUMMARYLOG_FILE="fmap_summary_log.txt"
if [ -f "$... |
3abe164259e8297118404045843fb31e224c7fe54505a48633675dceb8b1bf9a | Shell | 4,789 | 66 | #!/bin/bash
regions="/scale/gr01/shared/jjakobsson/backup/raquelgg_fs3_jakobssonlab/annotations/hg38/rmsk/hg38.fa.fulllength.L1HS_L1PA.bed"
grep L1HS $regions > L1HS_FL.bed
grep L1PA2 $regions > L1PA2_FL.bed
grep L1PA3 $regions > L1PA3_FL.bed
grep L1PA4 $regions > L1PA4_FL.bed
awk '(NR>1)' L1HS_FL.bed | awk '{{... |
cede83c22705d5e08eb363b2e95011a054d1e2fd22ab92c6802a3aa61c282fe1 | Shell | 4,816 | 125 | #!/bin/bash -e
####################################################################
# @ Filename : setup.sh
# @ Description :
# @ Arguments :
# @ Notes : run with "bash -e setup.sh all"
# @ Date :
####################################################################
. load_config.sh
## -... |
85d4e4e1cfc4f6978017abe9f7ac58f4f250a6e6c07af2e557d340fa2b8db31b | Shell | 4,819 | 107 | #!/bin/bash
#PBS -l select=1:ncpus=4:mem=8gb
#PBS -l walltime=08:00:00
#PBS -N secondary_scripts
#PBS -J 0-1699
# Secondary scripts do not depend on primary scripts.
# Each base job is run with 10 different seeds (0-9).
# Load environment
module load anaconda3/personal
source activate graphtrip
cd ~/projects/graphTR... |
b1e031c2af3ee8cd4977bf55806b5ff3eafe918000b617971f00e5ac1fda92fa | Shell | 5,025 | 159 | #!/bin/bash
# Build script to compile SimpleITK with Elastix
# Author: David Young, 2017, 2022
HELP="
Compiles SimpleITK with Elastix enabled.
Build the package in a clean build directory with support for Mac and
Linux with Python virtual environments.
Includes compiler flags to configure CMake to use clang on late... |
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