sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
489cacc344e023807f26d280071227455a926ef1c6681aa24fabeb7e24f4806f | Shell | 2,932 | 57 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Li2019_GSR
# remove useless stable projects
rm -r Standalone_Li2019_GSR/stable_projects/brain_parcellation/Kong2019_MSHBM
rm -r Standalone_... |
a79469d8ab449932020a3a08440d76c1d6ac820e8b12312fd38810fb037dfe88 | Shell | 2,933 | 105 | #!/usr/bin/env bash
set -euo pipefail
# ---------- defaults ----------
OUT_ROOT="../datasets"
RESULTS_ROOT="../results"
CONFIG="base"
MODEL_PATH="../models/pretrained/base/base.pth"
DATASET_TYPE="classification"
METRIC="rocauc"
SPLIT="strat-0"
EXP_NAME="KPGT-F"
PATIENCE=6
PATH_LENGTH=5
N_JOBS=32
N_SAMPLES=24
PYTHON_BI... |
4adad561bcc8b3516537be0f15fcee21a462e561456a9d2852ee1831e92c8863 | Shell | 2,935 | 60 | #!/bin/bash -l
set -e
#cd in the directory of the script in order to use relative paths
script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P )
cd "$script_path"
WORKING_DIR=/home/runner/work/gatk
set -e
echo "Creating tar.gz for Funcotator datasources =========="
pushd .
FUNCOTATOR_TEST_DS_DIR=${WORKING_DIR}/gat... |
e5e1ffcb14570f8cbc83be6400cfa7113b47651dcb41bdea02af1066614909c4 | Shell | 2,938 | 97 | #!/bin/bash
set -x -e
pip install --upgrade pip setuptools wheel cmake ninja
echo "Check CMAKE version"
cmake --version
mkdir -p be/install && cd be
echo "Checking folder structure"
ls -lh .
ls -lh ..
# Download and build VTK
LIB_LOCATION=build
if [[ $1 =~ ubuntu-.* ]]; then
VTK_BINARY=vtk-wheel-sdk-9.3.1-cp310... |
8f4bac8c43f9a8bd799ae0b7b3eaa596c7b4141a787d4d2a4e5cb9440c9d0dcc | Shell | 2,940 | 45 | #!/bin/bash
#BSUB -J VAL_A1
#BSUB -o ./VAL_A1_%J.out
#BSUB -e ./VAL_A1_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for PHENOVAR... |
5dcbbc3a978c71f1f80410616eaf40be0153390e4f559e3ce90c694277a5e10f | Shell | 2,941 | 92 | #!/bin/bash
# The behavior of the script is controlled by environment variabled defined
# in the .github/workflows/test.yml file defining the github action to run
# for the project.
#
# This script is adapted from a similar script from the scikit-learn repository.
#
# License: 3-clause BSD
set -xe
CLOUDPICKLE="cloudp... |
d7546761d84dcb24c2adcb21f9a025fce2aa9195697b42318ee5e5b68b905577 | Shell | 2,943 | 66 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
48d368e84c8dda7222451e939687fabde0098a64ba5b149763bc628300e3eabe | Shell | 2,953 | 44 | #!/bin/bash
#BSUB -J VAL_OMNI
#BSUB -o ./VAL_OMNI_%J.out
#BSUB -e ./VAL_OMNI_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 10000
#BSUB -R "rusage[mem=10000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for ... |
64f6e0b5d17cf2cb9539071f7667288ea11446b2e6ebc56d64cc6da4ee3f65b4 | Shell | 2,954 | 45 | #!/bin/bash
#BSUB -J THCVD_A1
#BSUB -o ./THCVD_A1_%J.out
#BSUB -e ./THCVD_A1_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for PH... |
f5f6c674deb799bade7cea8e0a5943efbdbaeba7129c97e48b5629d29af909db | Shell | 2,956 | 45 | #!/bin/bash
#BSUB -J VAL_AR
#BSUB -o ./VAL_AR_%J.out
#BSUB -e ./VAL_AR_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for PHENOVAR... |
c426f4bb3cee4574b842176ae0997185fd27828fa2ab37461ae9f027b352123b | Shell | 2,959 | 45 | #!/bin/bash
#BSUB -J VAL_A2GSA
#BSUB -o ./VAL_A2GSA_%J.out
#BSUB -e ./VAL_A2GSA_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for... |
181cd3f68ce8d647a4f0ad09153696c93ff574a85dfce1c7a58bb6a642ee0a5f | Shell | 2,961 | 75 | #!/bin/bash
#SBATCH --job-name=soBUSCO
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=100G
#SBATCH --error=joblog_error_yahs_%A_%a.txt
#SBATCH --output=joblog_output_yahs_%A_%a.txt
#SBATCH --array=0-11 # Updated array range from 0-5 to 0-11
#### source l... |
b6dbdad53200aee97222491aac99672a26fc927b2dcb14521660935df98aa841 | Shell | 2,963 | 66 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
878f75c9ca4be3626569dadc790f1f25d4370e8a142cc08bafd88e976b05abc3 | Shell | 2,966 | 45 | #!/bin/bash
#BSUB -J THCVD_OMNI
#BSUB -o ./THCVD_OMNI_%J.out
#BSUB -e ./THCVD_OMNI_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
... |
a8e8d2812bc012258a0968af763d19f13bae52ae28b18e9cd7c7ed2e04bf8bab | Shell | 2,972 | 44 | #!/bin/bash
#BSUB -J THCVD_A2GSA
#BSUB -o ./THCVD_A2GSA_%J.out
#BSUB -e ./THCVD_A2GSA_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
... |
5adfb72ebaa2d2a31368765642df5eea24a814454754f56de15bbfd154d80159 | Shell | 2,974 | 71 | #!/bin/bash
# Path to the folder containing subject folders
subjects_folder="/beegfs_data/scratch/iandrulyte-diffusion"
FA_folder="/beegfs_data/scratch/iandrulyte-diffusion/FA_maps/for_Ieva_FA_maps"
AF_divided_files="/beegfs_data/scratch/iandrulyte-diffusion/Divided_AF_five_parts"
# Create a CSV file for full AF FA... |
3afad56fac189d4bffa3e0f40c8f16a21f31b3fbfe5edee68b1b8bb1403d3194 | Shell | 2,978 | 68 | #!/bin/bash
# Copyright 2025 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
1007e44fa7d0bf180f050bd73ad0f225ed973b800e686a1ede281a0932b4d546 | Shell | 2,980 | 74 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SEGMENTATION OF ANTOMICAL SCAN (FREESURFER)
##
## R-fMRI master: Xi-Nian Zuo at the Institute of Psychology, CAS.
## Email: zuoxn@psych.ac.cn
## References:... |
45583e9ea4e06250b1769df72730b37b94f3ca284f818232c42affad60192254 | Shell | 2,982 | 109 | #!/bin/bash
# Uninstallation script for Membrane Kymograph Generator
# This script removes the system-wide installation
set -e # Exit on error
# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color
# Installation directories
INSTALL_DIR="/opt/membrane-kymograph"
BIN_LINK... |
25ef9e1aa43e5711f61ae867fae5879c58c46f6a49b298d33cb427e809790405 | Shell | 2,984 | 90 | #!/bin/bash
##########################
export project_work_dir=$1
##########################
if [ -f human_wg/data/histogram.txt ];
then
rm human_wg/data/histogram.txt
fi
if [ -f human_wg/circos.png ];
then
rm human_wg/circos.png
fi
cd $project_work_dir/Pre_Assembly
#/media/storage/HTS/VirusMeta/SAM_BAM/hg1... |
27d5c7d44e8dfa8929f187387e6569f7c91afa67995740000cbd0f7bb048dc4e | Shell | 2,986 | 45 | #!/bin/bash
#BSUB -J THCVD_ADC13t15
#BSUB -o ./THCVD_ADC13t15_%J.out
#BSUB -e ./THCVD_ADC13t15_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4... |
1e54aa93930eea99167312b00175b997dc146d4ee12ae86d010393d5cd41d5af | Shell | 2,992 | 64 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
44420db617b34b3515174ebdb27c36205f16116a85bc2771f4666c37a2ab61fb | Shell | 2,992 | 80 | #!/bin/bash
# =============================================================================
# STARsolo CLI - STRT-seq platform
# =============================================================================
# CB_UMI_Simple with a 96-barcode whitelist (8 bp CB, 8 bp UMI).
# NOTE: R1 is the biological read; R2 carries th... |
346f0a9ed7816d426d9a34c7b0e2986c422cc9cba5338fa431af0097f6182862 | Shell | 3,002 | 81 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licen... |
3cfcb70a94c89f1f276f9ef690eee74186f3b4b607f92ec4c2dc42326f10b81e | Shell | 3,006 | 92 | #!/bin/bash
set -e
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
CONDA_ENV="dnabert_aug_2025_jupyter"
PYTHON_SCRIPT_1="TSProm/src/3_attention/1_raw_attention_extract-gpu.py"
PYTHON_SCRIPT_2A="TSProm/src/3_attention/2A_save_meme.py"
PYTHON_SCRIPT_3="TSProm/src/3_attention/3_SHAP.py"
GPU_... |
29f3cab8a44261324cbbf91cfff7b21a92019b1f9726f1a4af14ecf748c2b9fa | Shell | 3,010 | 89 | #!/bin/bash
# The behavior of the script is controlled by environment variabled defined
# in the .github/workflows/test.yml file defining the github action to run
# for the project.
#
# This script is adapted from a similar script from the scikit-learn repository.
#
# License: 3-clause BSD
set -xe
ORIGINAL_PYTHON_VER... |
7331a254617db36575cb2047b77bae9f7459722a1e6387d4be872630ad7b49a9 | Shell | 3,027 | 86 | #!/bin/bash
#SBATCH -c 12
#SBATCH -t 0-11:59
#SBATCH -p short
#SBATCH --mem-per-cpu=10G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v3_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v3_%j.err
###############################################################################
# Whole-brai... |
d40bd17d8b0d040eccf65431668edf2a35895b099fbcdc4a1c7210c984d4cfdb | Shell | 3,027 | 67 | #!/usr/bin/env bash
set -euo pipefail
# One-time setup script for the ComptoxAI host on Amazon Linux 2023 ARM64
# (r7g.large or similar). Run as root or with sudo.
#
# Prerequisites this script does NOT handle (do them before running):
# 1. EC2 security group inbound rules:
# - 22 TCP from your admin IP only... |
2c9c4da5b2feff1027942380b68b49b8455c11f4722ada236d83309f5e804c97 | Shell | 3,029 | 60 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
project_dir=${1} # output directory
data_type=${2} # data_type = metric/label.
version=${3} # version = 20160827 or 20170508
fsLR_surface_dir=$CBIG_CODE_DIR/data/templates/surface
######################... |
acdd55d7fca3886f04b984cea2c73562b08c1eeda403d44dd3be8afe4cff44b5 | Shell | 3,029 | 101 | #!/usr/bin/env bash
#
# This script runs through the code in each of the python examples.
# The purpose is just as an integration test, not to actually train models in any meaningful way.
# For that reason, most of these set epochs = 1 and --dry-run.
#
# Optionally specify a comma separated list of examples to run. Can... |
fa574c1910b71b19f8bdcf8eba4333082ea1d317778953f75f5fa69a1512ac2b | Shell | 3,031 | 65 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
31dc6c1d286b70848633c0315db4087570fc74f1511cc9f5d7798f1ae0c0038a | Shell | 3,034 | 83 | #!/bin/bash
#SBATCH -c 12
#SBATCH -t 0-07:59
#SBATCH -p priority
#SBATCH --mem-per-cpu=10G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v2_priority_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v2_priority_%j.err
#######################################################################... |
e30e7d5619a84964f28a1d6a39fa8537aa42637031553291bc1b02ceefef6930 | Shell | 3,034 | 85 | #!/bin/bash
# nnU-Net v2 Training & Evaluation Pipeline for KiTS23
#
# End-to-end pipeline: data conversion, planning, 5-fold training,
# configuration search, and grouped Dice evaluation.
#
# Environment: conda activate convnextv2
# Estimated GPU time: ~2-3 days on a single A100 for all 5 folds.
# --------------------... |
331b3f7a283620a9ac19ee82952d302c48085bb5a76182810da8e20d13c7ecf1 | Shell | 3,048 | 51 | ###########Bench4############
BENCH4Q_BB=./dockq/only_backbone/bench4_dockqstats.csv
BENCH4Q_AA=./dockq/all_atoms/bench4_dockqstats.csv
BENCH4Q_RF=./dockq/only_backbone/bench4_dockqstats_RF.csv
BENCH4_KD=../../data/dockground/dockground.csv
#PCONSDOCK_BENCH4=./plddt/pconsdock-bench4.csv
PLDDT_BENCH4=./plddt/plddt_metri... |
1565dad78a517365a4a5e69cbd84cfdb979dd501d73bab84e57cedaa922f3114 | Shell | 3,051 | 84 | #!/usr/bin/env bash
# Full Phase A + B on Gadi (default photometry ON → completeness diagnostics + catalogue counts).
# Params: reff=5, nframe=5, ncl=400, galaxy=ngc1566 (override with env).
#
# Prerequisites (login node once):
# python3 -m venv .venv && source .venv/bin/activate && pip install -U pip && pip install ... |
50fb283c4c46b889b8b91b8066ef1103a16660965029ef9b830a47d6b4743c16 | Shell | 3,051 | 109 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# This is a simple little script to return the mean absolute error of data
# (image or timeseries) against a reference. The script is so simple, it might
# be helpful as a template script too.... |
7696625e31d111a2fc791d4f1100ebaf9d445586549af7f21d66b97aedac9692 | Shell | 3,059 | 29 | module load Anaconda3
conda activate geomx
python -m cellevaluation --vis_label_data cosmx_measuremens_flipped_y_dca.csv --h5ad_dir 'out/' --vis_name_pattern 'cosmx_6_6_[0-5]_all.h5ad' \
--num_subgraphs_per_graph 36 --num_hops_per_subgraph 1 2 3 5 8 11 --do_clustering_metrics --do_performance_metrics --do_path... |
b5dad84311f0cd8b54c46946c7d78115b61934508380b4a6a9d656267f6169b4 | Shell | 3,068 | 82 | #!/bin/bash -v
################################################################################
#
# subject_preprocess
# ----------------
#
# Pre-process the dMRI data for a single HCP subject using multi-shell CSD
#
################################################################################
#
# Usa... |
bab4873ce6c4e6ede5fe39a4a31705ebe1e475bc211fcc0359e4602684dc59e0 | Shell | 3,072 | 62 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
1a5734799a2053a62bcb6627546af15cdf6822515e5c111035fa73c86992411f | Shell | 3,081 | 83 | #!/bin/bash
set -e -u
# parse arguments
SubjectDir="$1" # /path/to/subject
Subject="$2" # subject ID
ASLVariable="$3"
ASLVariableVar="$4"
LowResMesh="$5" # 32
FinalASLResolution="$6" #2.5
SmoothingFWHM="$7" # "2"
GrayordinatesResolution="$8" # "2"
RegName="$9" # e.g., "MSMAll" or "MSMSulc"
CARET7DIR="${10}" ... |
aa5aafbe6388b2c5cdd700eff1cfe76005790e6f7ca036aeea123deb698e2583 | Shell | 3,087 | 100 | #!/bin/bash
# Copyright 2020 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
1b537c46a04a6597a532d61494665874756c30368f220c62049b58420264990c | Shell | 3,088 | 110 | #!/bin/sh
set -e
RED='\033[0;31m'
NC='\033[0m' # No Color
log() {
printf "uninstall.sh: %s\n" "$1"
}
err_and_exit() {
local Message="${1:-}"
local AdditionalInfo="${2:-}"
if [ ! -z "${td:-}" ]; then
rm -rf "$td"
fi
local info_suffix=""
if [ -n "$AdditionalInfo" ]; then
i... |
693c9f98f7958c39e52a488a88324a8f322f2d798442f2f02c3c1839170c9a8d | Shell | 3,090 | 68 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
project_dir=${1} # output directory
data_type=${2} # data_type = metric/label.
fsLR_mesh=${3}
version=${4} # version = 20160827 or 20170508
fsLR_surface_dir=$CBIG_CODE_DIR/data/templates/surface
######... |
c021fc4da9f4d044d13ef8c66e9550e20de2431c3126545793a1987e05df5044 | Shell | 3,090 | 99 | #!/bin/bash
USAGE=$(cat <<EOF
=== list-norm-files.sh ===
USAGE: $(basename $0) [flags] <output prefix>
Get a list of files that have been normalised. This requires that you have GWAS_DEST_DATA_ROOT set correcly in your ~/.bashrc or ~/.bash_profile
EOF
)
. shflags
# configure shflags
DEFINE_boolean 'verbose' false 'g... |
6392ca775d5415fe11a6d5a46bef3d70855f6d34b4703e155cc40ac32c5133cf | Shell | 3,103 | 86 | #!/bin/bash
#SBATCH --job-name=soSEQKIT
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --error=joblog_error_cleanHiFi_%A_%a.txt
#SBATCH --output=joblog_output_cleanHiFi_%A_%a.txt
#SBATCH --array=0-10
#### source library
path_script="/gpfs/scic... |
a8350b65e32a0322f90c6269bd1fc5ba0439111cd59c466ca43abbaf26f18b4d | Shell | 3,108 | 101 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Build habitat-sim using scikit-build-core.
#
# Usage:
# ./build.sh # Default build (GUI + Bu... |
dd771ef38645967f678f8303a316e7f84e58aa8a2fdb2200bf2ac3571d281612 | Shell | 3,108 | 74 | #!/bin/bash
# This scripts performs positive selection on the aligned sequences in script 08, using Hyphy FEL method.
# It uses the gene trees generated in script 10 and the species tree from Ronco et al. (2021).
# Hyphy version 2.5
source Scripts/functions_bash.sh # To access custom functions defined in functions_ba... |
48a4b20433770fa9cd1406967678acbbebfa699d18fd443e3d075778d0e7b8ca | Shell | 3,110 | 92 | #!/bin/bash
## check that all the runs have exactly 2 archived fastq files associated with them,
## and re-organise them according to sample_to_run.tsv
SERIES=$1
if (( $# != 1 ))
then
>&2 echo "USAGE: ./reorganize_fastq.sh <series_id>"
>&2 echo
>&2 echo "(requires non-empty <series_id>.sample.list, <series_i... |
ee8e0e28dfef86346a3d8d54c33dfda0e969e9fa0d81047f85a35cb6e852e6d1 | Shell | 3,111 | 121 | #!/bin/bash
# set -x -e
function usage()
{
echo "pybatch : Paul's SGE/SLURM/LSF launcher"
echo "Usage:"
echo " pybatch.sh [options] <command> [args]"
echo "Options:"
echo " -m <value> : Set memory requirement for job (e.g., 8G)"
echo " -n <number> : Set CPU core requirement for job (e... |
56903a3927f0f354f5b50278c45dc8b846806e7663256603e415f2d15ef890bd | Shell | 3,119 | 77 | #!/usr/bin/env bash
########this script run ccs_anat_preproc###########
#there are three inputs
# The first step of this script is to run on bash will move to python eventually
# 1.CCS_DIR
# 2.SUBJECTS_DIR
# 3.subject
######################################################
#set dirs
CCS_DIR=$1
SUBJECTS_DIR=$2
subject=... |
0f77e1a4a2e3595a343d1647bfb20fceb3fcb3de41c133a191460554ade77f63 | Shell | 3,121 | 84 | #!/bin/bash
#SBATCH --job-name=fsl_feat_batch
#SBATCH --cpus-per-task=4 # Adjust CPU allocation
#SBATCH --mem=16G # Memory per FEAT job
#SBATCH --time=24:00:00 # Adjust runtime
#SBATCH --nice=10 # Higher priority
#SBATCH --array=0-60 #Adjust based on number of subjects/sessions
# Load FSL module (modify if necessar... |
9693926837787e8d62855ca892872dc2a80b40b452936357057bbe16163bca1a | Shell | 3,136 | 76 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=iPSC_STR
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/iPSC_corrine/STR/src
#SBATCH -o logs/1_dumpSTR.log
#... |
78f8f2a9db64b9ff623277edacef7f122647aa4b4b9110be032e42c5fc36307d | Shell | 3,137 | 134 | #!/bin/sh
if test "$1" = "" ; then
echo "afer-install needs a host_cpu argument"
exit
fi
if test "$2" = "" ; then
echo "after-install needs a installation directory argument"
exit
fi
CPU=$1
prefix=$2
srcdir=$3
ivlibdir=$4
export CPU
NSRC="$3"
export NSRC
NVER="`sh $srcdir/nrnversion.sh`"
NDIR="NEURON-$NVER"
exp... |
38115f314cfd7b607a9841b90843a61136b126a329d84e18a381611135e619c7 | Shell | 3,139 | 87 | #!/bin/bash
#SBATCH --job-name=soGenome
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --error=joblog_error_pacbioclean_%A_%a.txt
#SBATCH --output=joblog_output_pacbioclean_%A_%a.txt
#### pacbioclean
function cleanhic {
local sample="$1"
... |
5cc4c43e15374a1e8185096576ef39ea448eac106bd3ebdecbd47a70dbcd23d3 | Shell | 3,145 | 86 | #!/bin/bash
#SBATCH --job-name=fsl_feat_batch
#SBATCH --cpus-per-task=4 # Adjust CPU allocation
#SBATCH --mem=16G # Memory per FEAT job
#SBATCH --time=25:00:00 # Adjust runtime
#SBATCH --nice=10 # Higher priority
#SBATCH --array=0-321 # Adjust based on number of subjects/sessions
# Load FSL module (modify if nece... |
69164254277c33d46498eaa77b9412444cf2505e251f0afb4b3cbec839d48b22 | Shell | 3,146 | 95 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE DTI SCAN (INTEGRATE AFNI AND FSL)
##
## R-fMRI master: Xi-Nian Zuo. Aug. 13, 2011.
##
## Last Modified: Dec., 12, 2015.
## Email: zuoxn@psych.ac... |
7f91e2ad7155dd60419c5e5dac7c8905ef974e9a63e4c70fe8f7ff5366fafa2c | Shell | 3,156 | 115 | #!/bin/bash
# Convert all the old XMLs in bulk GWAS norm into the new XML format
set -euo pipefail
# The input directly
indir="$1"
outdir="$2"
mkdir -p "$outdir"
cur_dir="$PWD"
cd $indir
# get all the file in the dir
files=($(find -type f -iname "*.xml.gz"))
for i in ${files[@]}; do
xml_file=$(readlink -f "$i")... |
694e7bd0a1c7c0e16d2ce74d20980f09ebf07cdf248f0caab692965f50161caf | Shell | 3,169 | 120 | #!/bin/bash
#
# Script to submit and update feedstock PRs from CircleCI
#
# Requires the following environment variables
#
# GITHUB_USER: The name of your user or bot
# CIRCLE_PROJECT_USERNAME: User under which repository is found
# CIRCLE_PROJECT_REPONAME: Name of repository
#
# One of:
# ... |
a0b4508f139b22fa22321bf3e57cc90373d38ff6ae96eb7641abe43ce2d4f3b3 | Shell | 3,171 | 100 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
e6b1f0695da9c226f3f722f87ada9df69bc5815c7204c4b6aa28dec5d67def5e | Shell | 3,176 | 120 | #!/bin/bash
#
# Script to submit and update feedstock PRs from CircleCI
#
# Requires the following environment variables
#
# GITHUB_USER: The name of your user or bot
# CIRCLE_PROJECT_USERNAME: User under which repository is found
# CIRCLE_PROJECT_REPONAME: Name of repository
#
# One of:
# ... |
55999887396123515416748aa4b0ea064ef483410a1108788ba00b42268e163c | Shell | 3,182 | 47 | #!/bin/bash
#BSUB -J THCVD_AADgte50
#BSUB -o ./THCVD_AADgte50_%J.out
#BSUB -e ./THCVD_AADgte50_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4... |
99ae2de0434c094d529645361e4164eabd5b8bae3a2ddec7e41a9d3f80b9ef99 | Shell | 3,182 | 112 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# This is a simple little script to return the root-mean-square-error of data
# (image or timeseries) against a reference. The script is so simple, it might
# be helpful as a template script t... |
5e6e3a1f5fe12cc2cee432b1dfff69851ba64fb43727e8998a9aa3e9a2333c61 | Shell | 3,187 | 107 | #!/bin/bash
umask 0000
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug87422/smithlab-shared/$projectname
scriptdir=$maindir/code
bidsdir=$maindir/bids
logdir=$maindir/logs
mkdir -p $logdir
#Keep scratch and derivatives dirs separate by sessions
for ses in {01..12}; do
if [ ! -d "$maindi... |
53c18195ad08420d2c13feb8e8fff68ea75ae71836e9a1af20bd8abb4223329c | Shell | 3,190 | 70 | #!/bin/bash
#nohup /media/StorageOne/HTS/VirusMeta/codon_usage/cutg_codon_usage.sh /media/StorageOne/HTS/Projects/test_cutg all_genbank
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export working_dir=$1
export taxonomic_order=$2 #all_genbank or only_virus
if [... |
7a66fc3c08790e0718819d089fa4670451f3a283e133fe0c5d2156c6f0c2812d | Shell | 3,190 | 90 | #!/bin/sh
# This function replicate the linear ridge regression results in the GSP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(pwd... |
197c56cc92cef90d49d36ab16bbc4d70db9d3deaf6a669799c2f2959e6bd6145 | Shell | 3,204 | 126 | #!/bin/sh
#
# -----------------------------------------------------------------------------
# Author: James Bonfield.
#
# This cross validation script is designed to run the htslib test_view
# and cramtools.jar CRAM implementations to test compatibility between
# implementations.
#
# The test set may contain many du... |
8d1ac2319a1bf67b9939686015342f5b111e3b02b0a752e2bb96374d91c14978 | Shell | 3,204 | 47 | #!/bin/bash
#BSUB -J VAL_AADgte50
#BSUB -o ./VAL_AADgte50_%J.out
#BSUB -e ./VAL_AADgte50_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.0... |
77baecaac44e9b6154ee48153231c717d617ec27c25c81f2e9e7d7adb40d8413 | Shell | 3,211 | 55 | #!/bin/bash
#BSUB -J MHEMOR
#BSUB -o ./MHEMOR_%J.out
#BSUB -e ./MHEMOR_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/s... |
22a6598ca7f296cbe524e9e04bfa66779d8a6ae1faf2f8eed6e356d05939affc | Shell | 3,217 | 55 | #!/bin/bash
#BSUB -J MWMRCAL
#BSUB -o ./MWMRCAL_%J.out
#BSUB -e ./MWMRCAL_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hih... |
d3e05d0fb481c9092eac7b5a60972a0e3cd125b11e95ec1612094a59ac6258cd | Shell | 3,219 | 97 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# when input arguments are provided, use these rather than the instruction file
[[ $# -gt 0 ]] && siteList="$*" || siteList=""
# ------------------- #
# GENERAL DEFINITIONS
# ----------------... |
a96a17eaa3d0f6d8c3ebc1ab7494c7c64638e960760fb1715e95b525f0330d42 | Shell | 3,226 | 47 | #!/bin/bash
#BSUB -J VAL_AADgte50
#BSUB -o ./VAL_AADgte50_%J.out
#BSUB -e ./VAL_AADgte50_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.0... |
66e4113983a6cdfdc3fe1612863ccebfa3f1ddfd466833e24bea77196e4d34c3 | Shell | 3,231 | 57 | #!/bin/bash
# this function runs all the control analysis of regression models
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
top_outdir=$1
###################################################################################################
# set co... |
cf7d4ca87d1d27367f4f590759d9a6ea55dad1bf9dbc02c916586ea249114ffa | Shell | 3,231 | 80 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <input_dir> -b <num_behav> -s... |
1c77add32cba47dc1521bd8ed172fb54632f92202ec7e2b33bee56f293d2f119 | Shell | 3,232 | 76 | #!/bin/bash
#SBATCH -c 16 # cores
#SBATCH -t 6-23:00 # Runtime D-HH:MM (just under 1 week)
#SBATCH -p long # 30-day cap; we fit comfortably
#SBATCH --mem-per-cpu=8G # 128G total
#SBATCH -o /... |
af9fa1912e8fe35c99426d77c35834e7fd798f775e79ead45545a7f87f817257 | Shell | 3,234 | 72 | #!/bin/bash
# Define the directories
DATA_DIR="/.../EMBARC/03_FSL_FEAT/Whole-data"
FSF_TEMPLATE="/.../EMBARC/03_FSL_FEAT/FSL_FEAT_model/Model.fsf"
# Loop through all subjects
for subject in $(ls $DATA_DIR); do
if [[ $subject == "sub-"* ]]; then # Ensure it follows subject naming convention
for session i... |
b0bb9fcd32ab3b29de533eb09c94be1219e90a67335c50f25cb141d9bd865940 | Shell | 3,238 | 78 | #!/bin/bash
#### hg38 ####
# add plasmid FASTA to hg38 FASTA
cp GRCh38.primary_assembly.genome.fa GRCh38.primary_assembly.genome.withdCas9.fa
cat pAAVS1_TetOn_zKRAB_dCas9_P2A_mCherry_insert.fa >> GRCh38.primary_assembly.genome.withdCas9.fa
grep ">" GRCh38.primary_assembly.genome.withdCas9.fa
# remove version suffix... |
ac3880214411b497a46d3d2a91557e775c7c94853283410807d4cc78ee84e90d | Shell | 3,239 | 79 | #!/bin/bash
#SBATCH --job-name=soMAPILMN
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=250G
#SBATCH --error=joblog_error_mapILMN_%A_%a.txt
#SBATCH --output=joblog_output_mapILMN_%A_%a.txt
#SBATCH --array=0-1
#### source library
path_script="/gpfs/scic/da... |
38ef3296b93fa8fc38ad732634574fb55158ffabac89942274a59ff1c500c3b3 | Shell | 3,240 | 47 | #!/bin/bash
#BSUB -J THCVD_AADgte50
#BSUB -o ./THCVD_AADgte50_%J.out
#BSUB -e ./THCVD_AADgte50_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4... |
79b34d8ccad57361709a0bc9cb48fb45a4251e7419a0f6cfbb9ad0a50208eed7 | Shell | 3,242 | 44 | ## VGGSound_100
#CUDA_VISIBLE_DEVICES=0,1 python train_incremental_ssil.py --dataset VGGSound_100 --num_classes 100 --class_num_per_step 10 --modality audio --max_epoches 300 --num_workers 0 --memory_size 1500 --lr 1e-3 --lr_decay False --milestones 100 --weight_decay 1e-4 --train_batch_size 256 --infer_batch_size 128 ... |
33e9dee276df21ab9f42cb1961af5da70ecc65247c1dd5be15a17dd8b93e69bf | Shell | 3,243 | 69 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
52a1653cdbca4b9269fef2772a2d35df5cdafdbf6d0158f4a3e1a091986b1bee | Shell | 3,243 | 67 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
f703d2e078aa5442fd2c71a434de3f344756d579a2d23950d52f6455e00f1fa3 | Shell | 3,257 | 92 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --mem=12G
#SBATCH -p long
#SBATCH --gres=gpu:1
#SBATCH -t 1-00:00:00
#SBATCH -o ./Logs/out_%j.log
#SBATCH -e ./Logs/error_%j.log
# Load the modules
module purge
module load Python/3.7.4-GCCcore-8.3.0
module load libs/cuda/10.1.243
module load libs/cudnn/7.6.5.32-CUDA-10.1.243
mod... |
2cd23827095ab69696c1697cf3fcc33d0434291c5a6db683512c8a79f454d0db | Shell | 3,258 | 136 | #!/bin/bash
usage() {
cat << EOF
Usage: batch-dl+direct [-h] [-c n_cpu] [-g n_GPU] [-b] [-m model_file] SRC_DIR DST_DIR
Batch processing using DL+DiReCT (with --bet), with N parallel jobs on CPU and GPU.
SRC_DIR is a directory with data to process, each subject should be in a separate subdirectory (with a T1.nii.gz in... |
859cd905075b4a6478dcaa23f7c699445209d7d702d7a6d5f090cb3d166e14d5 | Shell | 3,259 | 86 | #!/bin/bash -e
# Part of STARE: https://github.com/SchulzLab/STARE
# Small bash script to ease the normalization of .hic-files with Juicebox (https://github.com/aidenlab/juicer/wiki/Data-Extraction)
help="\n
Usage: ./Juicebox_KR_normalization.sh [-h hic-file to normalize]\n[-j path to the jar-file]\n
[-d folder to wr... |
7afb5fb76f60e2ac68861e78b9b16c883a347c4728693700037492151a6a4b56 | Shell | 3,261 | 88 | #!/bin/bash
# All raw reads are publicly available from the NCBI SRA database under BioProject PRJNA550295 (genomes) and PRJNA552202 (transcriptomes)
# I did not include the reference genome (Oreochromis niloticus) in the data but it is available from NCBI under the accession number GCF_001858045.2
# The following scr... |
12100d7abfbfc2ec45afb365c774a7853bb4e80ae4cf18fcfe80ff87d40dcded | Shell | 3,262 | 105 | #!/bin/sh
#####
# Example:
# $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG_diffusion_processing2022/AMICO/CBIG_DiffProc_runAMICO.sh \
# --subj_list /path/to/txtfile --dwi_dir /path/to/dwi_images \
# --output_dir /path/to/output --py_env name_of_AMICO_environment \
# --mask_output_dir /path/... |
02b15806a1e6c94cbcec283044d39d0183be3236b6b23e8a009b11d5c2bab70d | Shell | 3,265 | 96 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
8852db9b3888a94a3b763fec917a449872246e101717949553c1b9d9f18fc4a1 | Shell | 3,265 | 108 | #!/bin/bash
# Setup script for DP_GP_cluster monitoring
# This script helps configure notifications and test the monitoring system
set -euo pipefail
echo "DP_GP_cluster Monitoring Setup"
echo "=============================="
# Create logs directory
mkdir -p logs
echo "✓ Created logs directory"
# Check if email is ... |
0e682eada8d72ac8497e206bb4f76264a2293075d45c891e31335b32898f2aec | Shell | 3,267 | 55 | #!/bin/bash
#BSUB -J MCVD_S
#BSUB -o ./MCVD_S_%J.out
#BSUB -e ./MCVD_S_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/s... |
7b4ff73285f9fa4f4d5a2f16b9681e1c5b29aed9c2fffecba30a8b83017e8e29 | Shell | 3,273 | 55 | #!/bin/bash
#BSUB -J MINFA
#BSUB -o ./MINFA_%J.out
#BSUB -e ./MINFA_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/stud... |
f83475ce5533a8d07a6ae69ae28a5108f20a9db3d47eb5be4997b8075f96df65 | Shell | 3,273 | 55 | #!/bin/bash
#BSUB -J MMICR
#BSUB -o ./MMICR_%J.out
#BSUB -e ./MMICR_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/stud... |
7c3446935688d9d1207889fab6b68fdf821a9780338ed1c89a69746ca36af4df | Shell | 3,274 | 93 | #!/bin/bash
#SBATCH --job-name=soSEQKIT
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=32G
#SBATCH --error=joblog_error_cleanHiFi_%A_%a.txt
#SBATCH --output=joblog_output_cleanHiFi_%A_%a.txt
#SBATCH --array=0-10
#### source library
path_script="/gpfs/scic... |
28928acafa18fd8698b52f95c237a564ec7d20e47b5c4fb5d84a33f26ee6c127 | Shell | 3,280 | 90 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
# study-specific inputs
sm=0 # check templates to ensure no additional smoothing is being applied
sub=$1
ses=`ze... |
81073e2db9429013d3ef16ae1f47a7717f86b1f24174b4076616bf25a3afa161 | Shell | 3,281 | 98 | #!/bin/sh
# This is set as the minimum number of arguments for the script to run
ndefargs=2
# Parameters go here, where optionally, you can specify a default value
max_iter=100
bc_order=4
# Check number of args
image=$1
mask=$2
# Check mandatory args
if [ ! -f $image ]; then
echo "The image '$image' to be segme... |
edd1d0243f1bad97dee13b6b899b19f78422571fde9c8440da4a0a1c779d2f54 | Shell | 3,281 | 68 | #!/bin/bash
#SBATCH -c 4 # 4 cores (calc is ~single-threaded, need RAM)
#SBATCH -t 2-00:00 # 2 days (generous margin over ~28h expected per shard)
#SBATCH -p medium # Medium partition (>12h, up to 5 days)
#SBATCH --mem=64G ... |
10cc1f13da4e1597229ceb8d6dd4897c3ae16dacbb7c94b78822182595236215 | Shell | 3,285 | 79 | #! /bin/sh
# This script is part of a process to shrink packages
# by removing redundant files not used in the preprocessing pipeline.
# In summary, the shrinking process involves:
# 1. running fMRI preprocessing unit tests and using strace to identify files accessed during execution.
# 2. we can moved some of the ide... |
6a8d4fc25c31db38a048adb211f4252c4684deff405f7d5367429c35e5850ff6 | Shell | 3,287 | 55 | #!/bin/bash
#BSUB -J MWMR
#BSUB -o ./MWMR_%J.out
#BSUB -e ./MWMR_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/studies... |
a51c555b1e7d98c7566d2dc561016bdd592655852f215aab45a5a8703882cf28 | Shell | 3,287 | 55 | #!/bin/bash
#BSUB -J MCVD_ART_ANY
#BSUB -o ./MCVD_ART_ANY_%J.out
#BSUB -e ./MCVD_ART_ANY_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.0... |
e66d068daf3ac6632e52659d1206dfef834790224bfae3a8b34ca12c539b393c | Shell | 3,290 | 156 | #!/bin/bash
# ./run.sh gemm
# ./run.sh lazy_gemm
# Examples of environment variables to be set:
# PREFIX="haswell-fma-"
# CXX_FLAGS="-mfma"
# Options:
# -up : enforce the recomputation of existing data, and keep best results as a merging strategy
# -s : recompute selected changesets only and keep bests
ben... |
09e8f3b9e4ef52a2a3146ac8b79d56572349be4e5eea0313236a0b237546cc80 | Shell | 3,293 | 55 | #!/bin/bash
#BSUB -J MREAG
#BSUB -o ./MREAG_%J.out
#BSUB -e ./MREAG_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res='/hihg/stud... |
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