sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
80a45adbe1df1988f10c43794c972eeab95f52cf4e3e90b8fa7eca97d90e06a1 | Shell | 3,293 | 55 | #!/bin/bash
#BSUB -J MBRAA
#BSUB -o ./MBRAA_%J.out
#BSUB -e ./MBRAA_%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... |
d04fabfe7642272d297f4c83b3cf0d5792fc3512b7137bce57b2d3cc3f04cf3d | Shell | 3,293 | 55 | #!/bin/bash
#BSUB -J MADNC
#BSUB -o ./MADNC_%J.out
#BSUB -e ./MADNC_%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... |
0a77d7997d2aba4529ad01a03a19a022e22e13f1f6643f2bf8c5d4f119ee5563 | Shell | 3,299 | 55 | #!/bin/bash
#BSUB -J MTDP43
#BSUB -o ./MTDP43_%J.out
#BSUB -e ./MTDP43_%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... |
1314e27c515ce46986156ce4aae5b3e46c6aa1f13096778665d4a89652b74fd6 | Shell | 3,299 | 55 | #!/bin/bash
#BSUB -J MTDP_3
#BSUB -o ./MTDP_3_%J.out
#BSUB -e ./MTDP_3_%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... |
b40f049c090e6feb8a6ef9e28355c6685f57f50ae7fa1384bd127c1629b62359 | Shell | 3,299 | 55 | #!/bin/bash
#BSUB -J MAMY_A
#BSUB -o ./MAMY_A_%J.out
#BSUB -e ./MAMY_A_%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... |
c1a3150a540a04e36ce40fa22fb6d484ed2120d52de200e597a795851b5d236c | Shell | 3,303 | 83 | #!/bin/sh
#####
# This script calls the matlab function to run KRR. User needs to provide the following variables.
# 1. feature_path: path to feature mat file (without .mat extension)
# 2. outdir: output directory
# 3. sites: number of sites used for the test fold
# 4. innerFolds: number of inner fol... |
66e452aefe3a180f1fbc3831a2da9df20c6763b4d3479066064ed2d59e1cb5d4 | Shell | 3,309 | 55 | #!/bin/bash
#BSUB -J MHS_S
#BSUB -o ./MHS_S_%J.out
#BSUB -e ./MHS_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/stud... |
da82eae59899e7aca18d59b284a76f4f4c66150306c8ebc7384667b1b7634f36 | Shell | 3,310 | 137 | #!/opt/homebrew/bin/bash
#
# Function to display script usage
usage() {
echo "Usage: $0 [OPTIONS]"
echo "Options:"
echo " -h, --help Display this help message"
echo " -i, --in File path to input file"
echo " -g, --index File path to index file"
echo " -o, --out File path to output"
}
has_argument(... |
151432d997c4f63d3d4f17e436094b6c371fb1e3189c8708bb7a664c657e0885 | Shell | 3,311 | 55 | #!/bin/bash
#BSUB -J MCVD_ART
#BSUB -o ./MCVD_ART_%J.out
#BSUB -e ./MCVD_ART_%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='/... |
160595b066d627009a06fdd20d2b959f9fdb9949f715a345fe1b20c086397b5b | Shell | 3,311 | 55 | #!/bin/bash
#BSUB -J MCVD_CAA
#BSUB -o ./MCVD_CAA_%J.out
#BSUB -e ./MCVD_CAA_%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='/... |
995e5af0c2511ccde6d2213c5b53e19ad3c6b1ed655a3986eaab76e7318ab6eb | Shell | 3,311 | 55 | #!/bin/bash
#BSUB -J MB_SCORE
#BSUB -o ./MB_SCORE_%J.out
#BSUB -e ./MB_SCORE_%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='/... |
e600590d6ae6cdc182ec1206643fb83e30611d2acf47c17080386ff277eaedd9 | Shell | 3,311 | 55 | #!/bin/bash
#BSUB -J MCVD_ATH
#BSUB -o ./MCVD_ATH_%J.out
#BSUB -e ./MCVD_ATH_%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='/... |
2bfb14b84251484aaa0f0c814707e8be1d0c15acb141b425a21a1da84185d9f5 | Shell | 3,315 | 55 | #!/bin/bash
#BSUB -J MCVD_ATH_ANY
#BSUB -o ./MCVD_ATH_ANY_%J.out
#BSUB -e ./MCVD_ATH_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... |
e64af0045b2fe5d43f9d7f39b51e825d85e43907e52480ebf6bfca435c7a1718 | Shell | 3,316 | 54 | #!/bin/bash
#BSUB -J MAMY_THAL
#BSUB -o ./MAMY_THAL_%J.out
#BSUB -e ./MAMY_THAL_%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... |
a41e282a806442d24efdf822a77df303370f40cf7f473d9d8dc6a837bf6f052c | Shell | 3,317 | 104 | #!/usr/bin/env bash
# Fast LSS completion counter (glob-based)
# Counts trial files like:
# sub-101/LSS_task-mid_sub-101_ses-01_run-1_acq-single_space-T1w_confounds-tedana_sm-0/zstat_trial-01.nii.gz
set -euo pipefail
shopt -s nullglob
# --- anchor & roots (no cd) ---
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}"... |
acb629ca5728a5196e6f4242bb9da87bdaeb3329a8fd67f032e4e1c4e42740dc | Shell | 3,317 | 55 | #!/bin/bash
#BSUB -J MLEWY_grp
#BSUB -o ./MLEWY_grp_%J.out
#BSUB -e ./MLEWY_grp_%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... |
daf89537c963eed3a1ade2a0d76b228c541a7ec955628ec9ebfe44f3f51616ae | Shell | 3,317 | 71 | #!/bin/bash
if ! [[ "18.04 20.04 22.04 24.04" == *"$(grep VERSION_ID /etc/os-release | cut -d '"' -f 2)"* ]];
then
echo "Ubuntu $(grep VERSION_ID /etc/os-release | cut -d '"' -f 2) is not currently supported.";
exit 1;
fi
# Set non-interactive mode to avoid prompts in CI. `sudo` resets the
# environment, so t... |
eaea4180c1be19062d553ddb286890ae55a13b0ff4371be6a38cb0b6d92d4473 | Shell | 3,321 | 79 | #!/bin/bash
#SBATCH --partition=bcc # Partition (job queue)
#SBATCH --job-name=nodeRstudio # Assign an short name to your job
#SBATCH --nodes=1 # Number of nodes you require
#SBATCH --ntasks=1 # Total # of tasks across all nodes
#SBATCH --cpus-per-task=16 ... |
46a97f6e3a44cb50bccff035bebee8efb2cb9db697ea0b38555900e39a989a2d | Shell | 3,323 | 55 | #!/bin/bash
#BSUB -J MLEWY_full
#BSUB -o ./MLEWY_full_%J.out
#BSUB -e ./MLEWY_full_%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
#
... |
c8ec3adb59ae5fc8266bbf7ed2a8e12bbf313b819757e969e297f83b459c1db6 | Shell | 3,323 | 55 | #!/bin/bash
#BSUB -J MAMY_CERAD
#BSUB -o ./MAMY_CERAD_%J.out
#BSUB -e ./MAMY_CERAD_%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
#
... |
983651fbd2bbf00176114bd8b90ef8c2ee84698f312751e45232b1f2763baa29 | Shell | 3,329 | 55 | #!/bin/bash
#BSUB -J MWBVD
#BSUB -o ./MWBVD_%J.out
#BSUB -e ./MWBVD_%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... |
e7f90189245785c8b0f85e84330588790512f39c3ac3fae86b7527d52643ffd0 | Shell | 3,342 | 12 | # human wilcox
nohup /home/zoo/ball6395/software/miniconda3/envs/sc/bin/Rscript /mnt/data01/yuanzhen/01.Vertebrate_cell_evo/04.ohno_para_significance/0bin/Ohnologs_stats.v2.R -I /mnt/data01/yuanzhen/01.Vertebrate_cell_evo/04.ohno_para_significance/0bin/Hsap_background_genes.txt -P /mnt/data01/yuanzhen/01.Vertebrate_cel... |
2a5b256e49d0ae63bebffb3024fb66009bf104d9d59599feb0b4e58beaa5a5ee | Shell | 3,350 | 74 | #!/bin/bash
set -e
############ Convert data ############
python convert_dataset_to_nnunet.py \
/mnt/nor/wasserthalj_data/TotalSegmentator/zenodo_upload/Totalsegmentator_dataset \
/mnt/nor/nnunet/raw_v2/Dataset101_TotalSegmentator_public_part1 \
class_map_part_organs
python convert_dataset_to_nnunet.py \
/mnt/nor/wa... |
cb42f51cb3fc560f406e8c42123d2b379ad495f430d00e5e54594f6228644038 | Shell | 3,351 | 55 | #!/bin/bash
#BSUB -J MCVD_CAA_ANY
#BSUB -o ./MCVD_CAA_ANY_%J.out
#BSUB -e ./MCVD_CAA_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... |
75534657ba911a3c9092b9de60244e1080273c729d171bf1fcc223227894e693 | Shell | 3,354 | 45 | mkdir inputs
# Make sure these manual steps have been done:
# Download "BrowseTF TcoF-DB.xlsx" from https://tools.sschmeier.com/tcof/browse/?type=tcof&species=mouse&class=all# (a button at https://tools.sschmeier.com/tcof/home/)
# Open the file in Excel and save tab-separated as "inputs/TcoF-Db.tsv"
#
# You need to... |
5bcad2bc976e17ad98c14498c945b8acd1223ebe0cc9e30a48a9ae403fc656e6 | Shell | 3,360 | 113 | #!/bin/bash
#
# A script to generate the GATK tool WDLs for a specified GATK release, and publish them
# to the GATK tool WDL github repository broadinstitute/gatk-tool-wdls.
#
# Must be run from the root of a GATK clone.
#
# Usage: bash scripts/publish_gatk_tool_wdls.sh <gatk_version_tag>
#
# Eg., bash scripts/publi... |
1b58763f144f1a79b3c2d358e5ab20a03198ea8bae1ff1c045b79650630a45ca | Shell | 3,361 | 55 | #!/bin/bash
#BSUB -J MAMY_ANY
#BSUB -o ./MAMY_ANY_%J.out
#BSUB -e ./MAMY_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/4.1.1.036
#
res='/... |
d86191fb83a4fe0d8fda0d966598bff494537c41a5b2601d7b96202ba6e39070 | Shell | 3,366 | 108 | #!/bin/bash
PORT=8001
COMMANDS=()
DEFAULT_COMMANDS=("convert_nbs" "convert_src_nbs" "serve_docs")
RUN_DEFAULTS=true
errors=()
handle_error() {
local error_msg="$1"
echo -e "\n❌ Error: $error_msg"
errors+=("$error_msg")
}
show_usage() {
echo "Usage: $0 [commands] [options]"
echo "Commands:"
ec... |
d06179a5e0d4a2a8267064a17b787864b5c648adb99a1c72c725847df3577d96 | Shell | 3,370 | 74 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# NOTE: run this script from habitat-lab/ directory
# TO PLOT RESULTS SEE RUN `python scripts/hab2_bench/plot_bench.py`
mkdir -p ... |
23ade8aa0b1f70a86f68343a49b6a2e057e5d99f8dc234b13bcbb1623113a835 | Shell | 3,372 | 93 | #!/usr/bin/env bash
set -euo pipefail
# This script lives in .../masks
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
fmriprepdir="${maindir}/derivatives/fmriprep"
maskdir="${scriptdir}"
# Pick the study MNI grid (3-D boldref). Pass as $1 or auto-detect... |
1677125e4b3f578cba17f95b32fb8d3ae419781a9fd52d42c2fdaee844e75cd5 | Shell | 3,378 | 93 | #!/bin/bash
# ---------------
# Instructions
# ---------------
# 1. Align orientation and match to MNI152 space with FSL and Freesurfer
# 2. Pre-require:
# 1. WMH series（nii.gz）
# 2. WMH mask series（nii.gz）
# 3. Fundation brain MRI in MNI space: T2_FLAIR_brain_to_MNI.nii.gz
# 4. Fundation brain MRI to MNI spac... |
a6cf26ee9d3251b1345f0601d3abe439a705488df399de8a3f35bd539d5b430f | Shell | 3,386 | 55 | #!/bin/bash
#BSUB -J MLEWY_ANY
#BSUB -o ./MLEWY_ANY_%J.out
#BSUB -e ./MLEWY_ANY_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
res... |
5928b1768cf4f4f85d188617bb307589696c70ab0c2766a49dab569c27ed09fe | Shell | 3,387 | 66 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
52ca358a504a198fe335018e8c15abe3c8c6f08530845e2520b34cb1eabbef14 | Shell | 3,390 | 88 | #!/bin/sh
# This function replicates the variance component model results in the GSP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(p... |
4ab7b00b1c1c14c5922dbd69de4b748b75b974d6e9cba5bbb240031e22272744 | Shell | 3,400 | 72 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
6f38d236b8924ba8871b05de65643a4d632c4841cb268d22e14f09a08035ebda | Shell | 3,418 | 86 | #!/bin/bash
#SBATCH --partition=bcc # Partition (job queue)
#SBATCH --job-name=nodeRstudio # Assign an short name to your job
#SBATCH --nodes=1 # Number of nodes you require
#SBATCH --ntasks=1 # Total # of tasks across all nodes
#SBATCH --cpus-per-task=16 ... |
abcbef0ef96768649359403fda6ac40dbed849e91248089b7b4b3147bbe1a08b | Shell | 3,428 | 85 | #!/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: $0 -i <input_dir> -f <feature_file>... |
26cb776acf1d434ac66d1bafd7bdeacd561e9976f7c6ddff3fed37bced365a55 | Shell | 3,434 | 80 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Lice... |
7aff26779b36e80182752256840fe8fc5f200608dd2e38698e8e28632c71f06b | Shell | 3,436 | 113 | #!/bin/bash
set -e
# for nightly/weekly builds we test multiple compilers and build options
if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
if [ "$TRAVIS_OS_NAME" == "linux" ]; then
packages=(
"neuron@develop +python +mpi +shared %gcc ^python@2.7"
"neuron@develop +python +mp... |
9e40938a7a4e573a6807a11e98657ccb3139fcade6556df915462b5f675cf039 | Shell | 3,443 | 73 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
bc9ca51fe11d1d49a9b19fe0c087252573ff0082ac5323cc8121b5d9580b252c | Shell | 3,443 | 74 | #!/bin/bash
#SBATCH -c 4 # Request cores (influence calc is single-threaded, but need RAM)
#SBATCH -t 1-00:00 # Runtime: 24 hours (155K neurons * 0.4s + factorization)
#SBATCH -p medium # Medium partition for >12h jobs
#SBATCH --mem=64G ... |
d0ec07badcf1cbcb3f2213e283437ac97a3474d2f1bdd3ae6bc6cded51468cce | Shell | 3,449 | 73 | #!/usr/bin/env bash
##########################################################################################################################
## SCRIPT TO RUN GENERAL RESTING-STATE PREPROCESSING
##
## Written by the R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn.
##
#########################################... |
25396f9598eaeddb4feb75db5782d0f829be55f8c5e86f56e7ff444bc69a8f25 | Shell | 3,473 | 92 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SURFACE-BASED DIFFUSION IMAGE PREPROCESSING (FREESURFER)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## Written by R-fMRI master: Xi-Nian Z... |
64e496f45cf6ac43ca457c2ba47d8d1a48d99dd0fd6bad0ca6b17254c9b39342 | Shell | 3,473 | 83 | #!/bin/bash
#SBATCH -c 16
#SBATCH -t 3-00:00 # generous — we do not yet know WB+ensemble wall-time
#SBATCH -p medium
#SBATCH --mem=160G # extra headroom for ensemble re-rank buffers
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_probe_%j.out
#SBATCH -e /home/ab714/b... |
3ad40191123f404af2df9c054af7e83b3c293d1535b68173a0e195379a686770 | Shell | 3,480 | 149 | #/bin/sh
# from svn update to alpha on ftp site for linux, mswin, and mac osx
# usage:sh mkalpha.sh
# sh mkalpha.sh force
# with force, will continue even if an ftp distribution file matches the
# svn updated version number
# must execute in the top level source directory
NSRC=`pwd`
export NSRC
cd $NSRC
lastalpha="`s... |
020afa91763a558e9a308032e6c7ff57e82f395f302e4203f4a3d80f79f5a542 | Shell | 3,481 | 87 | #!/bin/bash
# Copyright 2017 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 di... |
09bf14f5b092fdd387f9e519869746ab5f4e8254dfb24019a8732e970f7ebf3f | Shell | 3,511 | 83 | #!/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
# "Lice... |
fd52daac21c509b1ebfbc8e2322d2cc903b9f202b159283218476e0c3b774873 | Shell | 3,511 | 110 | #!/bin/bash
# Define paths
AF_trk="/Users/neuro-240/Documents/BIL_and_GIN_Visit/AF_trk_files/"
CC_trk="/Users/neuro-240/Documents/BIL_and_GIN_Visit/CC_trk_files/"
# Function to extract subject IDs from file names
extract_subject_ids() {
local tract_dir="$1"
subjects=()
local file_list=("$tract_dir"*)
... |
6abfacfdd742df13ad19b90efbd6918ec1635f2a8071537b6538988eec7b6e84 | Shell | 3,519 | 78 | #!/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
#... |
9a2083bb8e7ff9cdc81f8b4903cbe37c1c5adc698e5ac4cac6ff86ab1f411762 | Shell | 3,519 | 74 |
GENOTYPE_DIR=$1
SAVE_DIR=$2
HASEDIR=$3
STUDYNAME=$4
START=$5
FINISH=$6
CHUNK_NUMBER=$7
get_vcf_chunk(){
echo "***"
echo $@
echo "***"
iter=0
file_ind=0
for i in $( cat ${SAVE_DIR}/files_order.txt | awk '{print }' ); do
echo $i
file=${i}
file_ind=$(($file_ind + 1))
... |
462cadd3c25de19fa3a61d55a2a186648a019180407775e8933a757cadc9f242 | Shell | 3,520 | 114 | #!/bin/bash
# Time and start
start=`date +%s`
# Define source and destination paths
A='/n/data1/hms/neurobio/wilson/banc'
B='/n/files/Neurobio/wilsonlab/banc'
# Check if directories exist
if [ ! -d "$A" ] || [ ! -d "$B" ]; then
echo "Error: One or both of the specified directories do not exist."
echo "A: $A"... |
82af7b2b6d2c0d56a41e86fdc0dfba4ce085b00dcfbf09674698a1b99f09530a | Shell | 3,530 | 91 | ##################################
# pull docker image into singularity
singularity pull docker://cibersortx/fractions
singularity pull docker://cibersortx/hires
singularity pull docker://cibersortx/gep
GSE="GSE160189_186538_Integration"
mixture="CIBERSORTx_adjusted_merged_matrix_1_TPM.txt"
GOIs=(
"H_gene_set_ERK"
... |
c0f1cc3f37d842df4b6fcacb0537e65f66543a2f0d5767bf779e2678fba521d8 | Shell | 3,543 | 89 | #!/bin/bash
# Function to sync folders for multiple subjects from AWS S3 to a local directory.
#
# Written by: Aleksij Kraljic and Jure Demsar, 2025
get_args() {
arg="$1"
shift 1
for fn in "$@" ; do
if [ `echo $fn | grep -- "^${arg}=" | wc -w` -gt 0 ]; then
echo $fn | sed "s/^${arg}=//... |
328782ca3c757191d740f36d086b7a87864a7144ff790e30dce9ed932d9ea5ae | Shell | 3,559 | 100 | ########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=$3
anat_dir=${CCS_DI... |
6c6a627a523e8cb521aed3177d895614ef077ab8937749a2f6ff7030ef8c30a8 | Shell | 3,559 | 100 | ########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=$3
anat_dir=${CCS_DI... |
1b4fd11f4ae7a32245b4cfa54e523a8a68fd10d23f77d1ca8bdd4125f09fa8d0 | Shell | 3,561 | 83 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
mkdir -p $pd/data/validations/ATAC_seq_FASTQ
cd $pd/data/validations/ATAC_seq_FASTQ
# download files
## experiment 1, human iPSC
wget https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR120/054/ERR12081954/ERR12081954_1.fastq.gz
mv ERR12081... |
d14f5d98e108fe1d3ddf7c17b80efc165fd76b8ac1d82a987f90cb2b466c1adb | Shell | 3,563 | 76 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=GATK
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to project dir
#SBATC... |
529d04d4be74d45b57a2056422468166f36d3cc91c6035422b06dd71f62a563a | Shell | 3,564 | 98 |
# /media/storage/HTS/VirusMeta/SAM_BAM/beta_actine_test/circos_pipeline.sh /media/storage/HTS/Projects/2013_H3_19RNA_SCC /media/storage/HTS/Projects/2013_H3_19RNA_SCC/diginorm/read_1.fastq /media/storage/HTS/Projects/2013_H3_19RNA_SCC/diginorm/read_2.fastq
##########################
export project_work_dir=$1
export p... |
059af0d33a7d7056c9e7b62ceaf38a734acf99917900717940dbbc971ae764fd | Shell | 3,565 | 98 |
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/circos_FPKM/circos_pipeline_v2.sh /media/storage/HTS/Projects/2013_H7_RNA-2libr /media/storage/HTS/Projects/2013_H7_RNA-2libr/diginorm/read_1.fastq /media/storage/HTS/Projects/2013_H7_RNA-2libr/diginorm/read_2.fastq
##########################
export project_work_dir=$1
export ... |
afc6ddc3976abec8c9fa3a0316b456199f13699645d90eadfcd00fa4248a18c5 | Shell | 3,571 | 98 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( 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... |
68de5b8d201b71876a3604b504bcae5983ba7b162bf81cccb17da541497c32b2 | Shell | 3,584 | 63 | #!/bin/bash
export project_work_dir=$1
export work_dir=$2
export fasta_sequence_ids=$3
export work_fasta=$(basename $4)
#sort index file according to id
export file1=$project_work_dir/Data/Intensities/BaseCalls/forward_index_name_sorted.txt
export file2=$project_work_dir/Data/Intensities/BaseCalls/reverse_index_name_... |
b10c81af6c3ba64bff5f9b267c00289fc616388e05a5a2ac375a54b0f1d103f1 | Shell | 3,593 | 79 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
d8b3e08ba74f165cf76b54ce683821e1d556b2bb5cd6c8373c629187d5415ee3 | Shell | 3,609 | 76 | # Author: Javier Gonzalez-Castillo
# Date: January 20th, 2023
#
# Description:
# This script takes two input parameters: subject and run name
#
set -e
echo "++ Load FSL, AFNI and ANTs modules"
module load afni
module load ANTs/2.2.0
# Unset DISPLAY variable
# ----------------------
echo "++ Unset DISPLAY variable"
uns... |
3c6df6181ec7fffffe9e0671c0c84a4e23ce146ca10891cd58c7e7b3b85688bf | Shell | 3,616 | 91 | #!/bin/bash
#PBS -l walltime=12:00:00
#PBS -N tedana
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=28
cd $PBS_O_WORKDIR
# ensure paths are correct irrespective from where user runs the script
projectname=night-owls
maindir=/gpfs/scratch/tug87422/smithlab-shared/$projectname
scriptdir=$m... |
df0e4ce91c84cbab7535d2325921df75cdf4cf62604b28217ae0ba4ceb84a841 | Shell | 3,618 | 211 | #!/bin/bash
#
#This is a shell program to batch count swc files based on different tracing algorithms
#
tarfile=$1
METHOD=$2
#APP1
if [ $METHOD == "1" ]; then
tar ztvf $tarfile| grep _app1.swc|wc -l
fi;
#APP2
if [ $METHOD == "2" ]; then
tar ztvf $tarfile| grep _app2.swc|wc -l
fi;
#MOST
if [ $METH... |
2f5f6ea847e266abf98e67bc27f4dab16061ca1a229653826e890b7b6017c7d1 | Shell | 3,619 | 119 | #!/bin/bash
####################################################################################################################################
# run_3_rigidRegistration.sh
#
# Performs rigid registration of preprocessed brain images to a resolution-matched MNI152 template
# using ANTs. The estimated transform is also... |
c1791e097b1dbe159a12d8975b2fec8ab7796ea55bb2c54bc6e2bbb0a78e12cc | Shell | 3,623 | 116 | #!/bin/sh
#
# If compiling at the BIC in /data/aces/aces1/, do "newgrp aces"
# before this script so that files are accounted for in the aces
# group quota.
#
umask 077
INSTALL_DIR=$PWD/`uname`-`uname -m`
INSTALL_RELATIVE_DIR=`uname`-`uname -m`
mkdir -p ${PWD}/bin
ANIMAL=no
MRISIM=no
MAGICK=no
GIT=yes
CVS=no
# Note:... |
02315822cb6c8d76c405848c63b9377b5c49842a72e4cad74e6430718c02681b | Shell | 3,624 | 112 | #!/bin/bash
usage()
{
base=$(basename "$0")
echo "usage: $base volume subject age [options]
This script runs the dHCP surface pipeline.
Arguments:
volume T2 volume to segment
subject Subject ID
Options:
-d / -data-dir <directory> The directory used to run the... |
fbffc2440ed1ddc0b87b78812d63d00d13dc75e0045924bf5a7d948d498f9aed | Shell | 3,626 | 103 | #!/bin/bash
# change to the dir of the script
cd $( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# change to the dir to the project
cd ../..
title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
train_config=AI/train.yaml
output_dir=${OUT... |
4e617e2189df309dca6404c58548e3656258662ffa81daca6a7aa68975f9a236 | Shell | 3,627 | 120 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# Reorient an image according to macaque standard
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<EOF
rsn_reorient.sh: Reorient an image accord... |
1ad7a55eba83904013390577d35c26e94b91163d249500d470cf82076c9a527a | Shell | 3,628 | 85 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psy... |
01308568cd1132b6b949f48f5d4546b241d4f0194249581ee5534d9cd5325b63 | Shell | 3,655 | 104 | #!/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
#... |
94af3fa038c6e7853a2cc6058f5f9368415043bf91833d87e81d11b5eae41ae4 | Shell | 3,659 | 62 | #!/bin/sh
#GW edits
#Sept2012
#
#Aug2021, TOL
# add checks for commands; quit if not found
echo "Looking for wb_command; If we exit here it means we couldn't find it."
command -v wb_command || exit 1
echo "Looking for msm; If we exit here it means we couldn't find it."
command -v msm || exit 1
#Script and Program L... |
3b7a03cbd4715678bc3160110ce5dbd6dbcda061bb394142c23567ae56435a44 | Shell | 3,660 | 98 | #!/usr/bin/env bash
set -euo pipefail
# --- standard header: paths relative to the code directory ---
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
fmriprepdir="${maindir}/derivatives/fmriprep"
# --- edit these if you want to target another subject/ses... |
f9a6c764e2bed7a1ff786a4b11350a5bc0c8d04723a5e27a678e8be732794d14 | Shell | 3,666 | 111 | #!/usr/bin/env bash
set -e
# run this script from the MsaServer folder
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
cd "${SCRIPT_DIR}"
# enable this if you want to start a GPU MSA server
#export GPU=1
# choose which pdb rsync server to use
#PDB_SERVER=rsync.wwpdb.org::ftp ... |
81cf855498e04f346e9d9bdde3c3c8a8d60e27d167471ffd5a8eee86824325a0 | Shell | 3,673 | 73 | #!/bin/sh
export path_htsa_dir=$1
export path_pipeline=$2
export diginorm_work_dir=$3
export PAIR1=$4
export PAIR2=$5
########################################
#DIGINORM
########################################
if [ -d $diginorm_work_dir ];
then
rm -r $diginorm_work_dir
fi
mkdir $diginorm_work_dir
cd $diginorm_wor... |
fb075d0b9e9fdb62a69c9d2cc740df526bc4949e5f61062ffe1f36f267ff4649 | Shell | 3,688 | 99 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( 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=$1
ses=`ze... |
a344084e601be20df6f7540903b87ca5509ea89d7f574a5c8ec7ec20cc8d50b2 | Shell | 3,696 | 146 | #!/usr/bin/env bash
#
# Author: Stefan Buck
# License: MIT
# https://gist.github.com/stefanbuck/ce788fee19ab6eb0b4447a85fc99f447
#
#
# This script accepts the following parameters:
#
# * owner
# * repo
# * tag
# * filename
# * github_api_token
#
# Script to upload a release asset using the GitHub API v3.
#
# Example:
#... |
686e5b04de02ed07dc178d1843c72d6bf7ed1de10a288b1f70546954699ebc75 | Shell | 3,699 | 152 | #!/bin/bash
usage()
{
BASE=$(basename -- "$0")
echo "Trim a GangSTR reference file
Usage:
$BASE {TRF_IN} {OUT_PATH}
{TRF_IN} path to results from TRF
{OUT_PATH} path to output file.
"
exit 1
}
die()
{
echo "[$BASE] error: $@" >&2
exit 1
}
if [ $# -eq 0 ]
then
usage
fi
if [ -z "$... |
ca4b56e695104adde02bd72bc2c9845e7be126374152fccbf1f8ebe134cbcf18 | Shell | 3,725 | 79 | #!/bin/bash
# This script extracts the consensus sequences for each gene and individual from the BAM files and merges them to create a consensus for each species obtained from genomic sequences
# To reduce space, the consensus sequences are only shown in the alignment files (Data 08)
# mafft v7.526
# seqtk version 1.4-... |
0f57f1e0e0d6d99b184f42f94228d4e9848877cae54001feac674baa779a4c33 | Shell | 3,733 | 100 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/HBB_test/circos_pipeline.sh /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3 /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read1.fastq.gz /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read2.fastq.gz
##########################
export proje... |
a2c8b4ca55d34d7b012d21b5b3cc276b3abadab1b9b9b5bc4d49f03723269f9a | Shell | 3,748 | 69 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF STRUCTURAL IMAGE REGISTRATION
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## for more information see lfcd.psych.ac.cn... |
bad40bb048a0f3894ba4582aeba83ad9a3676ec9c6cfb809cc57937db7d98fc3 | Shell | 3,750 | 157 | #!/opt/homebrew/bin/bash -i
# Find working directiory
# Function to display script usage
usage() {
echo "Usage: $0 [OPTIONS]"
echo "Options:"
echo " -h, --help Display this help message"
echo " -i, --reads File path to filtered reads "
echo " -n, --index File path to gene index"
echo " -g, --growth File... |
3222cc0565600edb86388205672634da7f3e7c6d0f37ba02a8173c2a6f53afd4 | Shell | 3,755 | 169 | #! /bin/bash
fix_key="fix"
if [[ "$1" = "help" || "$1" = "--help" || "$1" = "-h" ]]
then
echo "'$0 $fix_key' to fix (in place replace). Otherwise lint (return non-zero if fails)."
exit 0
fi
if [[ "$1" = "$fix_key" ]]
then
fix_flag="1"
fi
version=$(cat VERSION)
# latest_tag=$(curl 'https://api.github.co... |
fa8527f434ddd2c643e5b3491c4728b1a7755a8f151e96cc74ba406308a279d0 | Shell | 3,755 | 90 | #!/bin/bash
#module load python/3.8.x-anaconda
#conda activate /home2/gkonop/my_conda_env
#conda env remove --prefix /project/Neuroinformatics_Core/Konopka_lab/shared/For_Gozde/03_INTEGRATED_ALL/SPN/my_conda_env
#!/bin/bash
# Define input and output directories
input_file="/endosome/work/Neuroinformatics_Core/gkonop/0... |
8511f112a5c23e6538280d5fcd7d736f5ff328b422ad6910f5d1b7b78628a7d1 | Shell | 3,773 | 148 | #!/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
# "Lic... |
df5fa582f08d9b221332b54a2e6d5d9700a7a962e46c57edf350b3857da483aa | Shell | 3,786 | 127 | #!/bin/bash
REF=$1
TRF_IN=$2
VER=$3
OUT_DIR=$4
BASE=$(basename -- "$0")
usage()
{
BASE=$(basename -- "$0")
echo "Trim a GangSTR reference file
Usage:
$BASE {REF} {TRF_IN} {TRF} {NUMPROC}
{REF} is a for the reference (hg38, hg18, mm10, etc.)
{TRF_IN} path to results from TRF
{VER} version numbe... |
89047ad207369bd6f8de35bd0c32469db18df3e4153c6c4c8debd26048b0d14b | Shell | 3,793 | 120 | ######################################################################
## This script is used to compile libraries and to build Python
## distribution for openmm-velocityVerlet.
##
## Usage:
## ./build.sh [OPENMM_DIR]
## - [OPENMM_DIR] is optional. If not specified, defaults to:
## /usr/local/openmm
##########... |
e5b31c1fbd52a90d89260fe07632b65b1f43acba21d04af4ff16ee8e90a2c87a | Shell | 3,793 | 101 | #!/usr/bin/env bash
set -euo pipefail
ok() { echo "OK"; }
fail(){ echo "NOT OK"; }
sep(){ echo "==== $* ===="; }
sep "Devcontainer sanity checks"
printf "Python: "
if python -c "import sys; print(sys.version.split()[0])" >/dev/null 2>&1; then ok; else fail; fi
printf "R: "
if R -q --vanilla -e "invisible(TRU... |
20322890559eaede287b887034ee1817e51167b2496b42abb6bf76d75dfa8335 | Shell | 3,804 | 73 | #!/bin/sh
########################
#nohup ./indices.sh 2013_H5_RNA-NMSC_v3 nextseq UNBIASED /media/StorageTwo/blc_2013_H5_RNA-NMSC/Data/Intensities/BaseCalls > indices.log
########################
#cwd=$(pwd) #get current home directory
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export ... |
24e243b8f9e5ebe41c9c7229564336dbd67ba8a9867a38095e00a65c958b7a15 | Shell | 3,816 | 103 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=2
#PBS -N overlap
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="bulk-seq"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
exp... |
456cae843620dadbd4fa2771ed81609439d6fbac84cc8acc7078e3c519581607 | Shell | 3,822 | 94 | #!/bin/bash
export path_htsa_dir=$1
export path_pipeline=$2
export project_work_dir=$3
export work_fasta=$4
export PB_dir=$5
export aggregated_work_dir=$6
echo "annotating metagenomic sequences according using paracel blast..."
if [ -d $PB_dir ];
then
rm -r $PB_dir
fi
mkdir $PB_dir
cd $PB_dir
echo "paracel blast... |
ad9519fe14fc16103bf352a2c2707e8e071a4699ec6c3fc7a6e31725e837994d | Shell | 3,854 | 132 | #!/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 symmetric mean absolute
# percentage error of data (image or timeseries) against a reference. The script
# is so simple, it might be helpful as a... |
97e1ec59890ccd518978f18a33b4bd9d7542cad06381999fe33b3d5d96a83248 | Shell | 3,856 | 88 | #!/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... |
bb5b22c6c92cbdbeb9771ba34061bb10d7b71673c74c4baa0a0613a3995b620f | Shell | 3,856 | 121 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE DTI SCAN (INTEGRATE AFNI, FS AND FSL)
##
## R-fMRI master: Xi-Nian Zuo. Dec. 20, 2014.
##
## Last Modified: Dec., 16, 2015.
## Email: zuoxn@psyc... |
260674256dfe6cb783996db8cf40828278fc57688d175d898d10ff0c9462b74f | Shell | 3,857 | 89 | #!/bin/bash -e
## v3.1 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing (not possible for all platforms)
SIF="/nfs/cellgeni/singularity/images/starsolo_2-7-10a-alpha-220818_samtools_1-15-1_seqtk-1-13_bbmap_38-97_RSE... |
151e4bec38ac58373b0fc5528a7d78566a9e2abfecd44898f2140ae15fa626f6 | Shell | 3,868 | 78 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
c8f2ca55f0b89f401c3e7debd1da78d0150aa8fec522ed4dc794643cbb23770a | Shell | 3,896 | 95 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# TO PREPARE FOR THIS SCRIPT TO WORK:
# folder organisation: - main_root/ > where the data folders for one species are with folder raw in it and where the init file is
# - main_root/tem... |
6af32fb9a85781630196c85503d7bab35e0b3d734a1a94e21ce8ca06274d034e | Shell | 3,904 | 136 | #!/usr/bin/env bash
set -e # stop immediately on error
# Requirements for this script
# installed versions of: FSL (version 5.0.6)
# environment: as in SetUpHCPPipeline.sh (or individually: FSLDIR)
# give Lennart Verhagen (lennart.verhagen@psy.ox.ac.uk) a coffee or a pint
#==============================
# ov... |
27134f4cbba82df660dfe64b02c9625968c04d205b79d0f92ef2b7048dd8919e | Shell | 3,920 | 121 | #! /bin/bash -x
#/media/StorageOne/HTS/VirusMeta/assembly_module/sga.sh /media/StorageOne/HTS VirusMeta $project_work_dir/sga $project_work_dir/Data/Intensities/BaseCalls/forward.fastq $project_work_dir/Data/Intensities/BaseCalls/reverse.fastq
export path_htsa_dir=$1
export path_pipeline=$2
export working_dir=$3
expo... |
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