sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
42ae71fe7270a03ebb40fbcdaa61c4d4b4948074153a6cccb5035275b0ea8841 | Shell | 6,032 | 130 | # 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 disclaimer.
#
#... |
a3f286635229bdb033e93b9485b5a38c983515ad77eea6a874adc44d7ab4ddc0 | Shell | 6,040 | 145 | #!/bin/bash
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Master step 4 reliability pipeline.
# Usage: bash CBIG_LBC_run_step4_reliability.sh <step>
# step = 1 : submit per-subject FC compute jobs (4 conditions x all subjects)
# step = 2 : submit co... |
dad6cd89e8939a28cb4c97bb6e3c9dff14a7889c799c066e151ccfdc112be2c5 | Shell | 6,047 | 190 | #!/bin/bash
###### the recommended input for this script is the output of precon_all run on your volumetric template.
source $FREESURFER_HOME/SetUpFreeSurfer.sh
usage() {
cat <<EOF
Usage: $(basename "$0") [--cluster <config_file>] [--out-dir <avg_subject_name>] <template_subject_dir> <group_file> <ico_order>
Buil... |
9733f5ea3815c9e281a7d15a78bc57463b05c18a6c4826dff3ebead8380cd370 | Shell | 6,048 | 190 | #! /bin/bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); ... |
7e941de7e39ab28179f6689eb4a1da64788d5b7304aa5d8790475568aaab2e97 | Shell | 6,083 | 223 | #!/usr/bin/env bash
set -euo pipefail
ROOT="${ROOT:-${HOME}/benchmarks/macs3-release-benchmark}"
REPEATS="${REPEATS:-3}"
TIME_MODE="${TIME_MODE:-auto}"
BASELINE_REF="${BASELINE_REF:-v3.0.4}"
BASELINE_CMD="${BASELINE_CMD:-macs3}"
CURRENT_CMD="${CURRENT_CMD:-macs3}"
SRC_DIR="${ROOT}/src"
BASELINE_TREE="${BASELINE_TREE... |
9cdf58eed98aeb41718485551bdc6141d70428868a5af1260349c49ee6cbc0e5 | Shell | 6,099 | 158 | #!/bin/sh
# This function replicate the kernel ridge regression results in the HCP 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=$(pwd... |
e51b0d3fe56537171d5b0d90e811790cb19db0862e521538b26d04adfc7e7f05 | Shell | 6,113 | 90 | # #Pairplots of hhblits vs AF msas
# convert DockQ_AF_vs_paired.svg -pointsize 100 -gravity NorthWest -annotate +0+0 "B" DockQ_AF_vs_paired.svg
# convert DockQ_AF_vs_paired+AF2.svg -pointsize 100 -gravity NorthWest -annotate +0+0 "C" DockQ_AF_vs_paired+AF2.svg
# montage DockQ_AF_vs_paired.svg DockQ_AF_vs_paired+AF2.svg... |
8ceaaa54322b805e214d071ce861c487b23d4515df869973facaa0b481524d3a | Shell | 6,161 | 220 | #! /bin/sh
# Check if nrfjprog is already installed
command -v nrfjprog >/dev/null
nrfjprog_installed=$?
if ! [ $nrfjprog_installed -eq 1]; then
echo "installing nrf jprog"
wget "https://nsscprodmedia.blob.core.windows.net/prod/software-and-other-downloads/desktop-software/nrf-command-line-tools/sw/versions-1... |
d41f09ea668dacd715c3aef676d7f013e4cb9144964f95aee2eb4e4f618da31d | Shell | 6,162 | 132 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF ANATOMICAL SURFACE PROCESSING
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATION*****!!!!!
##
## Thanks go to Thomas Yeo for sharing his ex... |
7b91610ff126f8e0a76d3df4e75399677ac6fe59f7fc6c2615741d19a2ecb191 | Shell | 6,202 | 208 | #!/bin/sh
#
# This script does a binary search to look for the smallest input that will
# break something.
#
# The folder for us to store our temporary files. There may be many of them.
WORKDIR=tmp/search
# This setting determines where we save the input we generate.
# You should change it to something you have wr... |
6024f9d74cfd06345fec74b532e25ddcd339393e7048cf59bed166dbb166bada | Shell | 6,213 | 174 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
structRootDir="/Vo... |
1c553bfcd8ae68c28248e191a09115f2716bbc5402409af55cd5dd3fe08a2a85 | Shell | 6,216 | 147 | #!/bin/bash
set -euo pipefail
# Copyright 2017 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions an... |
7bf3dfefaa1e92f182a7f337a521507e4c386ed8f9bb7da095c0c8e254fdfdf1 | Shell | 6,297 | 183 | #!/usr/bin/env bash
set -euo pipefail
shopt -s nullglob
# -------- fixed locations (relative to THIS script) --------
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
rootdir="$(dirname "$scriptdir")" # project root (…/night-owls)
FSL_DERIV="${rootdir}/derivatives/fsl"
maskdir="${rootdir... |
89cd3e78bb2b29dadb5c106d27cc4cf548c9d142de96abf0296aa45d6602966d | Shell | 6,315 | 159 | # Based on original script of E. Cámara
export LC_NUMERIC="en_US.UTF-8"
#NUM_CORES=$(nproc)
#export OMP_NUM_THREADS=$NUM_CORES
# Read the subject number from the command line argument
if [ $# -eq 0 ]; then
echo "No subject number provided. Using default subject number: 01"
exit 1
#SUBJ="01"
else
SUBJ... |
d7bf33eee74b9696314bc7e2799cdf3ff6b8eda16cdf5469b2775bf47d01b37e | Shell | 6,315 | 116 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF ANATOMICAL SURFACE PROCESSING
##
## !!!!!*****ALWAYS CHECK YOUR SURFACES*****!!!!!
##
## Thanks go to Thomas Yeo for sharing his excell... |
4ddf115c36e5c39a2db2b2f35ef41068958ae6dbb09feabd83b7e43d74e345b4 | Shell | 6,336 | 133 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/beta_actine_test/circos_pipeline_v2.sh /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3 /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read1.fastq.gz /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read2.fastq.gz
##########################
e... |
fdd1fed624c3cfd31dad651ae682fbfd05737af92ea7ba12d88a53fdaecb9937 | Shell | 6,370 | 166 | #!/bin/bash
#
# extract_hic_trans_pairs.sh
#
# Extracts trans HiC pairs (pair_type=UU) between:
# (a) breakpoint scaffold pairs (defined per assembly)
# (b) control scaffold pairs: each control scaffold paired with the
# uninvolved scaffold of most similar length (from FAI)
#
# All pairs between each scaffold... |
449a84a69bcd9c22d6707826399e1b14b0f46a1f2a7f29e4b8e7af6f31c52f02 | Shell | 6,373 | 237 |
#!/bin/bash
####
################################## START OF EMBEDDED SGE COMMANDS ##########################
#$ -S /bin/bash
#$ -cwd
#$ -N wrapper_dcm2niix
#$ -j y #### merge stdout and stderr
#$ -l short
#$ -l h_vmem=1G
#$ -l tmpfree=2G
############################## END OF DEFAULT EMBEDDED SGE COMMANDS ############... |
d985d4b4d8c863144b1f9855737b3233d04596cbbad41173981929bc53fdf09d | Shell | 6,396 | 198 | #!/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 template script for a flexible instruction-based processing pipeline
# This script can be run over fsl_sub, for example using something like:
# fsl_sub -N runscript -q veryshort.q... |
37da29edf47b8c9c799416f5f699363462adf9c5f705159fab9a064cf5619556 | Shell | 6,440 | 206 | #!/usr/bin/env bash
set -e # stop immediately on error
# ------------------------------ #
# usage
# ------------------------------ #
usage() {
cat <<EOF
robustfov_macaque.sh: cropping the field-of-view for macaque in-vivo structural images
Usage: sh robustfov_macaque.sh <input> [<output>] [options]
Main robu... |
a552c43fba2a3973ffa5073719225b930d52ac5dcb65a627267f17dfbbf716d7 | Shell | 6,449 | 183 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# TODO: perhaps the structural should be specified in the instructFile
# for now, I'm simply taking the latest
# retrieve input argument to find correct instructions
instructDir="$1"
# -----... |
fb3817501115ed4f19b8879381b10fd4146958f49e113f2ca8aadc5f64a3e6b9 | Shell | 6,483 | 196 | #!/bin/bash
# Source in the task setup, this will deal with the command line input
# and cleanup functions, there are several variables that it will give
# access to:
# JA="$1"
# TMP_LOC="$2"
# STEP=$3
# IDX=${4:-$SGE_TASK_ID}
# WORKING_DIR : A location
# Store all the paths to the intermediate files, these will all ... |
78ec316e3ff16917bfb8d99acdacd671873fb860b3abdcf15f7d8cff8fa86361 | Shell | 6,490 | 197 | #!/bin/bash
# Display usage information
usage() {
echo "Usage: $0 -i INPUT_BASE -o OUTPUT_BASE [-g GPU_ID]"
echo " -i INPUT_BASE Base directory containing raw data and metadata.txt"
echo " -o OUTPUT_BASE Base directory where processed data will be saved"
echo " -g GPU_ID GPU ID to use for p... |
0269d85480b734559143fda2bc34511f19b92ddb9a95dbc33e3c94190e4d805a | Shell | 6,538 | 198 | #!/bin/bash
#
# count_hic_trans_background.sh
#
# Performs two streaming passes over a pairtools .pairs.gz file to count:
#
# (a) Trans pairs between all combinations of the top N scaffolds by length
# (negative control distribution for expected inter-chromosomal contacts)
#
# (b) Long-range intra-scaffold pa... |
22c04c03f7ae5c01a68d7354001bb7dd85bb0ad236f6fdf48313de05fdb057dd | Shell | 6,586 | 169 | #!/bin/bash
#PBS -l walltime=12:00:00
#PBS -N L2stats-subj
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
# module load fsl/6.0.2
# source $FSLDIR/etc/fslconf/fsl.sh
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct
shareddir=/gpfs/scratch/tug87... |
c76c4bc69ec5305f065ecd706c1aef1d467792be842306a429cdfbf2486da50a | Shell | 6,597 | 177 | #!/bin/bash
# This script contains functions for different parts of the pipeline
# Function 1: Create single-line fasta in-place
single_line_fa () {
fa_file=$1
sed -i "s/\r//g" "$fa_file"
awk -i inplace '/^>/ {print (NR>1?"\n":"")$0;; next} {printf "%s",$0;} END{print "";}' "$fa_file"
}
# Function 2: Crea... |
4faa976bf7b515acf70fb2cfca444822feff13e554662f63a593e4266f46b28c | Shell | 6,621 | 188 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# robust motion correction
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<EOF
rsn_motionCorr.sh: motion correction to a robust reference image... |
0cee8dc94228f289e628fce9ff1780a6109fad99aa39f8927a698137a5866439 | Shell | 6,622 | 159 | #!/usr/bin/env bash
#
# decode_crossover.sh — find where the parallel gzip decoder starts paying, in
# each of salmon's two mapping modes.
#
# WHY THIS EXISTS
#
# `-p` is one budget shared between inflating the input and mapping it. The
# serial decoder inflates inline on the mapping threads and is therefore
# work-con... |
247f3579baa225f590e464928746bc7a0fbb4c7b10f5c070b605ce93d6ebcca6 | Shell | 6,622 | 159 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# list of matches between HCP structures (left) and Freesurfer labels (right)
# Freesurfer labels: $HCPPIPELINEDIR/global/confib/FreeSurferAllLut.txt
# HCP/Freesurfer labels: $HCPPIPELINEDIR/g... |
5d792af013888d6ad6b0790d8727ba39d66731f06468bbe9f74cf01ffc1a8403 | Shell | 6,657 | 146 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/HPV16_test/circos_pipeline_v2.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 ... |
3a09bbbe34130c3178b04ed5a9b056322f28e5404d27b2b27e7df71c317d971f | Shell | 6,686 | 137 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2014-07-08 #
#compares sequence database with itself using ncbi blast #
###################################################################
#nohup /media/StorageOne/HTS/viral... |
2c56affa11f0e0ada397ad0b28d54327fd1cb2b9181c8da58f8269c71c37d5df | Shell | 6,688 | 274 | #!/bin/bash -e
#/*
#* SVRTK : SVR reconstruction based on MIRTK
#*
#* Copyright 2018-2020 King's College London
#*
#* Licensed under the Apache License, Version 2.0 (the "License");
#* you may not use this file except in compliance with the License.
#* You may obtain a copy of the License at
#*
#* http://www.apach... |
6c96afd9bc1eed3ce6d16826aee997ad0b0b7543a446138e1e7a998c5522c352 | Shell | 6,758 | 206 | #!/bin/bash
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Usage() {
echo " "
echo "Usage: `basename $0` [options] -i <Subject> -h <lh or rh>"
echo ""
echo " Compulsory Arguments "
echo "-s <Subject directory> : Directory containing preprocessed animal for surfac generation "
ec... |
c71b13dc9a83f12201c45bdbb6532ce74e8f5612b821b5355d46386425727776 | Shell | 6,761 | 219 | #!/bin/bash
# Author: Andrew Hamel
# Affiliation: Massachusetts Eye and Ear, Harvard Medical School
# Date: June 2022
#
# This is a shell script
# with a sample run of GeneEnrich
# for all available gene sets provided
# List of significant genes of interest
significant_file="../examples/artery_aorta_cad_sig_genes.t... |
c726895e47b2b34b0a6898374058dd6fc4728b66fb92fed71f7a9135f674505f | Shell | 6,799 | 212 | #!/bin/bash
usage()
{
base=$(basename "$0")
echo "usage: $base subject scan_age [options]
This script creates additional files for the dHCP structural pipeline.
Arguments:
subject Subject ID
Options:
-d / -data-dir <directory> The directory used to run the script and output the files... |
661480e8ebc1bad0d2262d6fc9205e27064d9865fb09a7bb1db30edfcc68e8fe | Shell | 6,832 | 220 | #!/bin/bash
# Author: Andrew Hamel
# Affiliation: Massachusetts Eye and Ear, Harvard Medical School
# Date: June 2022
#
# This is a shell script
# with a sample run of GeneEnrich
# for all available gene sets provided
# and concatenates the gene set enrichment results into a single table
# List of significant genes... |
ca0f55d768bd1048acd8176b92f77db42262028a4e52db7fbf27bf4035916def | Shell | 6,837 | 225 |
#!/bin/bash
####
################################## START OF EMBEDDED SGE COMMANDS ##########################
#$ -S /bin/bash
#$ -cwd
#$ -N wrapper_sortRename
#$ -j y #### merge stdout and stderr
#$ -l short
#$ -l h_vmem=1G
#$ -l tmpfree=1G
############################## END OF DEFAULT EMBEDDED SGE COMMANDS ##########... |
559528917178204a7755f2cd08135f88bc6453b4891f3a279f94f626f194b6c6 | Shell | 6,853 | 139 | #!/bin/bash
# Quick diagnostic for the iteration-degradation issue in alignment.
# Runs banc-alignment-run.py with cosine metric, 10 iters, 50% holdout,
# varying only the alpha schedule. Outputs go to data/optic_lobe/ with the
# diag_<case> suffix for easy comparison.
#
# Usage: sbatch alignment/diag_align.sh {baselin... |
c1b70fdac9ff3d4740d31c7a53bfeb28ec910affd29c942cfbc6734d09c8f6b9 | Shell | 6,896 | 166 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE AMPLITUDE MEASURES OF THE LOW FREQUENCY OSCILLATIONS IN THE BOLD SIGNAL
##
## This script can be run on its own, by filling in the appropriate parame... |
c24625342fbffad604cd06711a83d6bc5efcb7510ac808e2cd17e188b84fb274 | Shell | 6,992 | 183 | #!/bin/bash
is_float() {
[[ $1 =~ ^-?[0-9]*\.?[0-9]+$ ]]
}
dataset_path="../edm/dataset/pdbbind"
output_path="./results/guidance"
OPTIONS=$(getopt -o g --long use-glide -- "$@")
# OPTIONS=$(getopt -o g,f: --long use-glide,file: -- "$@")
# $? checks if getopt failed
if [ $? -ne 0 ]; then
echo "Incorrect options p... |
5692d7444526bde8311cec453e3b6c0a50dcb2f798b6e44bf048b7838aa8c6b9 | Shell | 6,998 | 220 | #!/bin/bash
# ---------------
# 参数设置
# ---------------
INITDIR="" # Working Directory
SOURCE_DIR="$INITDIR/data" # Data Path
RESULT_DIR="$INITDIR/RESULT" # Output Path
WMH_MASK_NAME="aligned_WMH_FLAIR_orig_ud_mask.nii.gz" # Mask file name
WMH_NAME="aligned_WMH_FLAIR_orig_ud.nii.gz" # Series Name
WMH_PROBMAP_NAME='alig... |
1fa189b1c67b049f17afa1bcb83f2fcb75c20d40d7ddd03f1d6657f76fb12c13 | Shell | 7,067 | 90 | # 捕捉中断/终止信号，终止所有后台任务
trap 'echo "中断信号收到，正在终止所有子任务..."; pkill -P $$; exit 1' SIGINT SIGTERM
##--------1. CREMAD datasets-----------
CUDA_VISIBLE_DEVICES=0 python train_snn.py --model AVresnet18 --node-type LIFNode --dataset CREMAD --epoch 100 --batch-size 32 --num-classes 6 --step 4 --modality audio-visual --alpha 0.8 ... |
9e53102424d003703102172789863980ec65cc077159cb426e20431b543a7d4d | Shell | 7,091 | 90 | # 捕捉中断/终止信号，终止所有后台任务
trap 'echo "中断信号收到，正在终止所有子任务..."; pkill -P $$; exit 1' SIGINT SIGTERM
##--------1. CREMAD datasets-----------
CUDA_VISIBLE_DEVICES=0 python train_snn.py --model AVresnet18 --node-type ReLUNode --dataset CREMAD --epoch 100 --batch-size 32 --num-classes 6 --step 1 --modality audio-visual --alpha 0.8... |
1a72d4711194701bd04e7c44925b06f49431a96811e84fbd5010dc2049926448 | Shell | 7,120 | 183 | #!/bin/bash
usage()
{
base=$(basename "$0")
echo "usage: $base entries.csv results_dir release_dir
This script uploads all the results.
Arguments:
entries.csv Entries for the subjects (subjectID-sessionID) used for the release
release_dir The directory used for the release.
data_dir ... |
886d648a119ed2cee821f007e605e31f959569a9c72e78b599cab1efd09a879b | Shell | 7,151 | 102 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Random walk
# Not truly a rondom walk as the generated structure will terminate \
# when a structural overlap occurs. Detecting and avoidin... |
534bee3c15a65aff90ffd18cac3ff4ad92ac2fd42c93e2e8387cd63feb134ac5 | Shell | 7,154 | 198 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=10:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --exclude=lnx-cm-21008
#SBATCH --job-name=repeatmasker_junctions
#SBATCH --error=joblog_error_%x_%j.txt
#SBATCH --output=joblog_output_%x_%j.txt
#
# run_repeatmasker_jun... |
75261fb40afadf57f0fc896b02fc286ce3ca97cb9a2aff99363356f2d0779a86 | Shell | 7,175 | 263 | #!/usr/bin/env bash
set -euo pipefail
ROOT="${ROOT:-${HOME}/benchmarks/macs-version-survey}"
REPEATS="${REPEATS:-3}"
MACS_REPO_URL="${MACS_REPO_URL:-https://github.com/macs3-project/MACS.git}"
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
TIME_MODE="${TIME_MODE:-auto}"
MACS1_REF="${MACS1_REF:-origin/macs... |
80d532e72e969da9a6c7e38360c524ed2a520e33bb2c5375fa275371ec16100a | Shell | 7,214 | 156 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE ANATOMICAL SCAN (INTEGRATE AFNI/FSL/FREESURFER)
##
## R-fMRI master: Xi-Nian Zuo.
##
## Email: zuoxn@psych.ac.cn or zuoxinian@gmail.com.
##
###... |
3c89b1c10c22d27bb699ed749772e85aa72405b13586270e4869780da8fb8c20 | Shell | 7,235 | 211 | #!/bin/bash
# Robust DP_GP_cluster execution script with logging and notifications
# Usage: ./run_dp_gp_monitored.sh
set -euo pipefail
# Configuration
INPUT_FILE="tissue_all/merged.txt"
OUTPUT_PREFIX="tissue_all/tissue_all"
PLOT_FORMAT="png"
ITERATIONS=2000
LOG_DIR="logs"
# Conda environment setup (modify these pat... |
53ea07e174e2df77972eaba05dc225655d636363bf73a0ab7952a8ccf95c5da1 | Shell | 7,241 | 230 |
##Rewrite the AF2 output to contain 2 chains instead of 1 for the DockQ evaluation
################################
############new_dimers###############
################################
##########AF std and HHblits n2 msas############
#model_1
#reycle 10
PDBDIR=/proj/berzelius-2021-29/users/x_patbr/results/af2/new... |
f8c0034a4a96d1bbd85359530466d562b29258820318c0c1aeb4c5be1df964da | Shell | 7,247 | 194 | #!/usr/bin/env bash
#
# Build (and optionally push) a GATK docker image.
#
# If you are pushing an image to our release repositories, be sure that you've followed
# the setup instructions here:
# https://github.com/broadinstitute/gatk/wiki/How-to-release-GATK4#setup_docker
# and here:
# https://github.com/broadinstitut... |
b659a409946e25dd6ea14b1d0d1da01ae6454dfc429f91a906ffc01ea4c4473b | Shell | 7,265 | 128 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO FINAL PREPROCESSING STEPS OF RESTING_STATE SCAN
##
## R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn or zuoxinian@gmail.com.
######################... |
21b86d70f5f85350e30368dfedb55a1be7ad34fa32197de4e12a89591289a3c6 | Shell | 7,288 | 282 | #!/bin/sh
set -x
#mingw='yes'
mingw='no'
nrnpy='yes'
#nrnpy='yes'
#nrnpy='no'
#nrnjvm='yes'
nrnjvm='no'
#nrnmpi='yes'
NPYVER=
#NPYONLY='yes'
NPYONLY='no'
if test mingw = 'yes' ; then
ltlibs=
else
ltlibs=
fi
if test "$NPYONLY" = "no" ; then
#all the .o files
find .. -name \*.o -print | sed '
/\/modlunit\//d
/... |
6a3a5be780fcff6954a3678d4b3591b78441cc4013680560f5b9ff775c1c20b0 | Shell | 7,329 | 138 | #!/bin/bash
# Function to create a directory and check if it was successful, then set permissions
create_and_set_permissions() {
local dir_path=$1
mkdir -p "$dir_path"
if [ ! -d "$dir_path" ]; then
echo "Error: Failed to create directory ${dir_path}."
exit 1
fi
chmod 777 "$dir_path"... |
9f2fe3a0c5c129ed209abe223f36ec2de73e729544bf2e9d98476134ff2b059b | Shell | 7,347 | 183 | #!/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... |
fffadf88a5c12cc8ebaaa1acd30f51dfbd0b784403d5d4454a9c996eb01c1998 | Shell | 7,351 | 271 | #!/bin/bash -e
#/*
#* SVRTK : SVR reconstruction based on MIRTK
#*
#* Copyright 2018-2020 King's College London
#*
#* Licensed under the Apache License, Version 2.0 (the "License");
#* you may not use this file except in compliance with the License.
#* You may obtain a copy of the License at
#*
#* http://www.apach... |
e1198b2a6e5e09decdc24e47d1a735ac9373aef0356ba2e0d0f8b277ea079462 | Shell | 7,395 | 245 | #!/bin/bash
err() {
echo "ERROR: $*" >&2
exit 1
}
usage() {
cat <<EOF
Usage: $(basename "$0") [options] <source_subject> <target_subject|target_template.tif> <hemi> [suffix]
Register a precon_all output directory to either:
1. another individual subject, or
2. a direct template tif file for mris_register... |
cd6f60bcb32d6e01b465c7cb81779d85857c8426cd0d5fc8d2e44fe8cd846bb6 | Shell | 7,415 | 222 | #!/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... |
9ca349fba46c21668c64bee792a505efed6a73104fc3612b11902f2b98ded74d | Shell | 7,474 | 190 | #!/bin/bash
#SBATCH --time=1-12:00:00
#SBATCH --mem=40G
#SBATCH --cpus-per-task=20
# Remember to prepare the reference genome in advance! Like this:
# ${bwa} index ${reference_genome}
# ${samtools} faidx ${reference_genome}
# ${samtools} dict ${reference_genome} -o ${reference_genome/.fa/.dict}
# prepare the environm... |
b8b64faf8adbef00b50d25feba8e392041aa21fe7a6cac9a5c26ce9929e90f9f | Shell | 7,499 | 313 | #!/bin/sh
# install from the build directories to the mswin destination
# uses the classical positions of files
# must be launched from a mingw terminal
set -ex
if false ; then
echo "top_srcdir $top_srcdir"
echo "top_builddir $top_builddir"
echo "marshal_dir $marshal_dir"
echo "ivbindir $ivbindir"
echo "host_cpu $host... |
5d36d52a32bdbba498b70a9b1bb93209c361d78d5aca1c2662dba8646983a5c1 | Shell | 7,508 | 173 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE VOXEL-MIRRORED HOMOTOPIC CONNECTIVITY (ON BOTH VOLUME AND SURFACE)
##
## This script can be run on its own, by filling in the appropriate parameters... |
db6fa89169a746fab55087fb0eeb913987afa6d093ef10dacc6698e5960e454e | Shell | 7,508 | 132 | #!/bin/bash
# this should run after you've invoked this in matlab
# create_CANLab2024_CIFTI_subctx('MNI152NLin6Asym','coarse',2,load_atlas('canlab2024_coarse_fsl6_2mm'))
# which will create a nifti file in this folder with all necessary subcortical volumes
#
# It assumes it's located in Atlases_and_parcellations/2024_... |
64e6b20512e5e957f5e952e6724d9c0dae24938e519056f29f75f814bfdeaaaa | Shell | 7,522 | 208 |
STUDYNAME1=$1
STUDYNAME2=$2
ROOTPATH=$3
HASEROOT=$4
OUT=${ROOTPATH}/OUTPUT/${STUDYNAME1}_${STUDYNAME2}/
rm -rf ${OUT}
mkdir -p ${OUT}/mapper/
mkdir -p ${OUT}/MA_without_b4/
mkdir -p ${OUT}/MA_with_b4/
mkdir -p ${OUT}/MA_encode/
mkdir -p ${OUT}/MA_encode_10/
mkdir -p ${OUT}/MA_encode_01/
mkdir -p ${OUT}/summary_MA... |
45e8901f4dc426e1516feb82b0f4ce2e9211a12163479166819d2d95415cc57d | Shell | 7,580 | 180 | #!/usr/bin/env bash
# -------- fixed locations (relative to THIS script), and required tools --------
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
rootdir="$(dirname "$scriptdir")" # project root (…/night-owls)
FSL_DERIV="${rootdir}/derivatives/fsl"
FMRIPREP_DERIV="${rootdir}/derivati... |
bf7e87cfed12bc998bc36438037a86849f12656113418a16d81c10d9337d20c3 | Shell | 7,586 | 199 | #!/bin/bash -x
### get script directory
BIN=$(dirname "${BASH_SOURCE[0]}")
pushd $BIN > /dev/null
BASEDIR=`pwd`
popd > /dev/null
### get input
PROT1=$1
PROT2=$2
CHAIN1=$3
CHAIN2=$4
### get prot IDs and define input format
SUFFIX=`echo $1 | awk -F . '{print $NF}'`
ID1=`basename ${PROT1%.$SUFFIX}`
ID2=`basename ${PROT... |
b18595b006d844e4e222a95370a332d5f6456c13e9ad392fc34dd009d2841444 | Shell | 7,592 | 212 | #!/usr/bin/env bash
set -euo pipefail
# Bump the shared workspace version and publish the salmon-* crates to crates.io
# in dependency order. Modeled on piscem's bump_and_publish.sh, adapted for a
# multi-crate workspace whose members all inherit `version.workspace = true`.
#
# This script publishes ONLY the salmon-* ... |
1c4762afcdf2bbe8ed15d03227b6eaf01dc23f8ec6d324dd1eaa0c41e5b0408a | Shell | 7,596 | 213 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 22 different methods.
#
# Last change: 2015-08-17. by Hanchuan Peng adding the anisotropic filtering.
#
function write_neuron_tracing_command {
outputScript=$1;
METHOD=$2;
vaa3dProgramPath=$3;
inimgfileTracing=$4;
finalfileFolder=$5;
... |
d539203d423dbe0b9f385b63dab2e35610d07a536f03f481376437cd3d444552 | Shell | 7,612 | 212 | #!/bin/bash
# This script is a wrapper for running the CBIG fMRI preprocessing pipeline
# with containerization technology, namely docker and singularity.
# It performs the following tasks:
# - Parses command-line arguments to determine container type (Docker or Singularity),
# paths for MATLAB Compiler Runtime (MCR... |
ae1e3c5be9d09ae5404bd754f25497c87b87ce19d0137cfa1a8df2754c14b366 | Shell | 7,644 | 209 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
usage() {
echo "Usage: $0 [-b]"
echo ""
echo "Build and push updated Captum site. Will either update latest or bump... |
a4f93b2c0b744c3f1c68ddb5878ca3a3c18ade6c0f636369c3612aafd148e2f5 | Shell | 7,672 | 191 | #!/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 dis... |
a9ef95e37798d123c14fd4de6bb6159163bcc9e4e5404fa1a58990896c10c10e | Shell | 7,728 | 132 | #!/bin/bash
# this should run after you've invoked this in matlab
# create_openCANLab2024_CIFTI_subctx('MNI152NLin6Asym','coarse',2,load_atlas('opencanlab2024_coarse_fsl6_2mm'))
# which will create a nifti file in this folder with all necessary subcortical volumes
#
# It assumes it's located in Atlases_and_parcellatio... |
e4c05d9102a1f14a4054cc4d4f9ddd5bd07bd4ae40a1214dfc5608f6ed7e8c47 | Shell | 7,748 | 220 | #!/bin/bash
# create_appimage.sh - Create Linux AppImage from PyInstaller output
# Requires: appimagetool (download from https://appimage.github.io/appimagetool/)
set -e
# Configuration
APP_NAME="Membrane Kymograph"
APP_ID="in.tatsatbanerjee.membrane-kymograph"
#Placeholder version; will be automatically updated du... |
84288a9c7c2a8ebf3f05334ab09bc735176d00da525260b02eb76aef7b186510 | Shell | 7,754 | 197 | #!/bin/sh
echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
gemma=../bin/gemma
gemmaopts="-debug"
export GSL_RNG_SEED=10
testBslmm1() {
outn=mouse_hs1940_CD8_bslmm
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 2 -a ../example/mouse_... |
41f50a7a45450c7bdc9299d5f3cea64c7b156415e0893f853f46bc7cfbce535f | Shell | 7,767 | 182 | #!/bin/bash
## check that STAR temporary dir is removed for all samples, and that archived unmapped reads are created
>&2 echo "Checking that all STARsolo jobs went to completion .."
for i in *
do
if [[ -d $i && -d $i/output && -s $i/Log.final.out ]]
then
if [[ -d $i/_STARtmp ]]
then
>&2 echo "WARN... |
9fbe750469b0a04bc1640cd933f615638f9cb021c1d6da1b66fc64ba65fe0179 | Shell | 7,767 | 212 | #!/usr/bin/env bash
###############################################################################
# Scheduled BANC alignment runs
#
# Re-pulls fresh data from GCS / SeaTable (meta, connectivity edgelists, NBLAST
# scores, forbidden-matches), then runs three alignments sequentially:
#
# 1. Optic both, ensemble metri... |
6d6610939a1f193871b71476a16392ed9918f6e2711eff931ddd85f775649e18 | Shell | 7,798 | 195 | # This script shows how scripts are sequentially called to generate cardiac models from MRI data.
# This info assumes you have thorughly read our article:
# https://doi.org/10.1101/2025.10.31.685788
# A folder must be set with the subfolders:
# init: with all segmentations and labels obtained from Slicer3D
# mesh... |
77e19edf28273bd9466510cdbea3b2880478c71e4adbb4457e773a23d26bb9e1 | Shell | 7,847 | 228 | DOCKQ=/proj/berzelius-2021-29/users/x_patbr/DockQ/DockQ.py
#############################
##########new_set############
#############################
NAMES=./new_dimers_names.txt
NATIVEDIR=../../../../data/new_dimers/PDB
#
# #model_1
# #reycle 10
# for run in {1..5}
# do
# MODELDIR='/proj/berzelius-2021-29/user... |
8655bd92153defb972bb38fd3ae03be7a80a5a60303a9c4b209caa72ce35810e | Shell | 7,849 | 243 | #!/usr/bin/env bash
# manage.sh — Operator convenience wrapper for the scorm-agents systemd service.
#
# Usage:
# ./deploy/manage.sh install — Install + enable the systemd service
# ./deploy/manage.sh start — Start the service
# ./deploy/manage.sh stop — Stop the service
# ./deploy/manage.sh restart ... |
830dbcf95a9b5271bb5cb02d052957f067ea1eac94981f9ba361a0c7cde881bd | Shell | 7,853 | 191 | #!/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... |
d6efd7b68667a2306c25052ead388282f05d2e2a1c2b3feaec6220e8a481c55a | Shell | 7,884 | 209 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=GATK
#SBATCH --ntasks=18
#SBATCH --cpus-per-task=8
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=10G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to project dir
#SBAT... |
c032a209a54a911ce1521215b363d68122b7d15b246630c732d522e1efcab5e0 | Shell | 7,904 | 186 | #!/bin/sh
#
# There are two subjects (with two sessions of data) in the CoRR_HNU dataset involved in the example. To be able to
# separate the data into training and test sets, these two subjects will be treated as 4 subjects (each session is
# considered as a subject). Then the RSFC of each session will be duplicate... |
aea3fce686814d237a506ba02ec26b97a56e09869605779099f8223d185e786e | Shell | 7,922 | 307 | #!/bin/bash
#
# Script: BIDSto3col.sh
# Purpose: Convert a BIDS event TSV file to a 3 column FSL file
# Author: T Nichols t.e.nichols@warwick.ac.uk
# Version: 1.2 5 September 2016
#
# Extension to give created 3 column files
ThreeColExt="txt"
# Replace slashes in event names with this character.
SlashReplace=""
# ... |
4a03f384e3b435be1d5f4fc0adb98354858c8b98c5d95e54e3324436c9bd5d54 | Shell | 7,924 | 245 | #!/bin/bash
# Ensure that you have installed docker(API >= 1.40) and the nvidia graphics driver on host!
############################################################
# Section 0: Project-Specific Settings #
############################################################
IMGNAME="brainseg"
CONTNAME="b... |
c73bca1e6da0bd3af8f458c20741aebac06610859e9084acced595fb6bf45dc5 | Shell | 7,933 | 155 | #!/usr/bin/env bash
umask 0000
# This script will perform Level 1 statistics in FSL.
# 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")"
logdir=/gpfs/scratch/tug87422/smithlab-shared/nig... |
4da63928e24a06c03d9f41b5f6ceb754714e0d47e0ad2481edfbf2889f1b99a8 | Shell | 7,950 | 224 | #!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o job_logs/job_log.$JOB_ID.$TASK_ID
#$ -j y
## Edit the line below as needed:
#$ -l h_rt=24:00:00,h_data=16G
## Modify the parallel environment
## and the number of cores as needed:
#$ -pe shared 3
#$ -t 1-12 # This will be replaced with actual number of files
# Ge... |
5fcf59a6021cc287e8a0fc8b53c5182a2c27d488225ef67413fb2fabb4306fc4 | Shell | 7,966 | 224 | #!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o job_logs/job_log.$JOB_ID.$TASK_ID
#$ -j y
## Edit the line below as needed:
#$ -l h_rt=24:00:00,h_data=16G
## Modify the parallel environment
## and the number of cores as needed:
#$ -pe shared 1
#$ -t 1-N # This will be replaced with actual number of files
# Get... |
ae89a23a67dff38c7bf118905b55bcc621850f9b7a1de5642a3f49dcde579112 | Shell | 8,030 | 218 | #!/bin/bash -e
# Setup everything for using mmseqs locally
# Set MMSEQS_NO_INDEX to skip the index creation step (not useful for colabfold_search in most cases)
ARIA_NUM_CONN=8
WORKDIR="${1:-$(pwd)}"
PDB_SERVER="${2:-"rsync.wwpdb.org::ftp"}"
PDB_PORT="${3:-"33444"}"
# do initial download of the PDB through aws?
# stil... |
47b12e29d4d1ec926db1373a01070ef6bcd7b58a5e0d51186daad0c920417c28 | Shell | 8,050 | 173 | # 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... |
9f5d0763c5aaf0cf25e3090961fe1e2478d5aa6e2cf7c867a2e20d48b9e90df0 | Shell | 8,065 | 177 | #!/bin/bash
# Create reference assembly FASTA file (5 chromosomes, 100 bp each)
cat > reference.fasta << 'EOF'
>chr1
ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT
>chr2
GCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA... |
8a762f2a3fa17be828d2da2a6aea63933b65e9752540bfb5cbf30f5f81c69b72 | Shell | 8,068 | 137 | #!/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.gz
export file2=$project_work_dir/Data/Intensities/BaseCalls/reverse_index_na... |
1476cd2daefb72f95654f13bafa11a0b249bfcbe0443f71a6a79da01ed20a000 | Shell | 8,088 | 137 | #!/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.gz
export file2=$project_work_dir/Data/Intensities/BaseCalls/reverse_index_na... |
d932d0e0e380d8055436716f37cdac2a78055041d95b3a4ec56b0303ba26e2d9 | Shell | 8,093 | 252 | #!/bin/bash
##### this script is to automate the surface generation process. A starting subject folder and list of subsequent subjects must be provided.
##### template generation is initialized via a single subject
##### mris_register all subjects to template using sulci in fisrt iteraton.
##### make template 1 usi... |
7614bf03337ae6fcc41845a9be9b52e47237f0bdb0de10f6abf65930d7efa10d | Shell | 8,138 | 222 | #!/bin/sh
echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
gemma=../bin/gemma
# gemmaopts="-debug -strict"
gemmaopts="-debug -check"
export GSL_RNG_SEED=100
testLinearModel() {
$gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 1 \
... |
bb2d9cbbcc5bb25794fb9a463bdec43b5fa1aae50979279999639b0960dc230a | Shell | 8,146 | 338 | #!/bin/bash
# TODO
# give user more control over parameters
#set -e
#set -x
# if py_bin not exported to script, use "python3"
if [[ -z ${py_bin} ]] ; then
py_bin=python3
fi
function checkisfile {
inFile=$1
if [[ ! -f ${inFile} ]] ; then
echo "file does not exist: $inFile"
exit 1
fi
}
EXEDIR=$(dirname "$(... |
d532818f93d2e43a0b27ecf5a4f697bdae30a30918a388dbdc2e55a785a2e37c | Shell | 8,149 | 208 | #!/bin/bash
Usage() {
echo " "
echo "Usage: `basename $0` [options] -i <deniosed T1 Brain image> "
echo ""
echo " Compulsory Arguments "
echo "-i <T1.nii.gz> : Image must include nii or nii.gz file extension "
echo "-a <animal>"
echo " Optional Arguments"
echo "-p u... |
49b43fe76eaa4fb794a1ff5e68598378b6afd6baca8a2f39f060d58c60ddcb21 | Shell | 8,154 | 265 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_DIR="$(cd "${SCRIPT_DIR}/../.." && pwd)"
DGX_USER="${USER:-$(id -un)}"
NNUNET_ROOT="${NNUNET_ROOT:-/nfs/home/${DGX_USER}/nnunet}"
NNUNET_RAW="${NNUNET_RAW:-${NNUNET_ROOT}/nnUNet_raw}"
NNUNET_PREPROCESSED="${NNUNET_PR... |
08f37609b80ce30d0c044b2dd1c20574c44ffaadc2e58a793278fd207ea61ac6 | Shell | 8,172 | 235 | #!/bin/bash
# ============================================================
# Build script for TheCrunchometer.app (macOS Apple Silicon)
#
# This script:
# 1. Checks prerequisites (Python, PyQt5)
# 2. Installs/updates PyInstaller
# 3. Downloads FFmpeg & FFprobe static ARM64 binaries
# 4. Creates macOS .icns icon... |
c3fa40cf00954ad63cd2d9cc7aa3aa8434a0898d138fd307fb6453691ff93a0a | Shell | 8,175 | 104 | #!/bin/bash
#BSUB -J THCVD_AR
#BSUB -o ./THCVD_AR_%J.out
#BSUB -e ./THCVD_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 PH... |
188a9f35a6510cace4fc7b4f7a33236cecc02e43030e6257287b6861990d43aa | Shell | 8,199 | 129 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
658a52f8cebf3aa0db6402b554a96d66e521c6578013a9b82ed2d622bf2c4f8e | Shell | 8,213 | 124 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
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