sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
49e0ca5c441f43e15dedb9fcb7810c88f4aff8de7ec6932481dd0e06aeab3c7d | Shell | 3,475 | 115 | #!/bin/bash
##############################################
# ARIMA GENOMICS MAPPING PIPELINE 07/26/2023 #
##############################################
# Below find the commands used to map HiC data.
# Replace the variables at the top with the correct paths for the locations of files/programs on your system.
# Thi... |
da18e2754036cb9f352ef79f112be4a5558872e6bf094523d1cdb95e81c9b881 | Shell | 3,484 | 87 | #!/usr/bin/env bash
# Smoke-test a Baysor binary from a release archive.
#
# packaging/smoke_test.sh <path/to/bin/baysor> [expected-version]
#
# Runs `--version` (compared with expected-version if given), `--help`, and a
# full `baysor run` on a small synthetic dataset (a grid of round cells,
# generated here with aw... |
7c0610dcfd383618823723468febac630d29a76d4b86f3c025ef0be4ceb5056e | Shell | 3,535 | 91 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
49816a164b16a5d8e00304d1d5cc5ea00e796cde3a10e210bc0d471373f36e50 | Shell | 3,544 | 113 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
c25169ff6ffad6348e8e9df3a3f3352ebc4c790c6413ae3c78dea6355a137453 | Shell | 3,604 | 121 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_preproc_study2.sh -i <Subject>
e.g. sbatch Functional_preproc_study2.sh -i Subject_1
EOF
exit 1
}
if [ $# -le 1 ];
then
Usage
exit 1
fi
while [ $# -ge 1 ];
do
case "$1" in
-i)
subject=$2;
shift;;
es... |
111b917fa8b36495a5a9c9913b64d9090de0666c42be4e11f40091962915aea9 | Shell | 3,611 | 90 | # Example:
# scripts/process_gbcIV.sh run all
#
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# Note we do not have a full reconstruction for cell 18
# in that dataset.
#####################################################... |
7c7cf8b204d21fde9c9c486ffc88b41ff22ecac451e74ff4a4d266befffc41cf | Shell | 3,625 | 115 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
3e5bfa69ae47007ffef5ce4c351e9f07d583a3cfd5b2447b439cd2e4ce3852df | Shell | 3,669 | 117 | #!/bin/bash
# This file contains the installation setup for running benchmarks on EC2 isntance.
# To run on a machine with GPU : ./install_dependencies.sh True
# To run on a machine with CPU : ./install_dependencies.sh False
set -ex
sudo apt-get update
sudo apt-get -y upgrade
echo "Setting up your Ubuntu machine to ... |
1516680e89fdbe79c9d116cad693f14f431e29f68ff792e33f626e89ba2e288e | Shell | 3,711 | 137 | #!/bin/bash
#rm -fr ${2}"_"${4}
start=${8}
end=${9}
type=${4}
mkdir -p ${2}"_"${type}
HEADER=$(head -1 $1)
SEQ=$(tail -1 $1)
LN=$(tail -1 $1 | tr -d "\n" | wc -c)
CENTER=$(echo "scale = 0; (${start} + ${end}) / 2" | bc -l)
DIFF=$(echo "scale = 0; ${CENTER} - (${LN} / 2)" | bc -l)
if (( $DIFF > 0 )); then
END=$(... |
903ce8de8c35d56dbaa985e7946a189c2458acc86075fc1ae4015e855ac4840f | Shell | 3,737 | 130 | #! /bin/bash
echo "Usage: ./_submit_bwa.sh <ref.fasta> <fastq.map> <out>"
ref=$1
fastq_map=$2
out=$3
if [[ "$#" -lt 3 ]]; then
echo "Not enough args given. Exit."
exit -1
fi
mkdir -p logs
if [ ! -s $ref.fai ]; then
cpus=4
mem=10g
name=$out.index
script=$VGP_PIPELINE/bwa/bwa_index.sh
args="$ref"
partition=q... |
b98294d40409cab89fc53bd55d3fa52017b2ab68860905a4ddf657ce4c755d20 | Shell | 3,742 | 109 | #!/bin/bash
genome=$1
if [[ -z $genome ]]; then
echo "Usage: ./telomere.sh <genome_id> <threshold> <ends> <asm.fa> [asm.csv]"
echo " <threshold>: threshold to define telomere window. Define from 0.0 to 1.0. Recommended: 0.4"
echo " <ends> : report ends.bed only if a window is found within <ends> ... |
f8fa4df7d6dd54fccf67df7e42761c00b0258d4ab72ce4076eb8d37d5ce6410e | Shell | 3,763 | 103 | #!/bin/bash
# asm-stats 0.0.1
# Generated by dx-app-wizard.
set -x -e -o pipefail
main() {
echo "Value of asm: '$asm'"
echo "Value of gsize: '$gsize'"
echo "Value of mode: '$mode'"
echo "Value of extract: '$extract'"
echo "Value of out_name: '$out_name'"
mem_in_mb=`head -n1 /proc/meminfo | ... |
23e4d642d2abbc95d50b8c90d08b384e3bda97b2fd32f1f45f23f202bacb7338 | Shell | 3,896 | 80 | #!/bin/sh
# ========================================
#SBATCH --partition=high_mem #Selecting “shared” Queue
#SBATCH --job-name="ROS_Subj17to24" #Name of Jobs (displayed in squeue)
#SBATCH --nodes=2 #No of nodes to run job #2
#SBATCH --ntasks-per-node=8 #No of cores... |
0694155c7cd920d0b9c09d4a3e47d0a41dec5b93f49af42cce55aa4a2e28a4d9 | Shell | 3,899 | 101 | #!/bin/bash
NUMPARAM=$#
if [ $NUMPARAM -lt 2 ] ; then
echo " Usage "
echo " $0 OUTNameAffine.txt *Affine.txt "
echo " assumes close to idetity affine transforms "
exit
fi
OUTNM=$1
shift 1
FLIST=$*
NFILES=0
PARAM1=0
PARAM2=0
PARAM3=0
PARAM4=0
PARAM5=0
PARAM6=0
PARAM7=0
PARAM8=0
PARAM9=0
PARAM10=0
PARAM11=0
PARAM12=0
... |
6c413e0e76d6dcde3cbd128d335641110b2f1cce8eaab7b337af783670fc8d43 | Shell | 3,902 | 75 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
b5c3d267fd118ed00efa832e3e2180f19ca738e83c31d34336c15cb31106092a | Shell | 3,930 | 72 | # dataset=USPTO50K-aug-untyped
seed=$1
dataset=USPTO50K-aug-untyped_${seed}
dataset_prefix=USPTO50K-aug-untyped
suffix=test-prediction
source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate retroxpert_
# propose 200, with seed
python3 ../../onmt/bin/translate.py --model ../../experiments/ch... |
40966adf489335a6130ff8b2751193278ac1af5ecba62819fb7df42f861a5fce | Shell | 4,018 | 128 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
b113f7ecf43398905ea28e397cca5bb07b6170662291ba15e03ef1fbd9662b39 | Shell | 4,029 | 122 | #!/bin/bash
# sttdev.sh: Standard Deviation
# Original version obtained from: http://tldp.org/LDP/abs/html/contributed-scripts.html#STDDEV
# 2009-03-09: Panagiotis Kritikakos
# Function stat_median() added for calculating the median value
# of the data set
# ---------------------------------------------------------... |
640aa9c32713978fce0b775de61fde6aa2c568b8f12b3cc5268a1c676ddcadab | Shell | 4,045 | 77 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
4dff67f7a693efeda4a4c6177f1faa33b7bf9c160bbbc11510628ddf305b536a | Shell | 4,107 | 77 | set -euo pipefail
gff=/data/human/Homo_sapiens.GRCh38.96.chr.gff3.gz
bcf=/home/brentp/src/varx/var.bcf
ped=/home/brentp/src/varx/var.ped
fasta=/data/human/GRCh38_full_analysis_set_plus_decoy_hla.fa
LCR=/data/human/LCR-hs38.bed.gz
mkdir -p vcfs/
cohort=exome
export SLIVAR_SUMMARY_FILE=$cohort.summary.tsv PATH=.:$PATH
... |
db19f1b8a73998bffc9f9d1d4734c493aeab444afc65094c10c6d78687748087 | Shell | 4,244 | 132 | #!/bin/bash
#this script (mtDNApipe.sh) is used to retrieve mitochondrial-like sequences from the raw Pacbio data
#generated in the framework of the Vertebrate Genomes Project and assemble them using Canu.
#it requires the following software (and their dependencies) installed:
#aws-cli/1.16.101, blasr/5.3.2-06c9543,... |
4c2b2ae9d47d215efaac6c649278e774039248ff8634633e262dd3d9c90becc4 | Shell | 4,281 | 111 | #first step is getting the protein restr files
#################
#USAGE genrestr_sequence grofile.gro topol.top pdbfile.pdb psffile.psf
#################
#make sure the pdb files contain the whole system. they don't need the right termini but they need all elements proteins ligands and lipids
#note weird sed delimiter... |
c69ff660cacf209d4d309ced8f8402bdcd6b8b6852d6eb39b05bd92425565997 | Shell | 4,288 | 132 | #!/bin/bash
#this script (mtDNApipe.sh) is used to retrieve mitochondrial-like sequences from the raw Pacbio data
#generated in the framework of the Vertebrate Genomes Project and assemble them using Canu.
#it requires the following software (and their dependencies) installed:
#aws-cli/1.16.101, blasr/5.3.2-06c9543,... |
e7ccbc5adcb266e65e456d7dfdb82ec726c2f130db6e2f7c933dba4bad54f229 | Shell | 4,388 | 155 | # Example:
# scripts/process_gbcIV.sh run all
#
proto="testIV"
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# This just computes for cell
#######################################################
CELLNAMES="09" # "02 05 06 0... |
72bfe4d16f6aed64d2b4d0cb5ab251caaddd9697a8096ead1f778fe2b7610e84 | Shell | 4,408 | 122 | #!/usr/bin/env bash
#
# Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
65897ab8809abab80ae4274511210f4f5c948d6a2c2a6497310182b53e2bb262 | Shell | 4,412 | 118 | #!/usr/bin/env bash
# We will be launching multiple tmux windows, which may not by default be using the same python environment as the current shell,
# so we specifiy to use the current shell's python executable.
PYTHON_EXECUTABLE="$(command -v python)"
echo "Using current python executable at ${PYTHON_EXECUTABLE}"
... |
e52c4d7e573f1077f86ab4e81695b1b303e56e3382e462e0276dc802daaa5bda | Shell | 4,455 | 146 | #!/bin/bash
NUMPARAMS=$#
MAXITERATIONS=30x90x20
if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " sh ants.sh ImageDimension fixed.ext moving.ext Subject/Moving-DT-To-Deform-To-Fixed-Image OPTIONAL-Subject/Moving-BZero-To-DistortionCorrect-To-Moving-T1-Image "
echo " Max-Iterations in form : JxKxL where... |
32a15ecbd4b0951ac660a823e819773284672c429561d96be2419f8704a7c914 | Shell | 4,555 | 183 | #!/bin/bash
VERSION="0.0.0 test"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
PROGRAMS[0]=ExtractSliceFromImage
PROGRAMS[1]=PrintHeader
PROGRAMS[2]=TileImages
PROGRAMS[3]=DenoiseImage
PROGRAMS[4]=ImageMath
PROGRAMS[5]=N4BiasFieldCorrection
for (( i = 0; i < ${#PROGRAMS[@]}; i++ ))
do
if ! comma... |
2f94a3d859a697d5ac2c17593dfa4b77dc3ee520eebd6bc323da5347eefcc0e5 | Shell | 4,697 | 142 | #!/bin/bash
NUMPARAMS=$#
MAXITERATIONS=30x90x20
if ! command -v "ANTS" &> /dev/null
then
echo "Cannot find the ANTS program. Please \(re\)define \$PATH in your environment."
exit 1
fi
if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " sh ants.sh ImageDimension fixed.ext moving.ext OPTIONAL-OUTPREFIX ... |
7b566b2c32a49c1e0f34c503fc25746f6f2afe431063c7262655f11feb6f2a19 | Shell | 4,724 | 93 | #!/bin/bash
# path to data
DATA_DIR=/home/goschv/CSB_NeuroRad2/goschv/DATA/Repro
cd $DATA_DIR
for s in CSB*
do
echo $s
mkdir $s/processed/fast4
mkdir $s/processed/ROC_fast4
mkdir $s/processed/ROC_fast4_dil
################################## USES REGISTERED BET IMAGES TO APPLY FMRIB's Automated Segmentation Too... |
bcd674beec0eb39c4ad07ac8f24786976ed3d3caa389b3e8285ea003fecdaf1b | Shell | 4,792 | 115 | #!/bin/bash
set -euxo pipefail
# Run after test_cc_local.sh: reuse its C API/backend installation and the
# matching LAMMPS checkout instead of rebuilding DeePMD or using the pip wheel.
SCRIPT_PATH=$(dirname "$(realpath -s "$0")")
REPO_ROOT=$(realpath "${SCRIPT_PATH}/../..")
DEEPMD_C_ROOT=${DEEPMD_C_ROOT:-${REPO_ROOT}... |
5531b97e2ff1f93df7e2ffd3455c179a0509bab2bda462738080ecce21fce559 | Shell | 4,830 | 126 | #!/bin/bash
usage=" $0 -d 3 -f fixed.nii.gz -m moving.nii.gz -o output_prefix "
:<<supercalifragilisticexpialidocious
here is a first pass at an unbiased registration between an image pair, A ( fixed ) and B.
the reference frame for the registration uses the header of A.
however, the image content ---- call it AB -... |
acadca7f5e01c17729a14ac5a053cba9e73ce60f97cda5bb2358355311b60535 | Shell | 4,836 | 160 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
201d6246c04bcf914ea5dd75b71aa3a3556ec25ad22f8560f75c18d1081f4a73 | Shell | 4,932 | 194 | #!/usr/bin/env bash
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
47570d1abea6e7edaae8bdd5e5bdeb61c78fc3efd341883dec8c60f15207ffe3 | Shell | 4,948 | 214 | #!/bin/bash
VERSION="0.0.1"
function Usage {
cat <<USAGE
Usage:
`basename $0` [-h ] [-r ] [-j nb_jobs ] command arg_list
Optional arguments:
-h: Shows help
-r: Replace asterix * in the command string with argument
-j: Number of concurrent jobs to run (default 2, must be more than 1)
Examp... |
2e94a3ac1cfc146a16ea38e9ececc8b0e1ca9bdb590dc9feff2aac658f28107b | Shell | 5,049 | 213 | #!/bin/bash
# Translated and modified from:
# https://s3.eu-central-1.amazonaws.com/avg-kitti/raw_data_downloader.zip
files=(2011_09_26_calib.zip
2011_09_26_drive_0001
2011_09_26_drive_0002
2011_09_26_drive_0005
2011_09_26_drive_0009
2011_09_26_drive_0011
2011_09_26_drive_0013
2011_09_26_drive_0014
2011_09_26_drive_00... |
4a6bafb887f5bac9b205fce0c9dd2c1ec067c48b22fbf7ccc98a9436308514c0 | Shell | 5,093 | 87 | #! /bin/bash
export FREESURFER_HOME="/usr/local/freesurfer-6"
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export LD_PRELOAD=/usr/local/gcc-7.2.0/lib64/libstdc++.so.6
#This script will be used to create aggregate files with CNR and Euler number values for freesurfer version 5.3
#The methods for this script were obtained... |
cc8a0aae240363a0f2561f5e664ee0e96e8f04dee152f9750583ee4344606ace | Shell | 5,126 | 117 | #!/bin/bash
# Copyright (c) 2008, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of con... |
a75246e06b95b1b28f58970709caff3a97dd69488d66bc7a47194efb37082ed9 | Shell | 5,133 | 168 | #!/bin/bash
# mitoVGP-re 0.0.1, mitoVGP read extractor
# based on mtDNApipe.sh, mitoVGP pipeline v1.1
set -x -e -o pipefail
main() {
echo "Value of ID: '$ID'"
echo "Value of REF: '$REF'"
ref_name=$REF_name
ref_prefix=$REF_prefix
dx download "$REF" -o ${ref_name}
#define working directory
W_U... |
b04e74cc92f0cf4a27e9b62cfd7bc1ad30cce262f4300f9b046df45d855229c6 | Shell | 5,171 | 119 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
3d369d90e7a968c31df99223f09d3bedbb38344f05e496801af596b0424d011e | Shell | 5,285 | 140 | #!/bin/bash
#
#
if [ $# -lt 5 ] ; then
echo this script will allow you to run \( Reg \) a pairwise segmentation, \( RegSegPSE or RegSegMSQ \) or run segmentation, then use segmentation output in registration or \( BTP \) build a template.
echo you call the script like this
echo $0 ImageDimensionality Opt OutputPrefix... |
effc67b75b82c17c1b454d3e5788a0d12a7c2ab080e36a61ff6a9272f0a8f8e8 | Shell | 5,418 | 74 | #!/bin/bash
# transform ROIs in MNI space to subject space, EEGSTV based ROIs
# Hengda He, Mar 16th 2021
ReD='\033[91m'
YelloW='\033[93m'
EndC='\033[0m'
#SUBJECTS=$1
SUBJECTS=(180607_Sub11 180618_Sub17 180624_Sub21 180725_Sub25 180829_Sub33 180608_Sub12 180621_Sub18 180626_Sub22 180807_Sub29 180830_Sub34 180612_Sub14... |
7e225b1fd632ad65a337a4732fa16c5556cf61f70e981eb3e86194dc3eff9ca4 | Shell | 5,432 | 129 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
e7452106df028d3c367e1188bbb7b8972077c6f769210612ff039b9f167b0bf0 | Shell | 5,562 | 169 | #!/bin/bash
### AUTHOR: Po-chia Chen chen.buo.jia@gmail.com
### MODIFIED: Miro A. Astore miro.astore@gmail.com
#source $HOME/scripts/functions.bash
#Designed to work with GROMACS ffbonded.itp
function grab-bond-angle() {
awk -v a1=$2 -v a2=$3 -v a3=$4 'BEGIN {
mode=0
bond1="" ; bond2="" ; angle=""... |
5a85fd6bffaf23c0003052312827dc44a86a30f983de1d3d2d593a0ce997c7fb | Shell | 5,654 | 109 | #!/bin/bash
#this script (ArrowPolish.sh) is used to polish the assembly generated by the script
#mtDNApipe.sh using Canu. It performs two rounds of Arrow polishing using the same reads used
#by Canu to generate the assembly. These are retrieved from the raw Pacbio data
#using information from Canu intermediate files.... |
febad87b581ec77419b02d24f14d92a72dacfab036b66b3da966c4a28e1bd6f3 | Shell | 5,665 | 109 | #!/bin/bash
#this script (ArrowPolish.sh) is used to polish the assembly generated by the script
#mtDNApipe.sh using Canu. It performs two rounds of Arrow polishing using the same reads used
#by Canu to generate the assembly. These are retrieved from the raw Pacbio data
#using information from Canu intermediate files.... |
9bdfb097cbb724ca768e90f2e154fefcf5ebc358d1dc00ea27f17d338edf6d2f | Shell | 5,692 | 167 | #!/bin/bash
#this script (map10x1.sh) is used for short read polishing of the long-read assembly
#resulting from Canu (mtDNApipe.sh) and Arrow polishing (ArrowPolish.sh).
#In the VGP pipeline it uses 10x data (currently with random barcodes) but it can be used
#with any short read data containing mitogenomic reads us... |
30955f4ee484f38fe3555bd5035554a9a0983dcac4e4ab3c060a2a71345d7356 | Shell | 5,706 | 166 | #!/bin/bash
#this script (map10x1.sh) is used for short read polishing of the long-read assembly
#resulting from Canu (mtDNApipe.sh) and Arrow polishing (ArrowPolish.sh).
#In the VGP pipeline it uses 10x data (currently with random barcodes) but it can be used
#with any short read data containing mitogenomic reads us... |
c7aa0345ce9dcab95f48546abcd5e07b45f98a6ea8d08b0c25cb0683c7684c3b | Shell | 5,851 | 164 | #!/bin/bash
set -e
#set variables species abbreviation
ABBR=$1
CONTIG=$2
FNAME="${CONTIG%%.*}"
FEXT="${CONTIG#*.}"
CONTIG_NAME=$(cat ${CONTIG} | awk '$0 ~ ">" {print substr($0,2)}')
if ! [[ -e "realigned_${ABBR}_all_sorted.bam" ]]; then
samtools sort -n aligned_${ABBR}_all_sorted.bam -o aligned_${ABBR}_all_paired... |
ea350dac1f9e29998b8796c145fa49708f13a00b80ea042616fb89740cec6694 | Shell | 5,973 | 166 | #!/bin/bash
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope tha... |
b8772d154ce0dfa8d58093e6d12585e2ad12e27fee4de534bdc095ccd0dc30bf | Shell | 6,024 | 178 | #!/bin/bash
#this script (map10x1.sh) is used for short read polishing of the long-read assembly
#resulting from Canu (mtDNApipe.sh) and Arrow polishing (ArrowPolish.sh).
#In the VGP pipeline it uses 10x data (currently with random barcodes) but it can be used
#with any short read data containing mitogenomic reads us... |
9c680f8e48fa0f0d4933fedc75edc459d36ab5f56de8a6fa5189ae244fd3c762 | Shell | 6,508 | 160 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
5d5708e55276553a38e3231d2c7e119abba96888e060c0f311b39ef0e86eb433 | Shell | 6,546 | 182 | #!/bin/bash
######################################################################
#
# Arguments
#
arg_input_seq=$1
arg_output_result=$2
arg_working_dir=$3
arg_output_evd_plot_feat_base=$4
######################################################################
#
# Constants: for the directory settings
#
MYOWN_... |
8f90088ea066e990d1b9e84f71e681b6784e4a883d4ff525311365c67aeb2b71 | Shell | 6,648 | 112 | #!/bin/sh
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... |
b7cccd74d9fbd8fc97a1de2f890826f75b248c8e3ff7ee499f51d027729cb6b8 | Shell | 6,694 | 158 | #!/bin/bash
NUMPARAMS=$#
if [ $NUMPARAMS -lt 2 ]
then
echo " USAGE :: "
echo " sh geodesicinterpolation.sh image1 image2 N-interpolation-points N-step-size Use-Affine-Initialization? Mask-Image Auxiliary-Template "
echo " N-interpolation-points -- if you choose 10 points and step-size of 1 then you will get 8... |
0e6493141959337eaa7038bd5d6c9f18d028fa03b813f007e4511d20b8dd9db6 | Shell | 6,771 | 187 | #!/bin/bash
######################################################################
#
# Arguments
#
arg_input_seq=$1
arg_output_result=$2
arg_working_dir=$3
arg_output_evd_plot_feat_base=$4
######################################################################
#
# Constants: for the directory settings
#
MYOWN_... |
22e7020213694044a5018a162d2c225035f3dfed3e8672c9f77d2614eac604e2 | Shell | 6,824 | 138 | #!/bin/bash
# Execute script via
# bash -x batch.ppfreesurfer.sh
export FREESURFER_HOME="/usr/local/freesurfer-6"
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export LD_PRELOAD=/usr/local/gcc-7.2.0/lib64/libstdc++.so.6
#https://github.com/PennBBL/conte/blob/master/freesurfer/QA.sh
#Runs the quality assurance pipeline f... |
54dd4ba2578c07d479b2f72eae1c2ce5bb5eb2902ddc31fea22798711dfcbf3d | Shell | 6,848 | 154 | #!/bin/bash
# freebayes-sp2 0.0.1
# Generated by dx-app-wizard.
set -x -e -o pipefail
# one_freebayes(){
# sudo chmod 777 /usr/bin/samtools
# sudo chmod 777 /usr/bin/freebayes
# sudo chmod 777 /usr/bin/bcftools
# mkdir -p out/vcf
# mkdir -p vcf
# dx-download-all-inputs --except ref
# dx c... |
3472b1d63ab7ff8f39f780155e02bfc9a5751795b3f612b788bcd5c7295fa9e3 | Shell | 6,882 | 58 | #!/bin/bash
#SBATCH --partition=medium
#SBATCH --time=24:00:00
#SBATCH --ntasks=5
#SBATCH --mem-per-cpu=8G
#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/sub-MDP001-dwi-FSL-preproc.txt
module load FSL/6.0.3
# Extract b0 images from AP and PA scans for both dir98 and dir99. Save in FSL directory
fslroi /d... |
b332180ebaf8421fbb00ad03db79a2b068aa618eec42c65aa40186ebe2c4da32 | Shell | 7,006 | 138 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
e5955043080dcfcde3ade91a52f69fc028cbe5595e06b47b1f3096660ca245ba | Shell | 7,243 | 175 | #!/bin/bash
set -e
if [ -z $1 ]; then
echo "use $0 -h for help"
exit 0
elif [ $1 == "-h" ]; then
cat << EOF
this script (ArrowPolish.sh) is used to polish the assembly generated by the script
mtDNApipe.sh using Canu. It performs two rounds of Arrow polishing using the same reads used
by Canu to generate the ... |
8efa30bf0b91eac808cd501fe91f35f14d92b0c8f959c1e36cd8bcb095b7bcd5 | Shell | 7,329 | 115 | #!/bin/sh
#
# Use as
# package.sh <sourcedir> <destinationdir>
SOURCE=$1
DESTINATION=$2
if [ -e ${SOURCE} ]; then
SOURCE=${HOME}/matlab/fieldtrip
fi
if [ -e ${DESTINATION} ]; then
DESTINATION=${HOME}/matlab/cifti
fi
echo Copying from ${SOURCE} to ${DESTINATION}
# update the version
svn info ${SOURCE} | grep ^Last... |
30ba42a7824843b3b82d90c932e8a8ce5c7586a16cbbb5dbbbba808f140e106a | Shell | 7,364 | 287 | #!/bin/bash
set -e
if [ -z $1 ]; then
echo "use $0 -h for help"
exit 0
elif [ $1 == "-h" ]; then
cat << EOF
Usage: '$0 species id reference genome_size mapper threads'
mtDNApipe.sh is used to retrieve mitochondrial-like sequences from the raw Pacbio data
generated in the framework of the Vertebrate Genomes ... |
b0b06492ab13fad70f404d92e46fc38bdf24d8c5404fa54edf722bbf06cec424 | Shell | 7,442 | 138 | set -euo pipefail
gff=/uufs/chpc.utah.edu/common/HIPAA/u6000771/Data/Homo_sapiens.GRCh38.95.chr.prefix.gff3.gz
fasta=/scratch/ucgd/lustre/common/data/Reference/GRCh38/human_g1k_v38_decoy_phix.fasta
LCR=/uufs/chpc.utah.edu/common/HIPAA/u6000771/Data/LCR-hs38.bed.gz
zip=/uufs/chpc.utah.edu/common/HIPAA/u6000771/Data/gnom... |
f7316bd5c4249a083c98ccc458be50f2748a1f62954628b770b253bec5f1fc54 | Shell | 7,480 | 211 | #!/bin/bash
# trap keyboard interrupt (control-c)
trap control_c SIGINT
WARP=antsApplyTransforms
AVERAGE_AFFINE_PROGRAM=AverageAffineTransform # NoRigid
if ! command -v ${WARP} &> /dev/null
then
echo "antsApplyTransforms program can't be found. Please (re)define \$PATH in your environment."
exit
fi
if !... |
6b50e01d4881f149a8edaea6f80cac655235edb2b0d6ab839e815114a0e58f4b | Shell | 7,508 | 185 | #!/bin/bash
set -ex
if [ "$DP_VARIANT" = "cuda" ]; then
CUDA_ARGS="-DUSE_CUDA_TOOLKIT=TRUE"
elif [ "$DP_VARIANT" = "rocm" ]; then
CUDA_ARGS="-DUSE_ROCM_TOOLKIT=TRUE"
fi
#------------------
SCRIPT_PATH=$(dirname $(realpath -s $0))
NPROC=$(nproc --all)
#------------------
echo "try to find tensorflow in the Python... |
0d28cd967de95c5f8c94ecd3cef985055ae1888b8e6288a7110ce6438850465c | Shell | 7,521 | 294 | #!/bin/bash
set -e
if [ -z $1 ]; then
echo "use $0 -h for help"
exit 0
elif [ $1 == "-h" ]; then
cat << EOF
Usage: '$0 -s species -i species_ID -r reference -g genome_size -t threads -m mapper (optional) -l filelist (optional) -c cluster (optional)'
mtDNApipe.sh is used to retrieve mitochondrial-like sequenc... |
592204220d6c6291e384e4633c0fbbb03a59cc8e66972864bdee760d47ee2198 | Shell | 7,590 | 246 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_preproc_study2.sh -i <Subject>
e.g. sbatch Functional_preproc_study2.sh -i Subject_1
EOF
exit 1
}
if [ $# -le 1 ];
then
Usage
exit 1
fi
while [ $# -ge 1 ];
do
case "$1" in
-i)
subject=$2;
shift;;
es... |
170807790d5f3428adcad2aba15366ec8dd8b9755bcbaa99ad2ab914258d6105 | Shell | 7,823 | 158 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
227deae4329e62db630637bd70c365b29acb01b4870a98567536b77c92310e80 | Shell | 7,897 | 59 | #!/bin/bash
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=//Users/nagehan/Documents/Github/curveball/curveball_scripts/curveball/Yale_vtk
input="/Users/nagehan/Documents/Github/curveball/curveball_scripts/curveball/subjects_yale_TD.txt"
while IFS= read... |
1cb3ceb293f8fa07279fbbe90544d7d9c5972cba9e3888617715eec8206a2cfb | Shell | 7,901 | 183 | #!/bin/bash
#this script allows to generate a trimmed version of the Canu mitocontig after short read
#polishing (map10x1.sh). The resulting contig has 100 bp overlapping ends on both sides.
#The script is still experimental.
#it requires the following software (and their dependencies) installed:
#bowtie2/2.1.0, samt... |
b383bdaa66b38d50dca5a16476a5669c6f4f4746f24f5605714c7ff264bcc665 | Shell | 7,909 | 183 | #!/bin/bash
#this script allows to generate a trimmed version of the Canu mitocontig after short read
#polishing (map10x2.sh). The resulting contig has 100 bp overlapping ends on both sides.
#The script is still experimental.
#it requires the following software (and their dependencies) installed:
#bowtie2/2.1.0, samt... |
f2fc757a89cdc3cc3f50328ab74a3854f34d348a97fb60864eb457c0702bea41 | Shell | 8,164 | 198 | #!/bin/bash -eu
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... |
2e337fd1900bd7f54117ada7df79a034fc5adcb0d75f68bbaf99a930af101c2d | Shell | 8,229 | 185 | #!/bin/bash
#this script allows to generate a trimmed version of the Canu mitocontig after short read
#polishing (map10x1.sh). The resulting contig has 100 bp overlapping ends on both sides.
#The script is still experimental.
#it requires the following software (and their dependencies) installed:
#bowtie2/2.1.0, samt... |
3f7a7386ce81b226dc17c65623cc2e36266c0d068256f012a12fed8e2ebf17ba | Shell | 8,231 | 185 | #!/bin/bash
#this script allows to generate a trimmed version of the Canu mitocontig after short read
#polishing (map10x1.sh). The resulting contig has 100 bp overlapping ends on both sides.
#The script is still experimental.
#it requires the following software (and their dependencies) installed:
#bowtie2/2.1.0, samt... |
fda49157156baebe6736ab9383c8a57659ddb6b00c57021899dc0e83127d85ae | Shell | 8,240 | 185 | #!/bin/bash
#this script allows to generate a trimmed version of the Canu mitocontig after short read
#polishing (map10x1.sh). The resulting contig has 100 bp overlapping ends on both sides.
#The script is still experimental.
#it requires the following software (and their dependencies) installed:
#bowtie2/2.1.0, samt... |
045716b0241c0c2c8196be0a89467120a0f323280fb0e5fcfe2e68748c6bbcfd | Shell | 8,647 | 204 | #!/bin/bash
folder_name=$1
analysis_starting_point=$2
user_name="$USER"
echo $folder_name
# check the folder's log what is the last step completed
step_completed=$(AnalysisProgress.sh $folder_name)
if [ -z "$step_completed" ]; then
# cannot determine the last step completed
step_completed=-1
fi
# if there was no ... |
e10f3fae928fad14792d4f8f51209cd851de9098fa49038e389bcbb05500137b | Shell | 8,794 | 204 | #!/usr/bin/env bash
#
# Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
fc37dd1287301e0a0eace36baccea23038b93b568d932a4ccf69e0d74667e625 | Shell | 9,204 | 261 | #!/bin/bash
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... |
bee1d3030791f748c67193e496c0fa1df0d98e942ec258461bbae8bf9d190e1b | Shell | 9,415 | 191 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
beec2128786f8575e8ffecb14b7f8c153ea0d2995a6abe629786c87c95e94d72 | Shell | 9,820 | 370 | #!/bin/bash
VERSION="0.0.0 test"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
ANTS=antsRegistration
if ! command -v ${ANTS} &> /dev/null
then
echo "antsRegistration program can't be found. Please (re)define \$PATH in your environment."
exit
fi
function Usage {
cat <<USAGE
Usage:
`b... |
d39690b09cf2937dcffaca146dbb2f7231c50f0359c68865b43c4aab06a5b9de | Shell | 10,056 | 269 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=10:00:00
#SBATCH --gres=gpu:1 ... |
9325eae93c1bae46515c9305d0b985cea36f0d276f670552544c7782ad60754e | Shell | 10,095 | 227 | #!/bin/bash
test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest
. ssshtest
set -o nounset
set -e
nim c -d:debug -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo --boundChecks:on -x:on src/slivar
set +e
exe=./src/slivar
run check_help_works $exe expr --help
assert... |
3c308c5f51eee44d3de928e91f91afe3691ab193bfd752378df5803291d320b9 | Shell | 10,262 | 355 | #!/bin/bash
if ! command -v antsRegistration &> /dev/null
then
echo "Cannot find antsRegistration. Please \(re\)define \$PATH in your environment."
fi
if ! command -v antsApplyTransforms &> /dev/null
then
echo "Cannot find antsApplyTransforms. Please \(re\)define \$PATH in your environment."
fi
if ! command -v a... |
d33fbfb1805a6e1e190cfc49b351d3da9f1ae7fdafad8d85971e1609abe92dfe | Shell | 10,874 | 264 | #!/bin/bash
# scaff10x 0.0.1
# Generated by dx-app-wizard.
#
# Basic execution pattern: Your app will run on a single machine from
# beginning to end.
#
# Your job's input variables (if any) will be loaded as environment
# variables before this script runs. Any array inputs will be loaded
# as bash arrays.
#
# Any cod... |
e101630abaae9c6d1aecd6e7d3e4213ba9759e011d167b2d0c1fd074d715fa45 | Shell | 11,058 | 257 | #!/usr/bin/env bash
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
1c01fbbb1d971501096baff0429802c343e88849ed2050939302b505ae720c71 | Shell | 11,841 | 382 | #!/bin/bash
VERSION="0.0"
if ! command -v antsRegistration &> /dev/null
then
echo "we cant find the antsRegistration program -- does not seem to exist. please \(re\)define \$PATH in your environment."
exit
fi
if ! command -v antsApplyTransforms &> /dev/null
then
echo "we cant find the antsApplyTra... |
08780e1f3754da7fc918702cb4549f5704e84be90c5cf1581debcebf0b813a8b | Shell | 12,049 | 346 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
0dcf016fa52dfa1dd65a05a4b201395c5a53b9b4534e6aa49a288f0eb7b81f9f | Shell | 12,050 | 352 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
207239d333d1a358447344b9fc4a58c9cbd9775d0de3b798db16e33632447549 | Shell | 12,370 | 357 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
4727ca6da258b1afaf562bfb7ad65fd32467604e15d47e8b25de3ebd06d49ca0 | Shell | 12,435 | 360 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
ee90dae95117164a38816e98355db72b3bc379df92d119d0523d4a78cf471dec | Shell | 12,487 | 221 | #!/bin/bash
# path to data
DATA_DIR=/home/goschv/CSB_NeuroRad2/goschv/DATA/Repro
cd $DATA_DIR
for s in CSB*
do
echo $s
mkdir $s/processed/algo
rm -r $s/processed/algo/1_run_pipeline1
mkdir $s/processed/algo/1_run_pipeline1
# This script combines ADC and TRACE information first by dividing them. Then the resu... |
fa79a62e87177281c0f6e044990110acbe7169f3723bdf190828181880c01537 | Shell | 12,614 | 342 | #!/bin/bash
# Run this script and fix *any* error before sending PR.
# For repeated runs, set the environment variables
# SKIP_DOWNLOADS=1 If files/uncompressed dirs exist don't download (if compressed files exist, just untar).
# SKIP_FULL_CLEAN=1 Don't remove anything downloaded/uncompressed.
LOG_FILE=/tmp/$$_pull_... |
4e7b2796a9f3eb5d99d6f426ad2ad2261d8e73aaa005c8a6c05c92779204cf97 | Shell | 12,980 | 362 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your... |
2221b8d191b4d30bf7848443f136f5a8c1285143f4a6838dce551e7730f01a26 | Shell | 13,351 | 463 | #!/bin/bash
# Usage: $0 imageDimension segmentationImage grayMatterProbabilityImage
# whiteMatterProbabilityImage outputImage
VERSION="0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
if ! command -v ANTS &> /dev/null
then
echo we cant find the ANTS program -- does not seem to exist. please \(re... |
8c06b997fb92c39e4fff51021f11675019daf1fb5130e941d606432f47d944b2 | Shell | 13,727 | 49 | # Original runs
asreview simulate data/brouwer_clean.csv -s simulation_output/nb_tf-idf.h5 --model nb --feature_extraction tfidf --n_queries min --seed 200 --n_prior_included 10 --n_prior_excluded 10 --init_seed 200
asreview simulate data/brouwer_clean.csv -s simulation_output/lr_tf-idf.h5 --model logistic --feature_e... |
4c31af2f0d00c78a3b45c17a4b8df06dd371ee786ca423e61ecda079d88aa2cb | Shell | 17,123 | 620 | #!/bin/bash
VERSION="0.0.0 test"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
ANTS=antsRegistration
#################
#
# default values
#
#################
DIM=3
FIXEDIMAGES=()
MOVINGIMAGES=()
INITIALTRANSFORMS=()
OUTPUTNAME=output
NUMBEROFTHREADS=0
SPLINEDISTANCE=26
LINEARGRADIENTSTEP=0.1
SYNGRADI... |
1b183b5365bc89821b5ec794090151cab4c8a305e262223041083a8aaf288819 | Shell | 17,837 | 626 | #!/bin/bash
VERSION="0.0.0 test"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
ANTS=antsRegistration
#################
#
# default values
#
#################
DIM=3
FIXEDIMAGES=()
MOVINGIMAGES=()
INITIALTRANSFORMS=()
OUTPUTNAME=output
NUMBEROFTHREADS=0
SPLINEDISTANCE=26
LINEARGRADIENTSTEP=0.1
SYNGRADIE... |
ed613d98f32df8ee09a315103547897e057a8875efdda5e26576b882fd21c87a | Shell | 17,982 | 413 | #!/bin/bash
usage=" $0 -d 3 -f fixed.nii.gz -m moving.nii.gz -t grouptemplate.nii.gz -b templatebrainmask.nii.gz -g f_auximage_tensor -n m_auximage_tensor -o output_prefix -h f_auximage_scalar -k m_auximage_scalar "
:<<supercalifragilisticexpialidocious
here is a first pass at an unbiased registration between an image... |
383df903da09fda8fe34aff938468dfd0cf5314904c7641c009b4a567cc61944 | Shell | 22,563 | 484 | #!/usr/bin/env bash
# configure.sh — one-stop configuration helper for the Baysor C++ build.
#
# Typical usage:
# ./configure.sh # detect deps, configure ./build (Release)
# ./configure.sh --build --install # ...and compile, install to ./install
# ./configure.sh --deps=conda --with-tests --b... |
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