sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
66ecf1b6cfed5430efc781bac350775fd73f13d4a181a42f45b4439d7b3f856b | Shell | 783 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
849a30af23fc42c2c4488f4fdde4565350b9bfdb0915c841dace75178a99867f | Shell | 788 | 31 | #!/bin/bash
if [[ -z $1 ]] ; then
echo "Usage: ./_submit_10x.sh <genome> [mean_cov]"
echo "Asset will run on aligned.bam from longranger and gaps.bed in this dir."
exit 0;
fi
if [ ! -e aligned.bam ]; then
echo "No \"aligned.bam\" found."
exit -1;
fi
genome=$1
mean_cov=$2
mkdir -p logs
#if [ ! -e 10x.bed ]; th... |
d23c3ae05d317bcda8e779aa064ee826b1c429ea9b227d7c2dda264f46be47cd | Shell | 789 | 27 | #! /bin/bash
[ $# -lt 1 ] && { echo 'Usage :
$1 : root directory
$2 : number of permutations (default 10000)
[$3 : prefix of the input file for randomise inside the subfolders]'; exit 1; }
dir=$1
if [[ ! $dir =~ /$ ]];
then
dir="$dir/"
fi
# randomise -i toto_filtered_4D.nii.gz -o toto_filtered_4D.nii.gz -d t... |
daeef0aa0c6818c2515852974dd6aeb81e014473ca87dd9ac1d0e7e3184363e6 | Shell | 791 | 24 | #!/bin/bash -l
#SBATCH --job-name=ali_to_anc
#SBATCH --output=ali_to_anc.out
#SBATCH --error=ali_to_anc.err
#SBATCH --partition=standard
#SBATCH --time=07-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=1
#Activate the topiary conda environment
source ~/miniconda3/bin/activate
export PA... |
b2163a8425a140506b02765a148fd9e4f1a0db2b9754d9a748462fc6eb78d42d | Shell | 793 | 31 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_nucmer.sh <ref.fasta> <qry.fasta>"
exit 0
fi
ref=$1
qry=$2
ref_prefix=`basename $ref`
ref_prefix=`echo $ref_prefix | sed 's/.fasta$//g' | sed 's/.fa$//g'`
qry_prefix=`basename $qry`
qry_prefix=`echo $qry_prefix | sed 's/.fasta$//g' | sed 's/.fa$//g'`
cpu... |
d49b041afd55eb96f8d6e830f2a1ff435257bdf6aa06177bd29c77fb419fe43d | Shell | 793 | 30 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_hybrid_scaffold_dle1.sh <name>"
echo -e "\t<name>: job name and output dir name"
echo -e "\tAssumes we have asm.fasta and DLE1.cmap in the same dir"
exit -1
fi
if [ -e $1 ]; then
echo "$1 already exists. Remove."
exit -1
fi
cpus=58
mem=980g
partition=large... |
3b6147c032bc8e794d60e850fc24aa057d6e925030c027674aec190a4d60dd67 | Shell | 800 | 27 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_cmap_assembly.sh <name> <bnx> <out> <xml>"
echo -e "\t<name>: job name"
echo -e "\t<bnx>: path to the bnx file"
echo -e "\t<out>: output folder for this bnx cmap assembly"
echo -e "\t<xml>: /bionano_path/RefAligner/7437.7523rel/optArguments_<haplotype>_<instr... |
210f1ed35c077c668c0b9ed2733de96a495b0a2bba194efbd083f1b2e37cb78b | Shell | 801 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
4b9c7ae14950ac0dc25ced1c834a9e39581d7c82cd12333e0d69d1aa28d2bd5b | Shell | 801 | 35 | #!/bin/bash
if [ -z $1 ] ; then
echo "Usage: ./longranger.sh <genome_id>"
echo "Assumes we have asm.fasta"
exit -1
fi
genome=$1
ref=asm.fasta
ref=${ref/.fasta/} ## if contains .fasta, remove it
if ! [ -e "refdata-$ref/genome" ] ; then
echo "No reference found"
echo "=== start indexing reference ==="
echo ... |
e71fba3ee53130036668749e831efb51cd1b5862980b19f013c6f6b54649b414 | Shell | 803 | 29 | #!/bin/bash
date_folder=$1
start_point=$2
next_step=$(($start_point + 1))
if [ -f "$date_folder/parameters.txt" ]; then
# this is a experiment folder
ProcessExperimentDirectory.sh $date_folder $start_point &
else
# this is not an experiment folder, repeat iteratively
# loop through all the directories in a date... |
e09c98b7a8523dcafcecfa342bbf1b5e22ca3a322d9a2b4defbb56cd99710a79 | Shell | 805 | 14 | #!/bin/bash
# This file contains the installation setup for running benchmarks on MAC.
set -ex
echo "Installing JMeter through Brew"
# Script would end on errors, but everything works fine
brew update
brew install jmeter
wget https://jmeter-plugins.org/get/ -O /usr/local/Cellar/jmeter/5.2.1/libexec/lib/ext/jmeter-pl... |
1a7f221b8cb5438a6e1cbaae197977586a7c1607238eba9181353becea17ccc3 | Shell | 806 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
c878813ff39871d4ae9a252013603f3099c9ffc0fc340fbc0918843e21da80c2 | Shell | 811 | 35 | #!/bin/bash
if [[ "$#" -lt 2 ]]; then
echo "Usage: ./nucmer.sh <ref.fa> <qry.fa>"
exit 0
fi
ref=$1 # ref.fasta
qry=$2 # qry.fasta
ref_prefix=`basename $ref`
ref_prefix=`echo $ref_prefix | sed 's/.fasta$//g' | sed 's/.fa$//g'`
qry_prefix=`basename $qry`
qry_prefix=`echo $qry_prefix | sed 's/.fasta$//g' | se... |
5d025a545cdcd3c9826bef31b49b85bb3df01874fab7c9e79b14e611805d7da3 | Shell | 813 | 26 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e asm.fasta ]] ; then
echo "Usage: ./_submit_scaff10x.sh <genome_id> [job_id_to_wait_for]"
echo "Requires asm.fasta, read-BC1.fastq and read-BC2.fastq"
echo "[job_id_to_wait_for]: Wait after the job finishes and launch"
exit -1
fi
mkdir -p logs
dependency=$2
if [ ! -z $depende... |
97ffbc12f07b65e59c842f7172eb28a68340af7c1d6f2badce3f05667ab7e384 | Shell | 813 | 26 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e asm.fasta ]] ; then
echo "Usage: ./_submit_break10x.sh <genome_id> [job_id_to_wait_for]"
echo "Requires asm.fasta, read-BC1.fastq and read-BC2.fastq"
echo "[job_id_to_wait_for]: Wait after the job finishes and launch"
exit -1
fi
mkdir -p logs
dependency=$2
if [ ! -z $depende... |
54bf66712af548f33d956afc25914fa9f98af047a8b1ca2f13a0479e72ee28a7 | Shell | 815 | 40 | #!/bin/bash
MACHINE=cpu
BRANCH_NAME="master"
for arg in "$@"
do
case $arg in
-h|--help)
echo "options:"
echo "-h, --help show brief help"
echo "-b, --branch_name=BRANCH_NAME specify a branch_name to use"
echo "-g, --gpu specify to use gpu"
exit 0
... |
db1cb6ac3190c4bc19689887759d656d745ff27e07dbf62f4188c61934b41d77 | Shell | 817 | 28 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./find_telomere.sh <fasta>"
exit -1
fi
file=$1
file_name=`basename $file`
if [ ! -e $file_name ]; then
ln -s $file
fi
file=$file_name
prefix=`echo $file | sed 's/.fasta$//g' | sed 's/.fa$//g'`
module load minimap2 # For sdust
$VGP_PIPELINE/telomere/find_telomere $fil... |
c7d344742f04b792de8d006caf31bbcefd0c4be31504eb1bbb03d585f2f6eb0f | Shell | 819 | 29 | #!/bin/bash
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.2 ...
module load R
#### Loading gcc 7.2.0 ...
#### Loading GSL 2.4 for GCC 7.2.0 ...
#### Loading openmpi 3.0.0 for GCC 7.2.0
#### Loading R 3.5.0_build2
export OMP_NUM_THREADS=$SLURM_... |
6a74e10ff14497f54a01eabfaaa4677217b7dd121f2771addb43dec0d54543df | Shell | 820 | 11 | onmt_average_models -output ./exp/USPTO-MIT_PtoR_aug5/average_model_230-239.pt \
-m exp/USPTO-MIT_PtoR_aug5/model.product-reactants_step_2300000.pt \
exp/USPTO-MIT_PtoR_aug5/model.product-reactants_step_2310000.pt \
exp/USPTO-MIT_PtoR_aug5/model.product-reactants_step_2320000.pt \
exp/USPT... |
a1f6518090731608abdaf5647233d18742418374bf1ceeb374d0a3f7c907badd | Shell | 820 | 36 | #!/bin/bash
if [ -z $1 ] ; then
echo "Usage: ./longranger.sh <genome_id> <lib>"
echo "Assumes we have asm.fasta"
exit -1
fi
genome=$1
lib=$2
ref=asm.fasta
ref=${ref/.fasta/} ## if contains .fasta, remove it
if ! [ -e "refdata-$ref/genome" ] ; then
echo "No reference found"
echo "=== start indexing reference ... |
c73a3c38d2a6fa4c9a62da86322bf7905ecba45eb53eaf49d723504327afb4da | Shell | 820 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
bc8d765803b9cf2f1f1aef2362151bc1d122571da47ef36821c2fed7a76d7b91 | Shell | 823 | 33 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_qv.sh <sample_id> [jobid_to_set_dependency]"
exit -1
fi
sample=$1
if ! [ -e aligned.bam ]; then
ln -s $sample/outs/possorted_bam.bam aligned.bam
ln -s $sample/outs/possorted_bam.bam.bai aligned.bam.bai
fi
mkdir -p logs
cpus=4
mem=4g
na... |
4f0e45a0d61cd35a1698458aca4579779af21aa75b6c6dc69089a7ca9c308b82 | Shell | 824 | 27 |
# BCI-HIL research framework start script.
# Suitable for the MacOS platform.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as your default web br... |
de6d6d357edbddf678a4b6946ccd643ace10761219b106d80343d00cbe9de4d4 | Shell | 829 | 27 |
# BCI-HIL research framework start script.
# Suitable for the MacOS platform.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as your default web br... |
3e98b7fe561b82f3460fc13842f7949cd76d9dafb447d0f4b8c905114db52f9d | Shell | 832 | 23 | #!/bin/bash
# In Nomine Functions Team
# distributed under license: GPL 3 License http://www.gnu.org/licenses/
SOURCE_FILE=$1 # File with preprocesed assembly code of functions
OUT=$2 # File where to write name predictions
MODEL=$3 # Path to the trained model
REFERENCE=$3 # Reference file to compute p... |
82e5bd9727c05c908c36b798586aaf36badc61fcb3c168c2071e5532f3808836 | Shell | 837 | 23 |
GENOME=/home/database/reference/hg38/hg38.fa.size
GENE=./eQTL/gencode.v39.annotation.gtf.pc.sorted.changed.bed.uniqGene.sorted.bed
TSS=./eQTL/gencode.v39.annotation.gtf.pc.sorted.changed.bed.uniqGene.sorted.bed.TSS.bed
python ./eQTL/getUniq_TSS.py $TSS $TSS\.uniq.bed
bedtools sort -i $TSS\.uniq.bed > $TSS\.sorted.be... |
4af3c148bfd7cb2e294b49517b634465261642a6599af5556f221875111ac5c6 | Shell | 840 | 18 | #!/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... |
d3968bcdca98e38f66c0d181f55d666e4119f1ae95776aca26e7521b525a52ce | Shell | 843 | 35 | #!/bin/bash
if [[ -z $1 ]] ; then
echo "Usage: ./_submit_hic.sh <name>"
echo " Run with an existing .bam file"
echo " Requires gaps.bed"
exit -1
fi
#export asset=$tools/asset
name=$1
mkdir -p logs
if [[ ! -e gaps.bed ]]; then
echo "No gaps.bed found. Exit."
exit -1
fi
if [[ ! -e hic.bed ]]; then
cpus=4
me... |
bfc45ccfc46ac7bf486bc56fb1c6859ea79d05c25d90ccd4db87318a2e31e260 | Shell | 850 | 18 | #!/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... |
1e5e96b6987d596332263d734b897a657a0350d2046211875b6854c41bebe71c | Shell | 853 | 35 | #!/bin/sh
name=$1
out=$2
bam=$name.bam
bed=$name.bed
if [ -z $name ]; then
echo "Usage: ./salsa2.sh <name>"
echo -e "\tSymlink re_sites.txt"
exit -1
fi
if ! [ -e $bed ]; then
module load bedtools
echo "bedtools bamtobed -i $bam > $bed"
bedtools bamtobed -i $bam > $bed
fi
source /data/Phillippy/tools/conda/et... |
b3cb312f602ca6ae46cd917fa4f1bc441ee546ee18bfbb3478dbcc8b041123ea | Shell | 855 | 27 |
# BCI-HIL research framework start script.
# Suitable for Linux/Ubuntu/Fedora/etc platforms.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as your... |
85842bbf137945fdc1e1a2cdd8b84d7bb64f0394b3614efcac89ffecc7c50c57 | Shell | 858 | 27 |
# BCI-HIL research framework start script.
# Suitable for the Linux/Ubuntu/Fedora/etc platforms.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as ... |
71e3960c19c78eb7406ce2798716465957dbe0f6aa64de64ce3c83267e0cf958 | Shell | 862 | 31 | #!/bin/bash
# Convert large CSV to Parquet chunks
python ./molbeam_fp/large_csv_to_parquet_chunks.py \
./molbeam_test/Enamine_REAL_strict_fragments_cxsmiles.cxsmiles.bz2 \
./molbeam_test/output_parquet_from_csv \
smiles \
idnumber
# Process SMILES to fingerprint Parquet
python ./molbeam_fp/process_smi... |
0d6afe3b208fe09d5e905a144443dfee702b919c2bac7b13a19fd73db73f3069 | Shell | 868 | 16 | #!/bin/bash
# Download data from https://doi.org/10.5281/zenodo.7265991 and place in here.
wget https://zenodo.org/record/7265991/files/ATF2_200.h5
wget https://zenodo.org/record/7265991/files/BACH1_200.h5
wget https://zenodo.org/record/7265991/files/CAGI_onehot.h5
wget https://zenodo.org/record/7265991/files/CTCF_200... |
c3d323a4eb7b9dafe8edd0c768c8ea1d9151a7ed4877bb68691382ee0f1f9c9d | Shell | 868 | 36 | #!/bin/bash
if [ -z $1 ] ; then
echo "Usage: ./longranger.sh <genome_id>"
echo "Assumes we have asm.fasta"
exit -1
fi
genome=$1
ref=asm.fasta
ref=${ref/.fasta/} ## if contains .fasta, remove it
if ! [ -e "refdata-$ref/genome" ] ; then
echo "No reference found"
echo "=== start indexing reference ==="
echo "\
... |
fb365a79c4b6dc566d75ed942d933b472b49e8e64f221a0084c638aa26b7a60d | Shell | 871 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
e60fa77fdc3958f78d21444d971eae4a87712fd1a383afdd64770425d1e4b05b | Shell | 874 | 30 | #!/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... |
aa3d631ee7e933e585956399f3c607745ac1f0100f5b4b0b54b0a98dbc65f4ad | Shell | 878 | 31 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_hybrid_scaffold_dle1.sh <name>"
echo -e "\t<name>: job name and output dir name"
echo -e "\tAssumes we have asm.fasta and DLE1.cmap in the same dir"
exit -1
fi
if [ -e $1 ]; then
echo "$1 already exists. Remove."
exit -1
fi
cpus=58
mem=980g
partition=large... |
3b1419de21afa26e6a8da3fcad6bdc86d6f36a7a4f97d6257543ff816f5c0b8a | Shell | 879 | 29 | #!/bin/bash
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.2 ...
module load R
#### Loading gcc 7.2.0 ...
#### Loading GSL 2.4 for GCC 7.2.0 ...
#### Loading openmpi 3.0.0 for GCC 7.2.0
#### Loading R 3.5.0_build2
export OMP_NUM_THREADS=$SLURM_... |
c9506a10958829e4ca5c280f26508b74f34308872364b9c89cc45b596a6957c5 | Shell | 883 | 41 | #!/bin/bash
name=$1
ENZYME=$2
BMAP=$ENZYME.cmap # DLE1.cmap
ASM=asm.fasta # ln -s to the asm.fasta
CONFIG=$3
RefAligner=$tools/bionano/Solve3.3_10252018/RefAligner/7915.7989rel/avx/RefAligner
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.2 ...
modul... |
080bb24c64ff6628b160f1d9d758374f427ad6c4b0c6abc623cee6dd518daf1d | Shell | 885 | 14 | #gmx editconf -f thyroglobulin_cg.pdb -d 2.5 -bt cubic -o thyroglobulin_cg_box.gro -c yes
#gmx grompp -p topol.top -f minimization.mdp -c thyroglobulin_cg_box.gro -o minimization-vac.tpr
#gmx mdrun -deffnm minimization-vac -v
#gmx solvate -cp minimization-vac.gro -cs water.gro -radius 0.21 -o solvate.gro -p topol.top... |
8b9dca8b821b5fb8ae1382402c0970ba85f2982e629a0c8e870aa50957c47137 | Shell | 886 | 22 | #!/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... |
e48e0696b82b3369193eb261b3fe2124e16cec637513ce3009a717a8d08eeba9 | Shell | 887 | 18 | #!/bin/bash
echo "Usage: \n sh weightedaverage.sh \"Faces*tiff\" \n "
count=9
for x in `ls -tr $1 `
do
count=`expr $count + 1` # Increment the counter
echo " count is $count and file is $x at it $i "
ANTS 2 -m PR[ template.nii,$x,1,8,-0.9 ] -t SyN[ 3 ] -r Gauss[ 3,1.5 ] -o ROBU{$count} -i 22x... |
210be7043fad593d1686d671a199acbe508bdaebc8743a1734f55258952edd4d | Shell | 895 | 51 | #!/bin/bash
# path to data
for DATA_DIR in /home/goschv/CSB_NeuroRad2/goschv/DATA/Repro
do
cd $DATA_DIR
for s in CSB*
do
echo $s
mkdir $s/processed
# DCM to nii0
dcm2niix_afni $s
# fslsplit
fslsplit $s/*_3.nii $s/
# rename fslsplit b0 image
mv $s/0000.nii.gz $s/b0.nii.gz
# gzip
gzip $s/*.nii
# b... |
111c48a4471af33a260f79d167f3519e9319309975ace29fbbf094c8bd865e2f | Shell | 897 | 26 | ENVNAME="cnmodel_venv"
python3 -m venv $ENVNAME
source $ENVNAME/bin/activate
pip install --upgrade pip # be sure pip is up to date in the new env.
pip install wheel # seems to be missing (note singular)
pip install cython
# # if requirements.txt is not present, create:
# # pip install pipreqs
# # pipreqs
#
# #Then:
#... |
1c945a41e5875f6f4383d13b68178c8b16df1d4a2ffe80690b61eedf9a1c5a3e | Shell | 898 | 41 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./minimap2 <ref> [num_line num_cpus]"
echo " Assumes we have <ref> and <input.fofn> in the same dir"
exit -1
fi
module load minimap2/2.17
module load samtools
ref=$1
ref=`echo $ref | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
... |
d9d5bcc07035164c69ba12c9376f40a26d0dfdb38a2b3539c71a61e7509bd65d | Shell | 900 | 22 | #!/bin/bash
##Provide an input file name (the query sequences) to the first position and the desired name of the outputfile to the second
##This is the same as the original submit_blast_mito.sh except the num_alignments and coverage parameters have been removed so I can
##get a look at the whole output.
inputfilen... |
f26ab97da13177d38e245e589ef422fa3e0b26d8f8ad1919d585498ab75e2cf3 | Shell | 903 | 26 | ENVNAME="cnmodel_venv"
python3 -m venv $ENVNAME
source $ENVNAME/bin/activate
pip install --upgrade pip # be sure pip is up to date in the new env.
pip install wheel # seems to be missing (note singular)
pip install cython
# # if requirements.txt is not present, create:
# # pip install pipreqs
# # pipreqs
#
# #Then:
#... |
086ca0990335a93d6af9efa65b4b66b33e2c530e8e0cc5f46adf2229caf717c1 | Shell | 908 | 30 | #!/bin/bash
asm=$1
if [ -z $asm ]; then
echo "Usage: ./trimNs.sh <asm.fasta>"
exit -1
fi
echo "Start running trim-N process on $asm"
name=`echo $asm | sed 's/.fasta$//g' | sed 's/.fa$//g'`
module load python/3.5
echo "
python3 $VGP_PIPELINE/bionano/trimNs/remove_fake_cut_sites_DNAnexus.py $asm $name.rmFake.fast... |
cc6b1028547c7e9aaebd04f580c3125e1fac4347fe6b852184bb03cec8e081c5 | Shell | 908 | 41 | #!/bin/bash
name=$1
ENZYME=$2
BMAP=$ENZYME.cmap # DLE1.cmap
ASM=asm.fasta # ln -s to the asm.fasta
CONFIG=$3
RefAligner=$tools/bionano/Solve3.2.1_04122018/RefAligner/7437.7523rel/avx/RefAligner
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.4 ...
mod... |
5bade40c9c91814f168a2d14670a970775905bc939e8beb3ccd921447391ceaf | Shell | 909 | 35 | #!/bin/sh
# BUILD THE MAN PAGES
INPUTDIR=input
OUTPUTDIR=man
HEADERFILE=${INPUTDIR}/ESTate.header.man
FOOTERFILE=${INPUTDIR}/ESTate.footer.man
mkdir $OUTPUTDIR
mkdir ${OUTPUTDIR}/man1
mkdir ${OUTPUTDIR}/man7
ls -1 ${INPUTDIR}/*.[17] | while read FILENAME
do
MANPAGENAME=`basename $FILENAME`
echo Building ma... |
493503fcc4d4040aa7a670f0ed0217542d9956a31bc72bee19e11bda0a4cf01d | Shell | 910 | 28 | #!/bin/env bash
#
#SBATCH -p all # partition (queue)
#SBATCH -c 6 # number of cores
#SBATCH -t 30
#SBATCH -o logs/array_jobs/step1_%A_%a.out # STDOUT #add _%a to see each array job
#SBATCH -e logs/array_jobs/step1_%A_%a.err # STDERR #add _%a to see each array job
#SBATC... |
f19d13d9bbb862f3d43167d22d116481b43ed4e3c99502d32ddca388d88a41c4 | Shell | 912 | 31 | #!/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... |
94b2934a97b87413dd2f74c9bb5db665d0af1afe1b39082dbbd2634ab76f7b9d | Shell | 913 | 37 | #!/bin/bash
if [ -z $SLURM_ARRAY_TASK_ID ]; then
i=$2
else
i=$SLURM_ARRAY_TASK_ID
fi
out_prefix=$1
r1=`sed -n ${i}p input.fofn`
r2=${r1/R1_001/R2_001}
if ! [[ -e $out_prefix.r1.$i.fastq && -e $out_prefix.$i.name ]] ; then
if [[ "$r1" =~ \.gz$ ]]; then
gunzip $r1
r1=${r1/.gz/}
fi
echo "scaff_BC-reads-1 $r1... |
6fea912f9c126dd04c6efe5e5fec21d9d2bd2a9b2b9b17067379976259d2dc4f | Shell | 916 | 45 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: map_hic.sh <asm.fasta> <input.fofn> [line_num num_cpus]"
echo -e "\tinput.fofn: tab delimited file for R1 and R2 reads. ex. R1.fastq.gz\tR2.fastq.gz"
echo -e "\t[line_num]: line num. to proceed in <input.fofn>"
echo -e "\t[num_cpus]: num. cpus used (if not running on SLU... |
1c2edea8a32bfa9a3deaddb0597ff514a62866cfcfe04560a7c0b563b9e7ece5 | Shell | 920 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
a4360f8f28127d7d1df3f378ef0def3818016b9218c2eb15e8b3d92aaa55df0b | Shell | 922 | 34 | #!/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... |
73c101064bb89293d7d1100206fb755c85e5b64235960dc1089d6a45d2784cdd | Shell | 925 | 24 | #!/bin/bash
# Copyright 2021 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... |
ab38475a0d379af3aa2f458972b8de41cc548de8b06a6046666e0737cc9f7cd9 | Shell | 927 | 26 | # Example:
# scripts/process_gbcIV.sh run all
#
proto="runIV"
#######################################################
# 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.
########################################... |
5e2d83f3dd13c09649103f66d7cc545afd8475dbfde8169d6ead0c2274deb94c | Shell | 929 | 25 |
# BCI-HIL research framework start script.
# Suitable for Linux systems using GNOME.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as your default... |
892865933542f6d3a885cfad17e5d30cb6910930e17f29c4b5760548fbfda07e | Shell | 930 | 25 |
# BCI-HIL research framework start script.
# Suitable for Linux systems using GNOME.
# Please make sure that your Python environment is setup before running this script
# This is done with something like "conda activate your_virtual_environment"
# Also, this script assumes that Google Chrome is setup as your default... |
e5a02eff3fcf25e4ff51eae50262ec0ac83457b231f5f68fbd36be5b38273eb4 | Shell | 931 | 35 | #!/bin/bash
# Helper script to download and install sktime from test PyPI to check wheel
# and upload prior to new release
set -e
# Version to test, passed as input argument to script
VERSION=$1
# Make temporary directory
echo "Making test directory ..."
mkdir "$HOME"/testdir
cd "$HOME"/testdir
# Create test envir... |
558a425ace12f48774f2d6b79fe0de71c4c9bbaa83c4d912686b0bc242a6e8b9 | Shell | 934 | 41 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ast.sh <out_prefix> [mean_cov]"
exit -1
fi
prefix=$1
mean_cov=$2
postfix=""
if [[ ! -z $mean_cov ]]; then
mean_cov=`echo $mean_cov | awk '{printf "%.0f\n", $1*2.5}'`
mean_cov="-M $mean_cov"
postfix="_M"
fi
#export asset=$tools/asset
pafs=`ls *.paf`
bed=pb${... |
8f58e87ecafe68adc87bb2fe1fcf8ede09ecbfe745aca975fdbffe2a32d54e28 | Shell | 935 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
a5aafc43b6d6ef8f48d411506bbb2464c35548f084a2d5a284eb5f90554249d1 | Shell | 937 | 47 | #! /bin/bash
echo 'Running all tests ...'
echo 'Running linter ...'
# check lint
npm run lint &> check_all_lint.log || exit
echo 'Linter complete.'
echo 'Running unit tests ...'
# unit test
NODE_ENV=test npm run test &> check_all_test.log || exit
echo 'Unit tests complete.'
echo 'Running server tests ...'
cd depl... |
b2e016f2e63a5906070ff47d4961c329fd44abf011671628b15d5841c068b624 | Shell | 941 | 11 |
TRACK_PATH=/home/disk/database/data/ICS_scHIC/f01_frontalCortex/tracks/
#nohup hicPlotTADs --tracks $TRACK_PATH\/track_NE.ini -o $TRACK_PATH\/figure_track_cortex_1_NE.png --region chr18:68682623-71733016 --dpi 300 &
#nohup hicPlotTADs --tracks $TRACK_PATH\/track_NI.ini -o $TRACK_PATH\/figure_track_cortex_2_NI.png --... |
b5423ec4083f7edb8ac7be09b0d3918a6763571aa30e73627a3f4c770a4c0ee7 | Shell | 943 | 43 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./minimap2 <ref>"
echo " Assumes we have <ref> and <input.fofn> in the same dir"
exit -1
fi
module load minimap2/2.17
module load samtools
ref=$1
ref=`echo $ref | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g'`
preset="$3"
if [ -z ... |
6719fbfd3bcc333bea3c3525853f13fc832075cb8c96bd9e014f15617fb4239e | Shell | 944 | 16 | #!/usr/bin/env bash
if [[ -z ${POKER_GAME_VERSION+x} ]]; then echo "POKER_GAME_VERSION is unset" && exit 1; else echo "POKER_GAME_VERSION is set to '${POKER_GAME_VERSION}'"; fi
if [[ -z ${POKER_GAME_PORT_PREFIX+x} ]]; then echo "POKER_GAME_PORT_PREFIX is unset" && exit 1; else echo "POKER_GAME_PORT_PREFIX is set to '$... |
325e18603070d89786243266c0096a4bda2fca014d2cbc16f61c850196942af0 | Shell | 956 | 45 | #! /bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]]; then
echo "Usage: ./_submit_kat_comp.sh <asm.fasta>"
echo "<asm.fasta>: Assembly fasta file"
echo "<input.fofn>: Full path to the fastq files"
exit -1
fi
asm=$1
input=input.fofn
for file in $(cat $input)
do
# read-BC[1-2].fastq.gz
file_name=`basename $file ... |
fbcc33197c42d663114e7b43f8a22f2a31f5ec1834b1e5a5d071e02ffdb2e8e7 | Shell | 965 | 50 | #!/bin/bash
# proc10xG 0.0.1
set -x -e -o pipefail
main() {
echo "Value of asm: '$input_fastq'"
dx-download-all-inputs --parallel
mv in/*/*/*.fastq.gz .
for e in ${input_fastq_name[@]}; do
echo $e
if [[ $e == *"R1"* ]]; then
echo $e >> fw.ls
elif [[ $e == *"R2"* ]]; then
... |
95d3176c6c0e1a0b80aaaa203f4676ad2909120d1b1a66eeb3ff6c7ced248e13 | Shell | 969 | 13 | dataset=USPTO50K-aug-typed
python ../../onmt/bin/train.py --data ../../data/${dataset}/${dataset} \
--save_model ../../experiments/checkpoints/${dataset}/${dataset}_model \
--seed 42 --world_size 2 --gpu_ranks 0 1 --save_checkpoint_steps 10000 --keep_checkpoint 10 \
--train_steps 300000 --param_init 0 --... |
1dbcb72268d9782c389d18072f25cff32a62cd4b3f9bc99b6e862245d2adcc23 | Shell | 970 | 21 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
gln_seed=$1
python gen_proposals/gen_union_or_clean_proposals.py \
--log_file gln_50_${gln_seed}_retrosim_50 \
--proposed_smi_file_prefixes GLN_200t... |
ddf555141846ba16eb3d6d05b12600920a3dffa254a9976480eeb9e88f1c426d | Shell | 974 | 22 | #!/bin/bash
if [[ $# -lt 3 ]] ; then
echo read script before using
echo $0 segmentationimage outputname thresholdlevel
echo e.g. $0 seg.nii.gz gm 2
exit
fi
TEM=$1
nm=$2
ThresholdImage 3 $TEM ${nm}_topo.nii.gz $3 $3
ImageMath 3 ${nm}_topo.nii.gz MD ${nm}_topo.nii.gz 1
ImageMath 3 ${nm}_topo.nii.gz ME ${nm}_... |
f26b76c3cdd7766ad60bd71eccc3e5ae73472fa8f88c5d956249ae7a96dbec4b | Shell | 981 | 30 | #!/bin/bash
# In Nomine Functions Team
# distributed under license: GPL 3 License http://www.gnu.org/licenses/
DATA_FOLDER=data/ubuntu_all_data/
TRAIN_SRC=$DATA_FOLDER/ubuntu_ds_train.asm
TRAIN_TGT=$DATA_FOLDER/ubuntu_ds_train.name
VALID_SRC=$DATA_FOLDER/ubuntu_ds_validation.asm
VALID_TGT=$DATA_FOLDER/ubuntu_ds_vali... |
3d61fd586d5661d0f16b56d6ad414b851afcb581375f3764110e405e6fe4da52 | Shell | 984 | 28 | #!/bin/bash
# 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 require... |
a1f0868601f92a11c2b586438f1aa46371a296f21d356e14aa6aaf8d3ab44ab9 | Shell | 989 | 38 | #!/bin/sh
# CONVERSION OF MAN PAGES TO HTML
# CHANGES OUTPUT FROM man2html A BIT.
# YOU NEED TO HAVE man2html IN YOUR PATH FOR THIS TO WORK.
STARTDIR=`pwd`
RESULTDIR="html"
INEXPR1='http://localhost/cgi-bin/man/man2html?[1-9]+'
OUTEXPR1='http://www.hgmp.mrc.ac.uk/~gslater/estateman/'
which man2html > /dev/null
if ... |
e3c5e7d38e889cf685b39dd184e336169ea64876e8c7e0c4adc45d267e672381 | Shell | 992 | 21 | #!/bin/bash
count=0
for x in phantomA phantomB phantomC phantomD phantomE phantomF phantomG phantomH
do
count=`expr $count + 1` # Increment the counter
echo " $x "
echo " LaplacianThickness ${x}wm.hdr ${x}gm.hdr 15 TEST{$count}thick.hdr 1 0.5 "
ThresholdImage 2 ${x}wmgm.jpg ${x}wm.nii 245 290
... |
766695e71752523a67a9ccf1713718f43a06c9dafb936f1644e0adabf3f4af27 | Shell | 995 | 36 | #!/bin/bash
#BSUB -M 500000
#BSUB -W 12:00
#BSUB -n 12
#BSUB -R "rusage[mem=500000] span[hosts=1]"
#BSUB -J rsem_quant
#BSUB -o rsem_quant.out
#BSUB -e rsem_quant.err
module load RSEM/1.3.0
BAM_folder='/data/aronow/Kang/induced_neuron/ChangHui_RNAseq_fastq/isoform_RSEM/star_align/BAM_transcripts/'
BAM_file='Aligned.... |
d3e288c91e8e6e3d85eced3b5236d8fa8d3e0e2e0e7ac5145fd510568e732783 | Shell | 995 | 32 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_telomere.sh <in.fasta>"
echo
echo "This script submits telomere_analysis.sh genome 0.4 50000 <in.fasta>"
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... |
7a14fa776d9739e31571e459b6a3e7b5e1cbe2d200be998dacbe29840f489757 | Shell | 998 | 28 | #!/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... |
d02f73f42a2f994ea2e441da8ce0a78c6bd5e8e164482bc6c884d70985f8cdd8 | Shell | 1,000 | 29 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate neuralsym
# cannot use too high LR, will diverge slowly (loss increases > 20)
# higher bs --> faster training (using CPU)
# 8 sec/epoch on 1 RTX2080Ti
sym_seed=$1
... |
d9ff80271117a29334edacaf165ba1d06bc582ad99cab6ba16fdbf92fefa86b8 | Shell | 1,003 | 35 | #!/bin/bash
CONFIG="toml/autoscale_multisite_0dB_parallel.toml"
RUNTEXT="running the individual initialization and running AN PSTH protocols"
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
TABLES="data_XM13A_nacncoop_normal data_XM13A_nacncoop_pasdend data_XM13A_nacncoop_actdend"
EXPERIMENT="all" # all=mean max=mean removel... |
3111a09ed1bb1dc0ba88fd8a561232d4a4a7a2bc8eab291088f74dc5753ef5b7 | Shell | 1,008 | 32 | #!/bin/sh
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... |
9d575042592924e1670ebc651ab5a391823177abbbaf1e2fd025cbae8fb1c467 | Shell | 1,008 | 23 | #!/bin/bash
while IFS=$'\t' read -r species id
do
mkdir -p $id
aws s3 cp --exclude "*" --include "*_MT_extracted_reads/${id}.fastq*" --recursive s3://genomeark/species/${species}/${id}/assembly_MT_rockefeller/intermediates/ $id
aws s3 cp --exclude "*" --include "mtDNA_*.fasta" --recursive s3://genomeark/species/${s... |
ac9dfb419addc546479faa742b68ae38887da68433c83ebc6ae6cde1cfde4c68 | Shell | 1,008 | 28 | TORCH_VER=1.6.0
CUDA_VER=10.1
CUDA_CODE=cu101
source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda create -y -n openretro_cu101 python=3.6 tqdm
conda activate openretro_cu101
conda install -y pytorch=${TORCH_VER} torchvision torchaudio cudatoolkit=${CUDA_VER} -c pytorch
conda install -y rdkit -c r... |
22e37fdf07e28574794256ff36c572c0c61277ece516276159559f3db3593f1b | Shell | 1,009 | 35 | #!/bin/bash
CONFIG="toml/autoscale_multisite_40dB_parallel.toml"
RUNTEXT="running the individual initialization and running AN PSTH protocols"
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
TABLES="data_XM13A_nacncoop_normal" # " data_XM13A_nacncoop_pasdend data_XM13A_nacncoop_actdend"
EXPERIMENT="all" # all=mean max=mean r... |
c34de866aa85d57b7b7297098719c828bbd6de47c9c7dc0490f9c8be53347e11 | Shell | 1,009 | 32 | #!/bin/bash
arg_input_evd_plot_feat_base=$1
arg_input_working_dir=$2
arg_input_query_id=$3
arg_output_file=$4
MYOWN_LOC=`dirname $0`; # XXX: some hacking:)
c_fetch_blast_report="$MYOWN_LOC/fetch_blast_report_by_index.pl"
c_extract_orf_seq_by_ids="$MYOWN_LOC/extract_orf_sequence_by_ids.pl"
blastx_report=$arg_input... |
f4b50fa911380b2bb2370239e74fbb6cb632780a29b101eb2ec3e550edd47389 | Shell | 1,009 | 34 | #!/bin/bash
if [[ "$(dirname "$0")" != "." ]]; then
echo 'Please change to the folder containing this script before execution. Exiting...'
exit
fi
# remove old api docs
mv source/index.rst source/index
mv source/readme.rst source/readme
rm -f source/vp_suite*.rst
mv source/index source/index.rst
mv source/readme ... |
7e756a0b2c988ba8ee72662627528890a8ad3cab07b84c6eac2ac6f28a0ebd3d | Shell | 1,010 | 37 | #!/bin/bash
BMAP=DLE1.cmap # DLE1.cmap
ASM=asm.fasta # ln -s to the asm.fasta
CONFIG=/data/Phillippy/tools/bionano/Solve3.2.1_04122018/HybridScaffold/04122018/hybridScaffold_config.xml
RefAligner=/data/Phillippy/tools/bionano/Solve3.2.1_04122018/RefAligner/7437.7523rel/avx/RefAligner
name=$1
module load python
#### P... |
9adff2df1352cf9778f60c7dd79029a1fae42536f6d0dcc77d7ef9f9b6166a1f | Shell | 1,012 | 37 | #!/bin/bash
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.2 ...
module load R
#### Loading gcc 7.2.0 ...
#### Loading GSL 2.4 for GCC 7.2.0 ...
#### Loading openmpi 3.0.0 for GCC 7.2.0
#### Loading R 3.5.0_build2
export OMP_NUM_THREADS=$SLURM_... |
51a34916839fc402acbfd8c3b0a20af298ad102f226cbf423117198fed4a5034 | Shell | 1,013 | 21 | #!/bin/bash
CONFIG="autoscale_multisite_parallel.toml"
RUNTEXT="running the individual initialization and running AN PSTH protocols"
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
DENDRITES="Full"
REPS=50
for f in $CELLNAMES
do
for d in $DENDRITES
do
python vcnmodel/model_run2.py VCN_c$f -D $d -P... |
6d0dc05713aeb366c86ea88b05973d663096761974933f372da3ce63bffdee9f | Shell | 1,015 | 37 | #!/bin/bash
BMAP=DLE1.cmap # DLE1.cmap
ASM=asm.fasta # ln -s to the asm.fasta
CONFIG=/data/Phillippy/tools/bionano/Solve3.2.1_04122018/HybridScaffold/04122018/hybridScaffold_DLE1_config.xml
RefAligner=/data/Phillippy/tools/bionano/Solve3.2.1_04122018/RefAligner/7437.7523rel/avx/RefAligner
name=$1
module load python
#... |
942bcc2b99986a6fa77ef6e359bc6c0a79e00526481b746ca5812d05ff07b27d | Shell | 1,015 | 41 | #!/bin/bash
#CONFIG="noscale.toml" #"autoscale.toml"
CONFIG="--configfile singles_multisite_parallel.toml"
RUNTEXT="running the AN Single protocols NoDendrites"
# sequentials:
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
TABLES="data_XM13A_nacncoop_normal" # " data_XM13A_nacncoop_pasdend data_XM13A_nacncoop_actdend"
DEN... |
4ade820b22453e33157c1b880bf606928b8b0e2237fc82d16263300c788f3764 | Shell | 1,018 | 58 | #!/bin/bash
#$ -S /bin/bash
dir=$1
cmd=$2
para=$3
naming=$4
fixname=$5
movingname=$6
echo $6
opta=$7
echo $7
optb=$8
echo $8
optc=$9
echo $9
optd=${10}
echo ${10}
opte=${11}
echo ${11}
optf=${12}
echo ${12}
optg=${13}
echo ${13}
opth=${14}
echo ${14}
opti=${15}
echo ${15}
optj=${16}
echo ${16}
optk=${17}
echo ${17}
op... |
69f3a68be27298d59a61007a9e2ce6c91798427566db3c97521e6c9e91415bc0 | Shell | 1,019 | 21 | #!/bin/bash
CONFIG="autoscale_multisite_parallel.toml"
RUNTEXT="running the individual initialization and running AN PSTH protocols"
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
DENDRITES="Full"
REPS=50
for f in $CELLNAMES
do
for d in $DENDRITES
do
python vcnmodel/model_run2.py VCN_c$f -D $d -P... |
8e2beaef97bdc46abef3653257f2e06be91873f06b24932dddf3777c78f2b321 | Shell | 1,020 | 32 | #! /bin/bash
ANTSPATH=$1
if [ ${#ANTSPATH} -lt 3 ] ; then
echo usage
echo $0 PATH_TO_ANTS_BINARIES image_to_label.nii.gz
exit
fi
if ! command -v ants.sh &> /dev/null
then
echo you need the file ants.sh - exiting
exit
fi
Image_To_Be_Labeled=$2
if [[ ! -s $Image_To_Be_Labeled ]] || [[ ${#Image_To_Be_Labeled} -lt ... |
ee858efe24c60fdef3380130ab85b564baa6a7547dfa0363629e42c0a0c3e565 | Shell | 1,022 | 24 | #!/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... |
df4e389798a639e4a186b283e3e3e0180796ab320834097fedee3df99d730f84 | Shell | 1,024 | 49 | #!/bin/bash
if [[ -z $1 ]] || ! [[ -e input.fofn ]] ; then
echo "Usage: ./_submit_juicer.sh <ref.fasta>"
echo "Assumes input.fofn in the same path"
echo "input.fofn should have reads with *_R1 and *_R2"
exit -1
fi
ref=`realpath $1`
# Create reference dir
if ! [ -e reference/asm.fasta ]; then
mkdir -p reference
... |
2b3cf94733aceee1d477e1af3ace1db192aae2733451f0d22dcfe5e6472a22c1 | Shell | 1,028 | 50 | #!/bin/bash
# repeat_mito 0.0.1
set -x -e -o pipefail
main() {
echo "Value of asm: '$mito_asm'"
dx download "$mito_asm" -o mito_asm
file_type=$(file mito_asm | grep -Po ': \K[^ ]+' | head -1)
if [[ $file_type == "ASCII" ]]; then
mv mito_asm mito_asm.fasta
elif [[ $file_type == "gzip" ]]; t... |
5b1585830673824d327db92544bf70b028cb749bbae0d010458a23fe16cbf3e5 | Shell | 1,032 | 41 | #!/bin/bash
#CONFIG="noscale.toml" #"autoscale.toml"
CONFIG="--configfile singles_autoscale_multisite_parallel_test.toml"
RUNTEXT="running the AN Single protocols Full"
# sequentials:
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
TABLES="data_XM13A_nacncoop_normal" # " data_XM13A_nacncoop_pasdend data_XM13A_nacncoop_actd... |
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