sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ccefac206d75dc5ec0ecf5fceebe3dc6c1a8737578eb14b0de2eddd316f96336 | Shell | 2,124 | 69 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./qv_subset_asm.sh <genome_id> <fasta.fai>"
echo -e "\tExtract variant calls for <fasta.fai> and get the QV only for those"
exit -1
fi
genome=$1
fai=$2
hap=${fai/.fai/}
hap=${hap/.fasta/}
threads=$SLURM_CPUS_PER_TASK
if [ -z $threads ]; then
threads=2
fi
echo "Load mo... |
3a9ff8324ca19ac33397d082ae0e490aaa4af69587cc3d3cef37ca73e3572bec | Shell | 2,138 | 45 | #!/usr/bin/env bash
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
./build.sh
VOLUME_SUFFIX=$(dd if=/dev/urandom bs=32 count=1 | md5sum | cut -c 1-10)
DOCKER_FILE_SHARE=picai_baseline_nnunet_semi_supervised_processor-output-$VOLUME_SUFFIX
docker volume create $DOCKER_FILE_SHARE
# you can see your output (to debug ... |
95ac35d7cc7e87e2a9a899e993447793625305f2eaf25306e48427ad8eef0f53 | Shell | 2,141 | 45 | #!/bin/bash
gro_file="../ionized.gro"
top_file="../topol.top"
top_root_dir=$(dirname $(readlink -f $top_file))
psf_file="../R352Q.psf"
pdb_file="../R352Q.pdb"
mkdir -p psf_buildfiles
#grab only the section that contains roots of topol.itp files, ignore comments and include statements
list_itp=$(cat $top_file | awk... |
ca42d7ca9ee5e87dcc723661b321e29d2fef19f34c74d2699ac0e8c136156cd8 | Shell | 2,141 | 68 | #!/usr/bin/env bash
#==========================================================================
#
# Copyright Insight Software Consortium
#
# 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 ... |
3465f9296e5d5cfa5d1308669fd951f27aa450c8152c319745aaf6f057be5063 | Shell | 2,157 | 62 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]] ; then
echo "Usage: ./_submit_minimap2.sh <ref.fasta> [genome_cov]"
echo -e "\tAssumes <input.fofn> in the same path"
echo -e "\t[genome_cov]: set ast_pb -M to genome_cov*2.5"
exit -1
fi
ref=$1
ref=`echo $ref | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fast... |
394a9f045b9f0b9daeeed96ad142ade3e5d707107824c241310a9aa09c89f9b6 | Shell | 2,160 | 74 | #!/bin/bash
# Bulk KR extraction: 4 cell lines × 22 chromosomes = 88 dense .txt matrices.
# Run from inside the `axialtad` conda env (see README for setup).
set -uo pipefail
: "${AXIALTAD_ROOT:?Please set AXIALTAD_ROOT to your working directory}"
ROOT="${AXIALTAD_ROOT}"
HIC_DIR=$ROOT/data_4dn
OUT_DIR=$ROOT/matrix_kr_... |
3d22bced41d29c177ae315d4208e93abc5a2b213b59b0cc181d1087181b9fed6 | Shell | 2,162 | 68 | #!/bin/bash
if [ $# -lt 7 ]
then
echo " USAGE \n sh command.sh fixed.nii fixedhipp.nii moving.nii movinghipp.nii outputname iterations DIM "
echo " the template = fixed.nii , the individual = moving.nii "
echo " iterations should be of the form 100x100x10 "
exit
fi
if ! command -v ANTS &> /dev/null
then
echo... |
cdc0586a3da66d7eda97fdeac8d3a030f095da9fc3fd5c79c8115c86583dfc74 | Shell | 2,166 | 33 | # dataset=USPTO50K-aug-untyped
seed=$1
dataset=USPTO50K-aug-untyped_${seed}
dataset_prefix=USPTO50K-aug-untyped
source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate retroxpert_
python3 ../../onmt/bin/train.py --data ../../data/${dataset}/${dataset_prefix} \
--save_model ../../experim... |
44241dd94281bdd93045160a3df45e8412839aa85f0086302af369b760eb59f4 | Shell | 2,167 | 65 | #!/bin/bash
echo "Usage: ./purge_haplotigs.sh [manual_peaks]"
if [ -e $1 ]; then
echo "$1 detected. Use values in this file for l m h."
l_cutoff=`sed -n 1p $1 | awk '{print $1}'`
m_cutoff=`sed -n 2p $1 | awk '{print $1}'`
h_cutoff=`sed -n 3p $1 | awk '{print $1}'`
fi
module load purge_haplotigs/0~201... |
5137bed0f9a9b28ce64e87afb4b1905df4835cd52e49b83e73bad5366aa21e0b | Shell | 2,169 | 69 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]] ; then
echo "Usage: ./_submit_bwa.sh <ref.fasta> [jid]"
echo -e "\t<ref.fasta>: no gz!"
echo -e "\tAssumes <input.fofn> and gaps.bed in the same path"
echo -e "\t[jid]: set --dependency=afterok:[jid]"
exit -1
fi
#export asset=$tools/asset
ref=$1
ref=`basename ... |
0e95eca7d3ad90394386fd6af72553c5399da6487163be5513d0eb694a75885f | Shell | 2,179 | 140 | #!/bin/bash
set -e
if [ -z $1 ]; then
echo "use $0 -h for help"
exit 0
elif [ $1 == "-h" ]; then
cat << EOF
bamextract.sh extracts reads from bam file(s) based on a text file with read names
Required arguments are:
-r the text file with the list of the reads to be extracted
-b the folder where bams file fr... |
8fd1ca6319e25c991854e996d2832f715b1a5765ee05af822bfc44bcc8fac94f | Shell | 2,181 | 87 | #!/bin/sh
# Measure performance of the astrocyte simulation for the specified number of processes (multiple runs).
# $1 - The minimum number of processes.
# $2 - The maximum number of processes.
# $3 - The step of process grid.
# $4 - The process distribution scheme:
# 1 - only master works,
# 2 - only slaves... |
e945f4051deb95fc485ce39bd045778cece6f9128cdccf2c2ac5e2c41099cc00 | Shell | 2,182 | 70 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]] ; then
echo "Usage: ./_submit_bwa.sh <ref.fasta> [jid]"
echo -e "\t<ref.fasta>: no gz!"
echo -e "\tAssumes <input.fofn> in the same path"
echo -e "\t[jid]: set --dependency=afterok:[jid]"
exit -1
fi
#export asset=$tools/asset
ref=$1
ref=`basename $ref`
ref=`ec... |
4a79e8806bed2cb5083c869caf5758599cf41f53ab267cf9d9f8454ff01fc079 | Shell | 2,183 | 58 | #!/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... |
b2f3f49259afb4c1f4f7ddec922d06ddd74d63f59538d8fa768b41dc4997ba21 | Shell | 2,198 | 75 | #!/bin/bash
solve_dir=/data/Phillippy/tools/bionano/Solve3.2.1_04122018
ref=$1
if [ -z $ref ]; then
echo "Usage: ./map.sh <ref.fasta> <input.fofn> [line_num]"
exit -1
fi
if [ -z $2 ]; then
echo "No input.fofn given. Exit."
exit -1
fi
i=$SLURM_ARRAY_TASK_ID
if [ -z $i ]; then
i=$3
fi
if [ -z $i ]; then
echo... |
7d86e93c6f9ded418e0f0bffa083fa8711b9aeaa145471d782e27591507fb60c | Shell | 2,203 | 63 | #!/bin/bash
# qv-calculator 0.0.1
set -x -e -o pipefail
main() {
sudo chmod 777 /usr/bin/samtools
sudo chmod 777 /usr/bin/bcftools
echo "Value of aligned_bam: '$BAM'"
echo "Value of variant: '$VAR'"
echo "Value of csv: '$CSV'"
bam_name=$BAM_name
var_name=$VAR_name
csv_name=$CSV_name
... |
e466ea774a48ecf12df9cb32eeb024ea6ebfb4662d0bba7e58244412d26eb6c6 | Shell | 2,217 | 49 | #!/usr/bin/env bash
# Copyright 2017 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... |
a7370ad05a8875c74ffd4635a145a328271e031bca320c691d5cb6a438f39d44 | Shell | 2,230 | 82 | #!/bin/bash
# Translated and modified from:
# https://github.com/kotaro-inoue/human3.6m_downloader
### CONFIG ###
TARGET_DIR=$1
if [ -z $TARGET_DIR ]; then
echo "Must specify target directory"
exit 1
fi
if [ ! -d "${TARGET_DIR}/training" ]; then
mkdir -p "${TARGET_DIR}/training"
fi
if [ ! -d "${TARGET_DIR}/tes... |
ea1ef575702d097519747c6d05ab2d3e162edc6807c8b0b69cb58260fe956630 | Shell | 2,249 | 63 | #!/bin/bash
if [[ -z $1 ]]; then
echo "Usage: reliable_block.sh <genome> <genomesize.map> [chromosome_assignments.csv]"
echo
echo "Run after asset.sh has fully finished its submitted jobs."
echo "Required files: asm.bed, asm.ends.bed, gaps.bed, and */*.support.bed"
echo
... |
adcc4737505b5b94f4893d1204d754b548e2a15b0b5e8017c44ba4b76a2d128e | Shell | 2,251 | 80 | #!/bin/bash
# 1. run scFusion with different downsampling
# output: knn_xy matrices, and cells (i)
# 2. within-modal clustering ...
# for each cell set from (i) -> run Leiden clustering with different resolution (r)
# output: clustering_results.tsv.gz (i, r): (i) separate tables, (r) columns per table
# 3. correlatio... |
cef7077a70c6bd79a852297a67b558d17a97efc51abd088de27209a7a230bd32 | Shell | 2,251 | 60 | #!/bin/bash
NUMPARAM=$#
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
LL=` head -n 4 $FLIST | grep Paramet | ... |
15f509f13e9cabbc0b72820fe425ecdaf9164f02266df234e8f645afb86f1dc4 | Shell | 2,268 | 67 | #!/bin/bash
######################################################################
#
# This software is based on:
# 'A Bash script to compute ETag values for S3 multipart uploads on OS X.'
# (https://gist.github.com/emersonf/7413337)
#
# Modifications are a 'United States Government Work', and
# are released... |
2134e2e49d7f01fb9d463fcd4db43e7633c1df39bda19f8e0f2b1c7e6e506b46 | Shell | 2,269 | 80 | #!/bin/bash
# 1. run scFusion with different downsampling
# output: knn_xy matrices, and cells (i)
# 2. within-modal clustering ...
# for each cell set from (i) -> run Leiden clustering with different resolution (r)
# output: clustering_results.tsv.gz (i, r): (i) separate tables, (r) columns per table
# 3. correlatio... |
b7eecf2cbdad52a383b1f4f2a5ae776b2be41f2ee7ff018ebd21af722315bcb0 | Shell | 2,284 | 60 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e re_bases.txt ]] ; then
echo "Usage: ./runArima.sh <name> [jobid]"
echo -e "\tSymlink fastq.map : <R1.fastq.gz path> <R2.fastq.gz path>"
echo -e "\tSymlink <name>.fasta : reference fasta file to align"
echo -e "\tSymlink re_bases.txt : Restriction enzyme site bases... |
8103b22f9cb72c92a8f1c34d996b2b64a556a477647f18958e313107cc5b899c | Shell | 2,289 | 96 | #!/bin/bash
set -e
echo "Usage: ./freebayes_v1.3.1.sh <sample> [array_idx]"
echo -e "\t<sample>: output prefix"
echo -e "\t[array_idx]: 1-100"
i=$SLURM_ARRAY_TASK_ID
sample=$1
if [ -z $i ]; then
i=$2
fi
if [[ -z $sample ]]; then
echo "No <sample> given. Exit."
exit -1
fi
module load freebayes/1.3.1
###... |
802293f149d0609711eaf4541eddc591303af90171be50f46c354c2e612bd7dd | Shell | 2,291 | 48 | # 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_
# added seed
python3 ../../score_predictions.py --beam_size 50 --invalid_smiles \
-... |
a362584b8c827777c315a3f0aab50c0579236f817678fcb5fb7b4f8e9992c769 | Shell | 2,318 | 56 | #!/bin/bash
#
dim=3 # image dimensionality
AP="" # /home/yourself/code/ANTS/bin/bin/ # path to ANTs binaries
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2 # controls multi-threading
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
f=$1 ; m=$2 # fixed and moving image file names
mysetting=$3
if [[ ! -s $f ]] ; then echo no fix... |
e76ceaca3c676701977b7e5a26cde7280ae9f55144d8cf4e8b13fe1fd5b906e6 | Shell | 2,318 | 52 | #!/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... |
d5081a4679965e265acb2b1a34ef0d461944d674a66e109747c81277686c8a0f | Shell | 2,367 | 80 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e re_bases.txt ]] ; then
echo "Usage: ./runArima.sh <fasta> [jobid]"
echo -e "\tSymlink fastq.map : <R1.fastq.gz path> <R2.fastq.gz path>"
echo -e "\tSymlink <fasta> : reference .fasta file to align"
echo -e "\tSymlink re_bases.txt : Restriction enzyme site bases. e... |
8b1281e42a554f5285ea86f1f5ee1faeda652590f6b83b42a08db65fd79c7b21 | Shell | 2,372 | 77 | #!/bin/bash
NUMPARAMS=$#
MAXITERATIONS=30x90x20
if [ $NUMPARAMS -lt 2 ]
then
echo " USAGE :: "
echo " sh $0 ImageDimension image.ext "
exit
fi
#initialization, here, is unbiased
DIM=$1
if [ ${#DIM} -gt 1 ]
then
echo " Problem with specified ImageDimension => User Specified Value = $DIM "
exit
fi
FIXED=$2
... |
e8876226b8701d6030a07f369c229b6e542f6c8ae43dbdf2c20f3edc9b204913 | Shell | 2,374 | 69 | # Takes one command line argument "local".
# if "local", then we use the local sources rather than calling down
# the sources from github.
# This does not apply to cochlea, which needs to be pulled from the upstream
# on pbmanis with the correct commit.
# define the "local" environment path. The required local source... |
c6a5bca2941fbae7bd7dc7055affaf04b7ee3506ebfa9a443485f7da9ea024c9 | Shell | 2,376 | 80 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e re_bases.txt ]] ; then
echo "Usage: ./_submit_salsa_2.1.sh <fasta> [jobid]"
echo -e "\tSymlink fastq.map : <R1.fastq.gz path> <R2.fastq.gz path>"
echo -e "\tSymlink <fasta> : reference .fasta file to align"
echo -e "\tSymlink re_bases.txt : Restriction enzyme site... |
f300f219967decca26a0139858c71c2f1bc8c13a88d9b874ccebb43764373dda | Shell | 2,380 | 80 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e re_bases.txt ]] ; then
echo "Usage: ./_submit_salsa_2.2.sh <fasta> [jobid]"
echo -e "\tSymlink fastq.map : <R1.fastq.gz path> <R2.fastq.gz path>"
echo -e "\tSymlink <fasta> : reference .fasta file to align"
echo -e "\tSymlink re_bases.txt : Restriction enzyme site... |
e52dfa64422656ba9c0e1b2da0a3dcb4dd3cc7da5dbe070c4fcfead01459ee30 | Shell | 2,415 | 76 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./qv_prim_hap.sh <genome_id> <primary_fasta> <alt_fasta>"
exit -1
fi
genome=$1
fa_primary=$2
fa_alt=$3
threads=$SLURM_CPUS_PER_TASK
if [ -z $threads ]; then
threads=2
fi
echo "Load modlues"
module load bedtools
module load samtools
echo
if [ ! -e $genome.changes.vcf.g... |
d5438aeb4f8822d3754003d60d54da1f8572dabee7d65f4f934a2039317cbbdb | Shell | 2,421 | 96 | #!/bin/bash
if [ $# -lt 6 ]
then
echo " USAGE \n sh $0 fixed.nii fixedhipp.nii moving.nii movinghipp.nii ITERATIONS LandmarkWeight "
echo " you should set LandmarkWeight yourself --- the intensity weight is 1. so the landmark weight should be in that range (e.g. 0.5 => 1 ) "
echo " the usage indicates .nii but yo... |
ef240fdbb249de87100d3f039472bee29d163f0e1674bf75d48f69582373b9cd | Shell | 2,435 | 92 | #!/bin/bash
# meryl_genomescope 0.0.1
# Generated by dx-app-wizard.
set -x -e -o pipefail
main() {
sudo chmod 777 /usr/bin/meryl
echo "Value of fastq: '${fastq[@]}'"
echo "Value of kmer: '$kmer'"
echo "Value of read_length: '$read_length'"
echo "Value of kmer_max: '$kmer_max'"
for i in ${!fastq[@]}... |
7e5366126f5b34be56ac62fded756dee7b536ffea6e3dc14bc405ee84bb5a851 | Shell | 2,454 | 86 | #!/bin/bash
if [[ "$#" -lt 3 ]] ; then
echo "Usage: ./_submit_pretext.sh <fasta> <fastq.map> <out_prefix> [jobid]"
echo " fasta : reference .fasta file to align"
echo " fastq.map : /path/to/R1.fastq.gz <tab> /path/to/R2.fastq.gz"
echo " out_prefix: prefix for output files. Final output will be a merge... |
efba27a3dcd3fc8b9060cf87f9e81cc28ad245db52671a1ce278de609c45bd40 | Shell | 2,454 | 63 | #!/bin/bash
# mitoVGP-canu 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... |
a92742b92406cc5ed8d96d82b7698e4f8ef40d74ff2564d18e92a2abd0b1f936 | Shell | 2,458 | 62 | #!/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... |
002d8895940cf6a4ae29244c57a664955571c18fe72ddfc5395c799536272d80 | Shell | 2,480 | 43 | # WORKDIR
WORKDIR=./
# DATADIR
DATADIR=../test/data/
# MASQUEDIR
MASQUEDIR=../
################
# 16S analysis #
################
# Even samples from MOCK communities
#sample=SRR072220
#sample=SRR072239
# Staggered samples from MOCK communities
#sample=SRR072221
#sample=SRR072223
#sample=SRR072237
for sample in $DATA... |
b217dc9299685c6c506cf3978f99a4dcfaae4202edc0ee1b3f5fe378ff8edaf7 | Shell | 2,490 | 102 | #!/bin/bash
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/Users/... # set the path for your subjects folder
# gather all your subjects in one folder, each subject put in a separate subfolder
# create a subfolder named surf (inside each subject folder),... |
e6ea0a0d17c945118a44fb07aad6bae7ee66af08c126b5c18971171d59f49733 | Shell | 2,525 | 61 | #!/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... |
466c8c4d0a0f5c96a08b2ddbd209a9ee290079c620a938979d33cf0a0d968b2e | Shell | 2,573 | 76 | # 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.
#####################################################... |
a199785182edee9a4e32a539022f360f4b70522e5fe9d2c46220241a9444d466 | Shell | 2,576 | 81 | #!/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... |
03303549405f82cd6ca44885cf1f34a18d5f908d14302e88e082ba281b912a58 | Shell | 2,579 | 76 | # 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.
#####################################################... |
8cee0c89b5732d9fdec72f67aaa6c202dab5e92d239372fc2def324b94e49452 | Shell | 2,583 | 68 | #!/bin/bash
# path to data
for DATA_DIR in /home/goschv/CSB_NeuroRad2/goschv/DATA/Repro
do
# path to template
TEMPLATE=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz
cd $DATA_DIR
for s in CSB*
do
echo $s
# register DWI (B0)
antsRegistrationSyNQuick.sh -d 3 -f $TEMPLATE -m $s/processed/*b0_bet.... |
ee6cb71db8bae05bd63170a06666bbef9003b71042dca187c29702d1084358b3 | Shell | 2,588 | 45 | #!/bin/bash
# Test 1:
# Basics of neuron dynamics
./../NeuralNetworkCode/main ../Test_Results/Test1/ Test1_Parameters.txt
# Test 2:
#Reproduces 4 panels of Fig. 8 in Brunel (2000) "Dynamics of Sparsely Connected Networks of Excitatory and Inhibitory Spiking Neurons" J Comp Neurosci 8, 183
./../NeuralNetworkCode/mai... |
1e3e236e442e281440e81cade066d87f338cd0d29a6124f662ecfafc5df1372f | Shell | 2,591 | 77 | # 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.
#####################################################... |
f1a8d8f79501e180cc4eb3ec7027b607db239f33a3b5bda55ad0ebc8aed698cd | Shell | 2,595 | 76 | # 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.
#####################################################... |
d1d69643a6906ebb548c6c4f8eed182c3e26839f9f6f9a3cc8dc47816172b445 | Shell | 2,596 | 76 | # 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.
#####################################################... |
8d41c0518b1e68e745ba68a9032bed2dafc13ccec639227724bfc09cec9ec17f | Shell | 2,617 | 53 | # 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_
# propose200, with seed
python3 ../../score_predictions.py --beam_size 200 --invalid_sm... |
fde79c490da598a2d2946cb7d1c27cccc36e2667f116ad098533c519133c858f | Shell | 2,622 | 60 | #!/bin/bash
#this script (map10x2.sh) is used for the final step of short read polishing. This step
#requires the output of the script map10x1.sh to be trimmed at the overlapping ends. This
#can be achieved using mummer or BLAST to determine the coordinates for trimming.
#Experimental script trimmer.sh may also be emp... |
a731890c058d45d8e51da79a155fc9b31050f1b4ef8264b684c6e1d38bb1c927 | Shell | 2,654 | 58 | #!/usr/bin/env bash
#
# Copyright 2026 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... |
6fa799528887f4f450d5eaeca8d2549eeb009cf2ec80870de007841d819da169 | Shell | 2,655 | 85 | #!/bin/bash
solve_dir=$tools/bionano/Solve3.3_10252018
ref=$1
if [ -z $ref ]; then
echo "Usage: ./map.sh <ref.fasta> <input.fofn> [line_num]"
exit -1
fi
if [ -z $2 ]; then
echo "No input.fofn given. Exit."
exit -1
fi
i=$SLURM_ARRAY_TASK_ID
if [ -z $i ]; then
i=$3
fi
if [ -z $i ]; then
echo "No SLURM_ARRAY_... |
6fe25100e8cbc5534ee86a102a4aaf6d438bf34d196aea28a85e60fcc9769bdb | Shell | 2,662 | 52 | #!/bin/bash
#PBS -P r16 #PBS -q gpuvolta
#PBS -l ngpus=1
#PBS -l ncpus=12
#PBS -l storage=scratch/f91
#PBS -l walltime=1:00:00
#PBS -o out.out
#PBS -e error.out
#PBS -l mem=16GB
#PBS -l wd
#PBS -m abe
#PBS -M yearlyboozefest@gmail.com
module purge
module load intel-mkl/2020.2.254
module load openmpi/4.0.3
module load ... |
37b804678f412280dad6042a8a24502dfe436dfdb0523afdb7b01d2cb07d2e94 | Shell | 2,665 | 60 | #!/bin/bash
#this script (map10x2.sh) is used for the final step of short read polishing. This step
#requires the output of the script map10x1.sh to be trimmed at the overlapping ends. This
#can be achieved using mummer or BLAST to determine the coordinates for trimming.
#Experimental script trimmer.sh may also be emp... |
2f3d85e045e3a39357f12d31dcf3fb7d22385bf1b9052354bc4bebbeffb3ca1a | Shell | 2,673 | 85 | #!/bin/bash
solve_dir=$tools/bionano/Solve3.3_10252018
ref=$1
if [ -z $ref ]; then
echo "Usage: ./map.sh <ref.fasta> <input.fofn> [line_num]"
exit -1
fi
if [ -z $2 ]; then
echo "No input.fofn given. Exit."
exit -1
fi
i=$SLURM_ARRAY_TASK_ID
if [ -z $i ]; then
i=$3
fi
if [ -z $i ]; then
echo "No SLURM_ARRAY_... |
a9dc165c01899259026d00eeed0dd16efa4f145e0335da2d5fc3618f3a4c43ec | Shell | 2,683 | 64 | # 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.
#####################################################... |
2a06a17991d03fe136db24d748832cfd6fb97e651e513ba85004bd05942ac880 | Shell | 2,690 | 59 | #!/usr/bin/env bash
# Reproduce the K562 within-cell row of the main per-cell evaluation table
# (Table 2 in the manuscript; Supplementary Table S6 holds the ten-seed values)
# on a small, fully bundled example dataset (K562 held-out chr20/chr21/chr22).
#
# This runs the bundled pre-trained checkpoint over ~6.5k labell... |
cef241e9b8a75e6a49452ae32731883a5de70b8c585450faee238f44d56658fc | Shell | 2,691 | 88 | #!/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... |
50ed874070e7a558326210df7e05614a7926a059638aa96de22c8bd8c8fec5bb | Shell | 2,726 | 77 | #!/bin/sh
# Wrapper script for docker.
#
# This is used primarily for wrapping the GNU Make workflow.
# Instead of typing "make TARGET", type "./run.sh make TARGET".
# This will run the make workflow within a docker container.
#
# The assumption is that you are working in the src/ontology folder;
# we therefore map the... |
1c14ab812614be5b3174846b5a388f973356047b95eb9279ab97237d406ab53f | Shell | 2,730 | 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... |
5f1d078b079dbbfcb2f46132ef4777c70f951c147d3f19f8d0a3de5ac3b9a627 | Shell | 2,747 | 88 | #!/usr/bin/env bash
# Copyright 2017 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... |
6f4bf79eade7a2a268f19df5876b4fbe4996c64cfe51ffa8dcad7093f59655aa | Shell | 2,756 | 60 | #!/bin/bash
#this script (map10x2.sh) is used for the final step of short read polishing. This step
#requires the output of the script map10x1.sh to be trimmed at the overlapping ends. This
#can be achieved using mummer or BLAST to determine the coordinates for trimming.
#Experimental script trimmer.sh may also be emp... |
a184b853c65c8fb5e632bb7bfb72adb127b06e6fca2c543551f9a680289f24cd | Shell | 2,763 | 74 | #!/bin/bash
# merqury 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 code... |
b5afd2383f66df4a7691324a929c1d127acf2fa3ca185b8ec2f651eaf6b971c1 | Shell | 2,779 | 87 | #!/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... |
4d4ad3d91d73457a75292dfe1c7538c76b439f0493f937ae9ece6c92f5e86206 | Shell | 2,782 | 46 | #!/bin/bash
#BSUB -M 128000
#BSUB -W 12:00
#BSUB -n 6
#BSUB -R "rusage[mem=128000] span[hosts=1]"
#BSUB -J rsem_de_isoforms
#BSUB -o rsem_de_isoforms.out
#BSUB -e rsem_de_isoforms.err
source_folder='transcripts/'
output_folder='differential/'
module load RSEM/1.3.0
# cell line A
rsem-generate-data-matrix ${source_fo... |
f68c34a7ec1a17dac3e2138fa703e96cea4cc503a726c1be28b01b60eb6b7cdf | Shell | 2,797 | 118 | #!/bin/bash
set -e
SPECIES=$1
ABBR=$2
CONTIG=$3
if ! [[ -e "${SPECIES}/${ABBR}_10x1" ]]; then
mkdir ${SPECIES}/${ABBR}_10x1
fi
if ! [[ -e "${SPECIES}/${ABBR}_10x1/${CONTIG}" ]]; then
cp ${SPECIES}/${ABBR}_arrow/${CONTIG} ${SPECIES}/${ABBR}_10x1/
fi
cd ${SPECIES}/${ABBR}_10x1
dw_date=`date "+%Y%m%d-%H%M%S"`; a... |
69bc393d130d00aeb486aefc66f1eee2facd718b0eba190f05fb5913a1c8b7fd | Shell | 2,811 | 66 | # # Retrain the models used for CI.
# # Should be done rarely, indicates a major breaking change.
my_python=python
############### TEST regular RNN choose either -rnn_type LSTM / GRU / SRU and set input_feed 0 for SRU
if true; then
rm data/*.pt
$my_python preprocess.py -train_src data/src-train.txt -train_tgt data/tg... |
8995f1dbe2862bd7060b643e2d5486cc3cbc8c0f94a335c171b8eefc48a04760 | Shell | 2,816 | 80 | # 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.
#####################################################... |
a2f1042c9abb096ebea8e04e0a127ae21b69f89059b5e3a167077fe46a177a13 | Shell | 2,823 | 108 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_higherlevel.sh -i <Subject>
e.g. sbatch Functional_higherlevel.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;;
esac
s... |
8043846459653a9ecf1769d86cdceaecf05c8421c1124ccaac36676d5c5f95bc | Shell | 2,833 | 83 | #first step is getting the protein restr files
#################
#USAGE bash genrestr_sequence topol.top pdbfile.pdb psffile.psf restr_groups.txt
#################
#make sure the pdb file is generated from the tpr file and output by editconf -conect
#note weird sed delimiters is because it won't distinguish /'s from di... |
d891134da4e5f338d34bb83bcf50ce9215d2f04de9596248d1165295ae626384 | Shell | 2,854 | 99 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: sh _submit_10x_trimbc_meryl.sh <k-size> <genome_id>"
echo "requires input.fofn: ls *R1*.fastq.gz > input.fofn"
exit -1
fi
k=$1 # 31
genome_id=$2 # genome_id
if ! [ -e input.fofn ]; then
echo "requires input.fofn: ls --color=never *R1_001.fastq* > input.f... |
1b1362acbe9690b7324198cdf5c3c7e936c01ab2029dc08c537f054a7b53a7d7 | Shell | 2,862 | 89 | #!/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... |
b11d5c92baaa733899a0e29e9ad089d8f2f9f0708a65ea16c3c0a0c3dab1e210 | Shell | 2,880 | 82 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]] ; then
echo "Usage: ./_submit_purge_dups.sh <asm.fasta> <input.fofn> [jid]"
echo -e "\t[jid]: set --dependency=afterok:[jid]"
exit -1
fi
asm=$1
ref=`echo $asm | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed 's/.fa.gz$//g' `
fofn=$2
wait_for=... |
15c6f8ef0da9e2e5ee1a0fa05c13f87cafd012e3886c889a21d2a002f7280ca6 | Shell | 2,894 | 70 | #!/bin/bash
# for each ROI in EEGSTV analysis
# extract time series from ROI
# Hengda He, May 25 2021
ReD='\033[91m'
YelloW='\033[93m'
EndC='\033[0m'
codepath='/media/hhshare/LAB_2021/Hengda/FunctionalConnectivity/Scripts'
ROIsubdir='/home/hengdahe/LAB_2020/Subjects'
FSdir='/media/hhshare/LAB_2020/Linbi/Subjects'
out... |
01f266b2bd30bc9eb6812cc1dd983b205b3244f5cc1e43a06fe377b3195e510c | Shell | 2,903 | 82 | # 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.
#####################################################... |
7474ae3bd8abbbeaae0661ff74af5d829a70654bff223579c1f1c9b806d6dfb4 | Shell | 2,924 | 49 | #!/bin/bash
#BSUB -M 128000
#BSUB -W 12:00
#BSUB -n 6
#BSUB -R "rusage[mem=128000] span[hosts=1]"
#BSUB -J rsem_de_transcripts
#BSUB -o rsem_de_transcripts.out
#BSUB -e rsem_de_transcripts.err
source_folder='transcripts/'
output_folder='differential/'
module load RSEM/1.3.0
# cell line A
rsem-generate-data-matrix ${... |
a9649ef628bf1fee8c57e7ac5334a8166ea449734d0d54ad45dcb982ab8c7ca2 | Shell | 2,951 | 85 | #! /bin/bash
if [[ -z $1 ]] ; then
echo "Usage: ./_submit_longranger_freebayes.sh <genome> [ref.fasta]"
echo "<ref.fasta> will be linked as asm.fasta."
echo "Assumes we have 10x reads located under /data/rhiea/<genome>/genomic_data/10x/."
exit -1
fi
if ! [ -e asm.fasta ]; then
... |
b78a3db34bc3b2007e9e2cb9e60f7c041ef72ae85bf995304826d4915c594e4f | Shell | 2,965 | 69 | #!/bin/bash
# EEGSTV regions transformed to native space, then project to surface
# 1. EEGSTV regions in MNI152 space warped back into native space
# 2. project EEGSTV regions to surface
# Hengda He, Feb 2021
ReD='\033[91m'
YelloW='\033[93m'
EndC='\033[0m'
SUBJECTS=(180607_Sub11 180618_Sub17 180624_Sub21 180725_Sub25... |
4556ed07610d742d43f90eabc368c571153e0e4ca84d0c7a71c2c1a52e6cf73a | Shell | 2,990 | 79 | #!/bin/bash
# wtdbg 1.2.8
# 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 code o... |
5c14576119dd0372a5d688dddac28186027cd7945d014017c53d5105ba58dcd6 | Shell | 3,012 | 112 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./asm_stats.sh <asm.fasta> <exp_genome_size (bp)> [p/s/c]"
echo "[ ]: By default, stats for scaffold / contig / gaps will be generated."
echo "[p]: set for getting primary / alt haplotig stats, in addition to default, assuming the primary begins with scaffold_ in... |
cc240b03a939b8be4b4d0dd7ac1ef1f39f13213775eb08e1b101a52ff9f7f1b0 | Shell | 3,029 | 92 | #!/usr/bin/env bash
set -euo pipefail
OUT_DIR="${1:-./outputs/tabby-pretrain-165k}"
: "${BLAST_DATA_ROOT:?Set BLAST_DATA_ROOT to the BLAST training directory}"
: "${SYNTHETIC_ARROW_ROOT:?Set SYNTHETIC_ARROW_ROOT to pre-generated KernelSynth Arrow shards}"
: "${BLAST_RATIO:?Set BLAST_RATIO to the actual BLAST fraction ... |
c21d5ced6d88e0a6325d6fbbd03d167a1aaa402deffd7ce42fd50f64371a9f69 | Shell | 3,035 | 91 | #! /bin/bash
if [[ -z $1 ]] ; then
echo "Usage: ./_submit_longranger_freebayes.sh <genome> [ref.fasta]"
echo "<ref.fasta> will be linked as asm.fasta."
echo "Assumes we have 10x reads located under /data/rhiea/<genome>/genomic_data/10x/."
exit -1
fi
if ! [ -e asm.fasta ]; then
... |
7a8de9d7e9213a59e72ccf95a5dcffd8a1a1339becce0844ea155017fa8a131b | Shell | 3,099 | 78 | #!/usr/bin/env bash
BASE=~/git/NIF-Ontology
BASESC=$(echo ${BASE} | sed 's/\//\\\//g')
TTLTARGET=${BASE}/ttl/
EXTERNALTARGET=${TTLTARGET}external/
UNUSEDTARGET=${TTLTARGET} #unused/ # XXX do the sorting after the conversion
TMPUNUSED=/tmp/temp_unused
#cd ${BASE}/ttl/
#find . -type l -exec unlink {} \;
#find ../ -nam... |
680ee4680204534ddc6ce6ba7823d3ba174a8f00114ac7115cd2e3d587396068 | Shell | 3,138 | 92 | #!/bin/bash
usage=" $0 -d 3 -f symmetric_template.nii.gz -m moving.nii.gz -o output_prefix "
:<<supercalifragilisticexpialidocious
here is a first pass at registration-based asymmetry based on mapping an image A to a symmetric-template.
note - care must be taken to look at prefix_L_aff.nii.gz to make sure that it's c... |
2216f61c8e046ff1b28ce19abbcbef28c7ea63c86a3f87bbcb0c748fb8e5a5f0 | Shell | 3,216 | 148 | #!/bin/bash
set -euxo pipefail
start_torchserve()
{
echo "Starting TorchServe"
torchserve --start --model-store model_store &
pid=$!
count=$(ps -A| grep $pid |wc -l)
if [[ $count -eq 1 ]]
then
if wait $pid; then
echo "Successfully started TorchServe"
else
... |
c4364bf2472718c0e8215913d564343bc69ba0aa5ebdf3f6c7ce6a4ac57ea60d | Shell | 3,245 | 47 | set -e
<<DONE
python plot-final-genome.py slivar-summ-results/genome.sarcoma.gatk.slivar.summary.txt slivar-summ-results/genome.sarcoma.gatk.ch.slivar.summary.txt slivar-summ-results/genome.sarcoma.dv.slivar.summary.txt slivar-summ-results/genome.sarcoma.dv.ch.slivar.summary.txt slivar-summ-results/genome.ped 2>err
m... |
4a888b43cd5b7ea8f9256427e2d952aa87e93a0374ca2d56f7998b1ec5ae664e | Shell | 3,249 | 90 | #!/bin/sh
## A shell pipeline for decontaminating VGP genome assemblies post-scaffolding.
## Help ########################
Help()
{
##command line syntax
printf "\n"
echo " Syntax for running VGP_decontamination_pipe.sh:"
printf "\n"
echo " sh VGP_decontamination_pipe.sh <scaffolded assembly... |
babe35b22121c4e6fce331493ab653ce17505a49a40e227cb6744372b83ef4ef | Shell | 3,251 | 58 | #!/bin/bash
set -e
SPECIES=$1
ABBR=$2
CONTIG=$3
cd ${SPECIES}
mkdir -p ${ABBR}_arrow
awk '$2 == "'${CONTIG}'" {print $1}' ${ABBR}_canu/${ABBR}.contigs.layout.readToTig > ${ABBR}_arrow/${ABBR}_contig${CONTIG}_IDs.txt
gunzip -c ${ABBR}_canu/${ABBR}.trimmedReads.fasta.gz > ${ABBR}_arrow/${ABBR}.trimmedReads.fasta
R... |
01a24a0384bcf92b5c0deb76fe1182690aaa0c052801965e45346e9fb425ba30 | Shell | 3,263 | 70 | #!/usr/bin/env bash
# Tiny end-to-end run: one short training epoch, then one evaluated config.
#
# smoke_test.py covers the model path only. This covers the two parts it cannot:
# the GIFT-Eval training loader (tabby.posttraining.data) and the evaluation
# harness. Those are where a fresh machine
# usually breaks: GIF... |
20e9c401292ea4e72bf2983bacacae11be6fc952c684da9104ab6cfd3745b3f4 | Shell | 3,270 | 88 | # 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 until late 2021.
# This file derived from process_gbcA... |
30bc898eee46d38c6a96ff301cca41d5ffd91ba7681bf888e76fe6171b3de577 | Shell | 3,270 | 88 | # 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 until late 2021.
# This file derived from process_gbcA... |
c4c5cbc8dd6e0c0405a0453acb1b9dd81aa5c48f345e9074677be86588b38a8e | Shell | 3,344 | 123 | #!/bin/bash
set -e
i=$SLURM_ARRAY_TASK_ID
sample=$1
if [ -z $i ]; then
i=$2
fi
if [[ -z $sample ]]; then
echo "sample=$sample"
exit -1
fi
module load freebayes/1.2.0
#### [+] Loading freebayes 1.2.0
module load samtools/1.9
#### [+] Loading samtools 1.8 ...
# This is co-installed with bcftools
modul... |
84054982c874db14e764c043e9c0ca6ce2719bc5175a309a33256cc007d33abe | Shell | 3,380 | 31 | #!/bin/bash
#SBATCH --partition=express
#SBATCH --time=2:00:00
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=8G
#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/register/sub-MDP001-reg.txt
module load FreeSurfer/6.0.0-centos6_x86_64
SUBJECTS_DIR=/data/user/mdefende/datasets/MDP/subs
% register clean b0 to struc... |
574da533783ad0a320affba20b84b053f599a210c60557ac1ceb4436d50a9ed0 | Shell | 3,393 | 108 | #!/bin/bash
set -e -x -o pipefail
check_cutoffs_are_logical() {
if [ ${high_cutoff} -lt ${low_cutoff} ]; then
dx-jobutil-report-error "ERROR: lot cutoff=${low_cutoff} is greater than high cutoff=${high_cutoff}."
fi
if [ ${midpoint} -gt ${high_cutoff} ]; then
dx-jobutil-report-error ... |
bff8a8f1656471549be19a54768fa5f65fab2803f06091cc4865aa8cd19c1127 | Shell | 3,419 | 81 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
ccbb4ebde8d7b6997e29ba889476b2f561e9fee9f3ebec11a0373935122284c3 | Shell | 3,430 | 70 | #!/usr/bin/env bash
# Train the prompt module on top of a frozen PatchTST-FM backbone.
#
# This reproduces the released configuration: prompt length 160, segmented
# context-aware prompts, gate initialised at sigma(+5), cosine annealing over 20
# epochs, 8096-step context window.
#
# Usage:
# GPU=0 CKPT=/path/to/step... |
b1c4518a206cba7b2c204b548ebefcbca63c3f157bb33da49d3d4a20f6b49c39 | Shell | 3,465 | 144 | #!/bin/bash
#
package=ANTS
repository=git@github.com:BRAINSia/ANTS.git
#
# when run by cron, the path variable is only /bin:/usr/bin
export PATH="/opt/cmake/bin:/usr/local/bin:/usr/sbin:$PATH"
#
# make the testing directory, based on current user name
#user=`who -m | sed -e 's/ .*$//'`
user=${LOGNAME}
ThisComputer=`h... |
a9a6c6d298216a932e8fa48bf8f301f68d0018f5cb424409963baaba52c30417 | Shell | 3,472 | 99 | #!/bin/bash
# purge_dups 0.0.1
set -x -e -o pipefail
main() {
echo "Value of ref_fastagz: '$ref_fastagz'"
echo "Value of raw_reads_pacbio_fastagz: '${raw_reads_pacbio_fastagz[@]}'"
echo "Value of custom_cut_off: '$custom_cut_off'"
echo "Value of max_genomesize: '$max_genomesize'"
echo "Value of co... |
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