sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
33caa67f27b6318d0e118adcb8e012dfe5ad2ed737c070dfbb8123b7ba837fa6 | Shell | 2,793 | 94 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# shellcheck disable=SC1091
. ./path.sh || exit 1;
fs=24000
num_dev=100
num_eval=100
train_set="train_nodev"
dev_set="dev"
eval_set="eval"
shuffle=false
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
d... |
37114cd3b392173d4800dbc237f76c6f82f74a2501876d3b312d958079be6c44 | Shell | 2,816 | 163 | #!/bin/sh
# mos2nrn2 zipfile simdir running
ARCH=x86_64
MODSUBDIR=x86_64
if test "x${NRNHOME}" = x ; then
prefix="/raid/zyc/code_for_dhs_paper/install"
exec_prefix="/raid/zyc/code_for_dhs_paper/install/x86_64"
NRNBIN="${exec_prefix}/bin/"
else
prefix="$NRNHOME"
exec_prefix="${prefix}/${ARCH}"
NRNBIN="${exec_pre... |
7b7bd71062d3d6366e462df33def525253efe32c263a5e1f73e678441be6f1b5 | Shell | 2,826 | 94 | #!/bin/bash
# WHAT IT DOES
# writes to path/pat/DWI a folder working_data with a copy of the data neded for the entire pipeline
# performs denoising and unringing of the diffusion image
# performs b0 distortion correction through synb0 ad writes the results in path/pat/DWI/synb0/OUTPUTS
# prepares data needed for synb... |
2f9e885270e2f2177b9fedcca1287fbbc8b1815aa837b7f355c405b9d1e9eeb5 | Shell | 2,869 | 74 | #!/bin/bash
# WHAT IT DOES
# coregisters DW image and T1
# creates and corrects wholebrain streamlines created with individual FOD, not used after.
# WHAT IT NEEDS
# The script ACT.sh already executed
# A good $path/$pat/DWI/working_data/b0_bet_mask.nii.gz
# A good $path/$pat/DWI/working_data/T1_unb_bet_mask.nii.gz
#... |
8e270548fa6a573e282ec557fbe0bf2c28d11944bac1ddc713e0813ea8805974 | Shell | 2,878 | 96 | #!/bin/bash
# ============================================================
# Extract all reads from a target BAM whose QNAMEs appear in
# a query BAM.
#
# Both inputs can be coordinate-sorted. We extract QNAMEs from
# the query BAM into a hash set, then stream the target BAM and
# keep any record whose QNAME is in the ... |
a11b252a3db112e462c23b74d65f4efce5794a91c47c7365a269abf7716cd6f3 | Shell | 2,879 | 98 | #! /bin/bash
set -xe
if [[ -z "${TMPDIR}" ]]; then
TMPDIR=/tmp
fi
set -u
if [ "$#" -lt "1" ] ; then
echo "Please provide an installation path such as /opt/ICGC"
exit 1
fi
# get path to this script
SCRIPT_PATH=`dirname $0`;
SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
# get the location to install to
INST_PATH=$1
... |
ada851bb6d56be242fc2bf2e0a88a8388dd22c796aab6640e05beb97da7fd5ec | Shell | 2,905 | 93 | #!/bin/bash
# WHAT IT DOES
# transforms leadDBS fixed() in FSL fixed (), where fMRi images are defined
# by doing antsRegistration (takes some time)
# WHAT IT NEEDS
# The transformation diff2struct.txt created in streamlineCreation.sh
# OUTPUT STRUCTURE (only additions shown)
# path/pat
############... |
824ef8d8070896a2adcf03c34e4542ec919ec86c90e8cb6ec845cb25a38c24e6 | Shell | 2,921 | 57 | # Encoder-decoder ICON (Single-Modal):
CUDA_VISIBLE_DEVICES=0 python3 run.py --problem 'icon' --epochs 100 \
--train_batch_size 32 --train_data_dirs '/home/shared/icon/data/data0910c' \
--model_config_filename 'model_icon_config.json' \
--train_config_filename 'train_icon_config.json' \
--test_config_filename ... |
1d271035f2e2b3e390c35356e23a0d0bb437cf670b8ab66e5b9980365af07ce7 | Shell | 2,941 | 25 | set -ex
#python train.py --dataroot ./datasets/edges2handbags --name edges2handbags --model pix2pix --netG resnet_9blocks --direction AtoB --lambda_L1 100 --dataset_mode aligned --norm batch --pool_size 0
#python train.py --dataroot ./datasets/stroke_ct --name stroke_ct --model pix2pix --netG resnet_9blocks --direction... |
09af08dfab896cb5c1b758a55ed6153313dd9afe48a05f3a33dae4554e549505 | Shell | 2,945 | 25 | set -ex
#python train.py --dataroot ./datasets/edges2handbags --name edges2handbags --model pix2pix --netG resnet_9blocks --direction AtoB --lambda_L1 100 --dataset_mode aligned --norm batch --pool_size 0
#python train.py --dataroot ./datasets/stroke_ct --name stroke_ct --model pix2pix --netG resnet_9blocks --direction... |
7da28f732211a7bddf116a747c14681bc8671c88e86f0a2034d6c512567d4608 | Shell | 2,958 | 73 |
# Set these environment vars to point to
# your local installation of WASP
WASP=$HOME/proj/WASP
DATA_DIR=$WASP/examples/example_data
# These environment vars point to the reference genome and bowtie2.
# in the examples below, the reference genome is assumed
# to be indexed for use with bowtie2
INDEX=$HOME/data1/exter... |
721986449d20b5e68eca7057efbb3446a7e5cc042000fe57733fc5575e8910bb | Shell | 2,969 | 31 | gpu=0
dir=data0511a
testeqns=100
testquests=5
traineqns=1000
CUDA_VISIBLE_DEVICES=$gpu python3 datagen.py --dir $dir --name test --eqns $testeqns --quests $testquests --length 100 --dt 0.01 --eqn_types series_damped_oscillator --seed 101 &&
CUDA_VISIBLE_DEVICES=$gpu python3 datagen.py --dir $dir --name test --eqns $te... |
97f0b2d1f55ea94eee5feef9c0d09c329b90db91aae7492dacb32158b7bd2e96 | Shell | 3,027 | 44 | #!/bin/bash
#SBATCH --job-name=HANE # Job name
#SBATCH --nodes=1 # Number of nodes
#SBATCH --cpus-per-task=32 # CPU cores/threads
#SBATCH --gres=gpu:1 # Number of GPUs (per node)
#SBATCH --mem=400000M # memory (per node)
#SBATCH --time=30-30:00 # time (D... |
65dac84e099e68e509ef05d2b2038b21712bd672194f603fc80c49493bd2991e | Shell | 3,057 | 69 | #!/bin/bash
#!/bin/bash
source ./utils.sh
#Data path of all the project
echo "Enter the complete data path of the project: "
path=$(get_path ) #E.g. path="/home/brainstimmaps/20xx_Projects/2023_Deep/03_Data"
# Patient subfolder
echo "Enter the patient ID: "
pat=$(get_patient )
pat_exist=$(check_original_data $path/... |
b5f9da07839a17ac18603ec903fa914e655701f10af9bf589c6c72e992f207bd | Shell | 3,121 | 62 | #!/bin/bash
# The purpose of this script is to register the HCP-output T1wDividedByT2w.nii.gz and T1wDividedByT2w_ribbon.nii.gz files provided with the Human Connectome Project (HCP)
# download from native to MNI152 space.
## PREREQUISITES:
# Before running the script you need to download:
# 1. The publicly availabl... |
4f50fe9e79f474875285a9c986072ce3aaa6212914b1584bdd61b067d77f6b83 | Shell | 3,123 | 75 | #!/bin/bash
echo activate conda environment
eval "$(conda shell.bash hook)"
conda activate tensorflow2_latest_p37
# check if data are already there, if not download from s3 bucket
DIR=""
DIRCode=""
if [ -d "$DIR" ]; then
### Take action if $DIR exists ###
echo "${DIR} exists"
else
### Control will jump here if... |
d50ea1db4c21025c42b025c2b6de99224d412027d323f09603c5d4fd89e16715 | Shell | 3,129 | 113 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# shellcheck disable=SC1091
. ./path.sh || exit 1;
num_dev=100
num_eval=100
train_set="train_nodev"
dev_set="dev"
eval_set="eval"
shuffle=false
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
db_root=$1... |
f8c0303cde975c5d717303a3574edf3fd97a5567b9aa1c27c6f32b21c2298a10 | Shell | 3,197 | 29 | set -ex
#python train.py --dataroot ./datasets/edges2handbags --name edges2handbags --model pix2pix --netG resnet_9blocks --direction AtoB --lambda_L1 100 --dataset_mode aligned --norm batch --pool_size 0
#python train.py --dataroot ./datasets/stroke_ct --name stroke_ct --model pix2pix --netG resnet_9blocks --direction... |
8abc410a4a81383db340c4edfe1213103e62a368ae8320dde5ffce0aaa788169 | Shell | 3,227 | 57 | #!/bin/bash
# Add subcortical structures from freesurfer default parcellation into brodmann parcellation
# Generate connectivity matrix
path='/home/alba/00_WorkingData/2025_MDD/Patient2'
fs_LUT='/home/alba/00_WorkingData/2025_MDD/LUT/' #folder containing all the required LUT (I think the freesurfer one has
# changed ... |
2a4b71e6fc4c9739bde52e417519f2cbca1b609ca719526f9f7143a1f3f48790 | Shell | 3,237 | 113 | #!/bin/bash
########## LICENSE ##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of AscatNGS.
#
# AscatNGS is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published b... |
c6be5a06b22eb7f079df8e1933185651f3b4fb19005b75553ceed60b98a12eda | Shell | 3,328 | 75 | #!/bin/bash
install_cplex() {
local CPLEX_BIN_NAME=$1
local CPLEX_INSTALL_PATH=$2
local CPLEX_DIR="$CPLEX_INSTALL_PATH/CPLEX_Studio"
local CONTAINER_NAME="jabba_cplex_container"
local NEW_IMAGE_NAME="jabba_cplex_image"
local IMAGE_NAME="mskilab/jabba"
echo "Installing CPLEX..."
docker ... |
b861c0021070d6fa87ec945518b10ba85c5a929a28beb408a2f086f07514e925 | Shell | 3,333 | 31 | gpu=0
dir=data
testeqns=100
testquests=5
traineqns=1000
CUDA_VISIBLE_DEVICES=$gpu python3 datagen.py --dir $dir --caption_mode test --name test --eqns $testeqns --quests $testquests --length 100 --dt 0.01 --eqn_types series_damped_oscillator --seed 101 &&
CUDA_VISIBLE_DEVICES=$gpu python3 datagen.py --dir $dir --capt... |
dad9a9de6d40514679d2a79ddbd71e0541b0d77162be57cad82167ce0e129130 | Shell | 3,337 | 100 | #!/bin/bash
# WHAT IT DOES
# performs cortical reconstruction (recon-all)
# creates a tissue type mask for Anatomically Constrained Tomography
# performs preliminary step to improve coregistration
# WHAT IT NEEDS
# a freesurfer license
# a zip package working on the terminal
# the same folder structure as defined in... |
4ab06fe26a3d35d5f07a1fa22b4a41fb87d5add1d19e539af23e1bddd6a6e603 | Shell | 3,349 | 106 | #!/usr/bin/env bash
#
# filter_contig_supporting_reads.sh
#
# Filter a svaba *.corrected.bam down to just the reads whose r2c (read-to-
# contig) BWA alignment landed on a single named contig. The contig name is
# matched against the `bi` aux tag that svaba writes onto each corrected
# read (one tag value per r2c hit, ... |
c972a068acc73488bfc0a5dcd56707eecd12db3ffc2efa5a38baf29457c93eec | Shell | 3,371 | 29 | gpu=0
prefix=data0520
# light dataset
quests=1
ood_coeff1_grids=10
ood_coeff2_grids=11
CUDA_VISIBLE_DEVICES=$gpu python3 datagen_ood.py --seed 202 --ood_coeff1_grids $ood_coeff1_grids --ood_coeff2_grids $ood_coeff2_grids --quests $quests --eqn_types ode_auto_const --dir ./${prefix}_ood_odeconst_light >out_data_ood_ode... |
e824e0bdc9906650f99bea78189d6e51d101ae7609b14c5c42ec5bc9cee2e1dd | Shell | 3,371 | 118 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# shellcheck disable=SC1091
. ./path.sh || exit 1;
fs=24000
num_dev=10
num_eval=10
train_set="train_nodev"
dev_set="dev"
eval_set="eval"
shuffle=false
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
db_... |
e77db0966f75f8106c38a43861de665ba7a6c4ef32d67ba510b02d200ca70aac | Shell | 3,456 | 31 | set -ex
#python train.py --dataroot ./datasets/edges2handbags --name edges2handbags --model pix2pix --netG resnet_9blocks --direction AtoB --lambda_L1 100 --dataset_mode aligned --norm batch --pool_size 0
#python train.py --dataroot ./datasets/stroke_ct --name stroke_ct --model pix2pix --netG resnet_9blocks --direction... |
c7c9f4c65872ef095c5a7be8f0e7ecf32e883f48ae769b82efef72f68446cc44 | Shell | 3,484 | 121 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# shellcheck disable=SC1091
. ./path.sh || exit 1;
fs=24000
num_dev=10
num_eval=10
train_set="train_nodev"
dev_set="dev"
eval_set="eval"
shuffle=false
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
db_... |
a520fa265cd93187727897cc91c5f3d3513c1ba060f5b12fc6acf90c857d21c5 | Shell | 3,560 | 80 | #!/usr/bin/env bash
#
# mix_tumor_normal.sh -- in-silico tumor impurity (admixture).
#
# Builds an IMPURE tumor BAM by mixing simulated-tumor reads with normal reads
# at a target purity and depth:
# impure_tumor = purity * (tumor reads) + (1-purity) * (normal reads)
# A somatic variant that is heterozygous in the ... |
1e157a4f91816a52d68fd4849d6a89a4d74d54eda6840cf829cb1e9df2f02934 | Shell | 3,587 | 146 | #!/bin/sh
if [[ $1 == "" || $1 == "--help" || $1 == "-h" ]];then
echo "
wrangle_annotation.sh
-------------
finds introns, exons and splice sites in a GTF file
usage
sh wrangle_annotation.sh <GTF> <outfile_prefix>
GTF can be gzipped
outfile_prefix can be file name or full path
WARNING: this has only been tested ... |
721e9dc0335ddc2f0d29c3a72eddc115316d974eaf09b099cabbcf8356e7f229 | Shell | 3,631 | 97 | #!/bin/bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey);
# Arnab Ghoshal, Karel Vesely
# 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.ap... |
a55b33529e4e8223052e5ef37ede7ca57a6fc4ff45c5d73dae38cfd130bc5c99 | Shell | 3,679 | 91 | # ====== About run.pl, queue.pl, slurm.pl, and ssh.pl ======
# Usage: <cmd>.pl [options] JOB=1:<nj> <log> <command...>
# e.g.
# run.pl --mem 4G JOB=1:10 echo.JOB.log echo JOB
#
# Options:
# --time <time>: Limit the maximum time to execute.
# --mem <mem>: Limit the maximum memory usage.
# -–max-jobs-run <njob>: ... |
f074fca5f0275641bd4916f3d4dd50c76a19f8a2dc67d69c57810a700d7c6fb1 | Shell | 3,680 | 91 | # ====== About run.pl, queue.pl, slurm.pl, and ssh.pl ======
# Usage: <cmd>.pl [options] JOB=1:<nj> <log> <command...>
# e.g.
# run.pl --mem 4G JOB=1:10 echo.JOB.log echo JOB
#
# Options:
# --time <time>: Limit the maximum time to execute.
# --mem <mem>: Limit the maximum memory usage.
# -–max-jobs-run <njob>: ... |
d3987697e0ad4d4735dbe412e3a40deb3a53b1a4a49bd5e9813d73019d9d31fe | Shell | 3,837 | 136 | #!/bin/bash
# Requirements are:
# XCode
# Command line tools (check if installed with "xcode-select -p", otherwise install with "xcode-select --install")
# MacPorts or homebrew as package manager
# PackageMaker (https://developer.apple.com/downloads ::search::
#----------------------------------------
# managing inpu... |
90a63104765bc31cbd75eb5b52e161fd4238b8a389787ea0826fd7cbec9adb83 | Shell | 3,865 | 42 | #!/usr/bin/env bash
python spike_generation_script_large_scale.py -gs 0 -ps 2000 3000 1 -t 75 -s "non-shuffled" -n "full" &
python spike_generation_script_large_scale.py -gs 0 -ps 11000 12000 1 -t 73 -s "non-shuffled" -n "full" &
python spike_generation_script_large_scale.py -gs 0 -ps 101000 102000 1 -t 70 -s "non-shuf... |
1e563b7dc8dece18ca37565569780019c2e521ef60b4532cafcc6ddc30a7495d | Shell | 3,942 | 111 | savedir="../analysis/analysis0521-ood"
suffix="_light" # for light dataset
# suffix="" # for heavy dataset
figs=10
testdatas=(
"data0520_ood_odeconst$suffix"
"data0520_ood_odelinear1$suffix"
"data0520_ood_odelinear2$suffix"
"data0520_ood_pdeporous_randbdry$suffix"
"data0520_ood_seriesdamped$suffix"
"data052... |
81dda2fcbbf69f9e880573a0ba5e330b6f24352fe280315083a31f607370df34 | Shell | 4,064 | 98 | #!/usr/bin/env bash
# discordant_for_cluster.sh
#
# Pull every read pair belonging to one svaba discordant cluster into a small
# sorted+indexed BAM for IGV, and (optionally) print the cluster's row from
# discordant.txt.gz so you can see the tumor/normal read split that drove the
# call. Handy for "why is this discord... |
79c91c9b6f80891971039adbff8bbbae5c6bc2e861f3f21745f209b6b02c60bb | Shell | 4,069 | 145 | #!/bin/bash
## activate the `master` conda environment before running this script
# conda activate master
echo "Running this on ### $(hostname) ### \(* w *)/"
echo "Currently in conda environment: ### $CONDA_DEFAULT_ENV ###, located in: $CONDA_PREFIX"
echo "Starting at $(date)"
echo "multiBigwigSummary path: $(comman... |
5d4664b4eb394a7200db374e8f71c2aeef49124216a04f396e83d547115916a4 | Shell | 4,091 | 101 | #!/usr/bin/env bash
# Validate the torch / warp-lang / nvalchemiops coupling on a CUDA box across
# the supported PyTorch range. For each version: fresh venv -> resolver-coherent
# install -> `pytest -m gpu` -> deterministic energy/force dump. A same-run
# torch-2.10 baseline is then used to diff every other version.
#... |
4acf5dad438aa26b5e7eea1470ab83302bb3b91435b110b40934365a5a7cdc3c | Shell | 4,120 | 137 |
#Set the folder where your images are stocked
set in_path = /your/path/to/input/images
#Set the folder containing the anatomical T2 and mask
set t2_dir = /your/path/to/anatomical/images
#Set the folder where contrast images will be stocked
set out_path = /your/path/to/the/output/directory
#If the output directory... |
c74304cb8f5ca5c57940e6f454dc256e5cc95f691bfadbb308d6c4f8b7d4bb21 | Shell | 4,141 | 72 | #!/bin/bash
source ./utils.sh
#Data path of all the project
echo "Enter the complete data path of the project: "
path=$(get_path ) #E.g. path="/home/brainstimmaps/20xx_Projects/2023_Deep/03_Data"
# Patient subfolder
echo "Enter the patient ID: "
pat=$(get_patient )
pat_exist=$(check_original_data $path/$pat)
echo "... |
4672a5c2c322966b89f02fe73b239c9dac2807ce8fa4d2ea5905c5b117836f11 | Shell | 4,145 | 79 | #!/bin/bash
# The purpose of this script is to register the T1w/T2w ratio files obtained from the Human Connectome Project (HCP) Pipeline
# (located under /cbica/home/panosf/Q7/structure_function_coupling/HCP_Processing_Pipeline/$subj/T1w/*) from MNI -> b0 space.
## PREREQUISITES:
# 1. Process the T1- and T2-weighte... |
8c6abe1e14aec89f4d3e07aacac055238efdf3ad6e8654b04792dac069de95c7 | Shell | 4,217 | 78 | #!/bin/bash
# OUTPUT STRUCTURE (only additions shown)
# path/pat
# - lead_recon
# - anat_t1.nii.gz
# - anat_t1_bet.nii.gz
#
source ./utils.sh
#Data path of all the project
echo "Enter the complete data path of the project: "
path=$(get_path ) #E.g. path="/home/brainstimmaps/20xx_Pr... |
bd10327485c4da53ea58fda3a892f54e3c2dda7db8bb15bb2ad1d84a0ea6ed83 | Shell | 4,232 | 89 | #!/usr/bin/env bash
#
# build_asan.sh — build svaba with AddressSanitizer (ASan) to pinpoint the
# teardown heap crash ("final flush" abort / segfault).
#
# Why this script exists: svaba's build has THREE compilation domains and
# ASan only helps where the code is instrumented:
# 1. svaba src + seqlib -> CMake-buil... |
57fd7cf74a657a62a30c3e2ce7d4d398b849cca626a943e66a76d81642e26181 | Shell | 4,342 | 129 | #!/usr/bin/env bash
set -eo pipefail
# Input json
input=/batchx/input/input.json
# Input BAMs
tmpBams=/tmp/tmpBams/
mkdir $tmpBams
# BAM Files
bamFilesString=''
for bamFile in $(cat $input | jq -r .bamBaiFiles.bamFile[]);
do
ln -s $bamFile "$tmpBams"
bamFile="$tmpBams$(basename -- "$bamFile")"
if [ "${#bamF... |
e9d4ef1a50b7eb36a70b360b33106fdadfbf102677c085ae1a0efc273f66a05e | Shell | 4,419 | 153 | #!/usr/bin/env bash
# plot_learn.sh — plot per-RG insert-size distributions from svaba learn data
#
# Usage:
# plot_learn.sh <ID_or_file> [output.pdf]
#
# If the argument ends in .tsv or .tsv.gz, treat it as the learn file directly.
# Otherwise treat it as a run ID and glob for ${ID}.*.learn.tsv.gz in the
# current d... |
b92315d67de0d1ca8090e316ad55b116d3ad4f5e5a78a964f2c00d6da9ff92c2 | Shell | 4,429 | 145 | #!/usr/bin/env bash
# Copyright 2013 Johns Hopkins University (author: Daniel Povey)
# Apache 2.0
# This script operates on a directory, such as in data/train/,
# that contains some subset of the following files:
# feats.scp
# wav.scp
# vad.scp
# spk2utt
# utt2spk
# text
#
# It copies to another directory, pos... |
d8ed422de257b9d194dd7da8054811715a46d224aa708a949dbbd7094014f8f3 | Shell | 4,461 | 97 | #!/usr/bin/env bash
# To start, set "python_path" to be the path to Python 2 on your system, and
# set "root" to be the directory containing this script and the other provided scripts.
# Then, make a new directory, which we will call "mycnvs". Then make the directories mycnvs/erds, mycnvs/cnvn, mycnvs/erds/original, ... |
528e712354f038148851c60eb4d44bf5116bcaa4624d945d3c0f7d497ae629e7 | Shell | 4,498 | 154 | #!/bin/bash
## activate the `master` conda environment before running this script
# conda activate master
# usage: ./04.run_multiBamSummary_in_consensus_peaks.sh cell_type
echo "Running this on ### $(hostname) ### \(* w *)/"
echo "Currently in conda environment: ### $CONDA_DEFAULT_ENV ###, located in: $CONDA_PREFIX"
... |
9b92a44e0ce6aaa686d55d99ccaa6bccda7cb81290c1b29095d6c26ef846cef8 | Shell | 4,567 | 166 | #!/usr/bin/env bash
#
# sort_and_dedupe_bps_old.sh — sort + dedup + PASS-filter for legacy
# (pre-2.0) svaba bps.txt.gz files.
#
# Same logic as the v3 postprocess step but with auto-detected column
# positions from the header row. Works on any bps.txt.gz schema as
# long as the header has #chr1, confidence, and either... |
98c287fada1cf395d4c345d79497f910b918126df8a46c64d0f1614848e384ed | Shell | 4,605 | 130 | #!/usr/bin/env bash
# r2c_for_contig.sh
#
# Given a svaba contig name, reconstruct the per-contig read-to-contig
# (r2c) alignment BAM for IGV. Uses the `bz:Z` aux tag that svaba writes
# on every r2c-aligned read (cname-keyed) to pick the right reads out
# of corrected.bam.
#
# Usage:
# r2c_for_contig.sh CNAME CONTI... |
bfd03efbeccc4ca8976c43822b7076017731be5b64cd11f9c6f0982a20cb3992 | Shell | 4,770 | 121 | #!/bin/bash
# WHAT IT DOES
# transforms broadmann atlas defined in MNI ICBM 2009a Nonlinear Symmetric space into the FSL functional space (MNI152 nonlinear 6th generation)
# by doing antsRegistration (takes some time)
# regrids it to the FSL voxels representation
# relabels it with increasing codes (only known areas)... |
9a087c2689d5950cc0de353dcc1352c04335a5f203aeef63f1b4786e442c64ba | Shell | 4,864 | 98 | #!/bin/bash
set -ex
# code checking
pyflakes .
# activate the fedml environment
source "$HOME/miniconda/etc/profile.d/conda.sh"
conda activate fedml
wandb login f01534a5607f98fefbff8aa5947e3fa66a160df0
wandb off
assert_eq() {
local expected="$1"
local actual="$2"
local msg
if [ "$expected" == "$actual" ];... |
6b9ed6a727a7a4494c21fd6b392e39878debc1d3a497791ead1978a58261350a | Shell | 4,901 | 165 | #!/bin/bash
## activate the `master` conda environment before running this script
# conda activate master
# keep track of which server is used to run this script
echo "Running this on ### $(hostname) ### \(* w *)/"
echo "Currently in conda environment: ### $CONDA_DEFAULT_ENV ###, located in: $CONDA_PREFIX"
echo "Star... |
d8010392f23fde44a2b86c4e23f5d5ca3b9d61d87032cd82926efb6cd67c3c8d | Shell | 4,909 | 151 | # This document contains examples of commands used to run BWA and the CNV-detection algorithms.
# Of course, details will differ depending on how your system is set up, so these commands
# are intended only as a guide.
### BWA
bwa mem -M genome.fa read1.fastq read2.fastq > output.sam
### GATK
# Followed standard best... |
3a3d222a25ca9fca789bf5eda62e3cee3e668e45e9a2835c0248d50914594d7a | Shell | 4,960 | 159 | #!/usr/bin/env bash
###
# OpenViBE – SonarQube analysis script
#
# Generates coverage + sonar-project.properties + runs sonar-scanner
###
set -e
set -o pipefail
eval "$(pixi shell-hook)"
PROJECT="$CI_PROJECT_NAME"
run-clang-tidy -p "$BUILD_FOLDER" -j2 > clang-tidy-report.txt
cppcheck --enable=warning,style,perfo... |
bc0006641a8ddbecf7be1e895df42b323aa09974d908d7b203bc16639e4bf045 | Shell | 4,987 | 96 | #!/bin/bash
# The purpose of this script is to register the BOLD files output by the CONN software from MNI to native diffusion (b0) space and prepare the necessary files to
# create voxel-based functional connectivity matrices for each Penn subject
## PREREQUISITES:
# Before running the script you need to:
# 1. Pro... |
8c0e27c0a3701500212187d024c9369924192e918f8166bfb1a06d5eaa5fa4e0 | Shell | 5,045 | 153 | test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest
. ssshtest
set -o nounset
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
... |
b8cacd7bb7ecf50a16f09a82da161680108750e2cb86163e171ce4ce46168578 | Shell | 5,170 | 40 | python save_syn.py --dataroot /research/cbim/vast/qc58/pub-db/MMWHS/processed/fsl/2d --name FSL_exp1 --input_nc 3 --output_nc 2 --model pix2pix --netG resnet_9blocks --direction AtoB --dataset_mode fsl1db --modality mri --epoch 200 --results_dir results/FSL_exp1_acdc_mri
python save_syn.py --dataroot /research/cbim/va... |
c60802f374594a29065d53fffb00a1fc62fbe60c14e31de524f4aceb4cd2aec7 | Shell | 5,204 | 135 | #!/usr/bin/env bash
# Copyright 2016 Johns Hopkins University (author: Daniel Povey)
# Apache 2.0
# This script operates on a data directory, such as in data/train/, and adds the
# utt2dur file if it does not already exist. The file 'utt2dur' maps from
# utterance to the duration of the utterance in seconds. This ... |
d7331369fbf0782ef5599a5ccf92dab23e55ca1b41e4445a82587616846e3a71 | Shell | 5,228 | 160 | #!/bin/bash
# Copyright 2010-2013 Microsoft Corporation
# Johns Hopkins University (Author: Daniel Povey)
# 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.ap... |
b834bd0cd437a5839690ac61f84f52c6a12fc262a9b84a2d8ae8a7e056d42ef9 | Shell | 5,257 | 163 | #!/bin/bash
get_path(){
read base_path
echo $base_path
}
get_patient(){
read patient_id
echo $patient_id
}
get_fsl_subject_path(){
read fsl_path
echo $fsl_path
}
compute_Brodmann_average()
{
functional_image_path="$1"
output_path="$2"
LUT_path="$3"
separated_path="$4"
echo c... |
cef4cc1730efc8e902c7d22815e839a874617971d8f49d91705e4c2ace9e973a | Shell | 5,277 | 154 | #!/bin/bash
# STAR mapping & RSEM quantification
# Inputs
read1=$1 #fastq file for read1
read2=$2 #fastq file for read1, use "" if single-end
STARgenomeDir=$3
RSEMrefDir=$4
dataType=$5 # RNA-seq type, possible values: str_SE str_PE unstr_SE unstr_PE
nThreadsSTAR=$6 # number of threads for STAR
nThreadsRSEM=$7 # numbe... |
8deca3fdae72f8160fb9ebd0ad5dd6ab3ca5682a4e266b2340a47b0885c7b551 | Shell | 5,408 | 138 | #!/bin/bash
# Split data direcoty into two data direcotries
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# shellcheck disable=SC1091
. ./path.sh || exit 1;
shuffle=false
num_first=0
num_second=0
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
if [ $# -ne 3 ]... |
2ab942c85aafa768bc7a6bdd08ac689ac449f9be6f54a846e12718736483d262 | Shell | 5,446 | 151 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
fab36032eecdf016548edfc5da153b8e03675cd30b5364e24068554a3233852f | Shell | 5,457 | 193 | #!/bin/bash
# PASCAL VOC dataset http://host.robots.ox.ac.uk/pascal/VOC/
# Download command: bash data/scripts/get_voc.sh
# Train command: python train.py --data voc.yaml
# Default dataset location is next to /yolov5:
# /parent_folder
# /VOC
# /yolov5
start=$(date +%s)
# handle optional download dir
if [ -z... |
57aa85e7b916bd69a1929032c566f127c4de22f15ef3ada9a1515a961e699bd6 | Shell | 5,535 | 119 | #!/usr/bin/env bash
#
# build_svaba_image.sh — build a svaba worker image from a specific git commit.
#
# Boots the builder VM, checks out the requested commit/branch/tag, rebuilds
# (submodules + svaba at -O3 -march=native, the cloud-perf build), VERIFIES it
# compiled, installs svaba onto PATH, then snapshots the bui... |
a37a9c0bee4283d5124b6372a91c62dde3c9f26ed26f011d2aa3b3d2f4282757 | Shell | 5,676 | 150 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
be4026e2d3897cce065309fc9c0ee5c03bad88d3f1422f2fd2ddade9b4a12267 | Shell | 5,880 | 134 | #!/bin/bash
set -e
if [ $# -eq 0 -o x$1 = "x-h" -o x$1 = "x-help" -o x$1 = "x--help" ]; then
echo "Usage:"
echo " $0 source-file(s)"
exit
fi
for i in $@
do
echo Update $i...
TMP=`mktemp`
sed -e "s/\<undirected graph\>/_gr_aph_label_/g"\
-e "s/\<undirected graphs\>/_gr_aph_label_s/g"\... |
cf1f7d90c839e8a7e3bfbd9071386bd21b3f2f5c80622ad29b7259f59235ceeb | Shell | 5,972 | 180 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
# Prepare kaldi-style data directory for JSSS corpus
fs=24000
num_dev=50
num_eval=50
train_set="train_nodev"
dev_set="dev"
eval_set="eval"
shuffle=false
# shellcheck disable=SC1091
. utils/parse_options.sh || exit 1;
d... |
455bb28d5e3e2e9288e589016aed897df8fecca2f07c06769901f72e439dacda | Shell | 6,248 | 204 | #!/usr/bin/env bash
#
# sort_bps.sh — sort a svaba bps.txt.gz file by (chr1, pos1, chr2, pos2, -somlod)
#
# Reads: ${ID}.bps.txt.gz
# Writes: ${ID}.bps.sorted.txt.gz
#
# Preserves the leading "#chr1 ..." header row, then sorts the body by:
# 1) chr1 (natural/version order) ascending
# 2) pos1 (numeric) ... |
a9682d6bddb8a9cef49c806eacb62ae934259fff9c0447765231c175fa8cab94 | Shell | 6,352 | 158 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
459036ac3e30287c1aba0b4450018ec9d81de2f98d4e21733f70c01b16bd8386 | Shell | 6,359 | 158 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
49e1575321bbf17d55b289a8e0d2cddf605d138f282c4e15ddbf50f3ed44bcb3 | Shell | 6,522 | 163 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
d7316d05a066f98f5224df963825798754633354cfc7b80252fe4747a8cb9ddf | Shell | 6,555 | 164 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
4014abf00088d7baa3089e3a6c8c1f84514a98e10101253bf7b7fb8c11aca562 | Shell | 6,576 | 164 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
40204c85842162c8527de5bf84a044cea08331724504f2d5e4182c1d6071cb21 | Shell | 6,580 | 164 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
e3a173e5d347f8d98f21f6e5a5e2bd4438151f389841c2bde73dcd6f4e0638dc | Shell | 6,722 | 167 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
dc96e84faea427757d6c52fd3a38fcdab0eef79c341fce5dfe95480023f63b4c | Shell | 6,746 | 145 | #!/usr/bin/env bash
#
# run_sim.sh -- end-to-end svaba SV simulation:
# 1. generate non-overlapping SVs + diploid donor genome + truth set
# 2. ART -> paired FASTQ from each haplotype (half coverage each)
# 3. BWA-MEM align back to the reference -> sorted/indexed tumor BAM @ MAXCOV
# 4. downsample to each reque... |
fdd87b3f0f78dee567863de70835f6651536a9efedba11b96cba5d9d303ffa6e | Shell | 6,753 | 215 | #!/usr/bin/env bash
# This script makes sure that only the segments present in
# all of "feats.scp", "wav.scp" [if present], segments [if present]
# text, and utt2spk are present in any of them.
# It puts the original contents of data-dir into
# data-dir/.backup
cmd="$@"
utt_extra_files=
spk_extra_files=
. utils/pa... |
3216aa7d6d40fbb2cb9ed9c2e981d3a5f92c9f8b3694097fa39ad50d20ceeab8 | Shell | 6,795 | 117 | #Commands needed for extracting data of MikJo from Freesurefer to Zeffiro.
#Atena Rezaei, 2019.
#System specific variable definitions
SUBJECT_DIR="/media/datadisk/atena/Carstendataset/Carsten_freesurfer"
SUBJECT="Carsten"
OUT_DIR="/media/datadisk/atena/Carstendataset/Carsten_freesurfer/output"
#Reconstructing the da... |
d48bee8ceb0d59818ed858692938a1859d924a5c44700a03931e5ebaba6e8a3c | Shell | 6,963 | 176 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in trainin... |
fc964f1c020d1ae4807e5dc40d6efa81f3c6a815d200f7e5aadd0f5790aa025b | Shell | 7,054 | 173 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
8c36ed5df49bdc205ef11f0a82f302b1fc4df6cab4f557d39c36dabf8c2d58b7 | Shell | 7,064 | 173 | #!/bin/bash
# Copyright 2022 Jiatong Shi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
lang=english # language for training
verbose=1 # verbosity level (lower is less info)
n_gpus... |
e449b80da9c5d5f46548301d75c3be8531791d3aa5df5712208d22284191a687 | Shell | 7,087 | 172 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
989852b3a19c6b9ce1067565bdb4a19d4cb6b1c3679239d4bd10ad78f9f3b320 | Shell | 7,093 | 172 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
6779d422536190456b977e00be760764b669370dae4e0ec55c32afc4f7e10595 | Shell | 7,094 | 192 |
# Set these environment vars to point to
# your local installation of WASP
WASP=$HOME/proj/WASP
DATA_DIR=$WASP/examples/example_data
#
# Convert SNP files to HDF5 format. This program can be used
# on output from impute2 or on VCF files. Note that
# you do not need to repeat this step here if it was already
# done in... |
1d25023568c2d22b730fb857d9e337ad3a5ac078ca98e5f871640b4f220728a0 | Shell | 7,116 | 173 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
302eaeb9e030214718805fb97cd631c541e88909d9b4a2bccc9ff8bb033a5472 | Shell | 7,138 | 173 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
57c72fe0acdace74d2c40297f0a1645a04a6997f865f20a5e6c6994b16062532 | Shell | 7,159 | 173 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
f795b94ecbfc00af2d482dccfb8eb37b0069ae075b28e0aac5f5471afdfcf878 | Shell | 7,164 | 178 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=0 # number of gpus in traini... |
63e9692f90ec9c16c185fe5631fa3d4401b7a241e2aeed44e55811dfd39d4aea | Shell | 7,247 | 176 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in train... |
930d8ba5087f43195404f5f60ed46bf70ca40b151770cc28534645341e211a48 | Shell | 7,247 | 178 | #!/bin/bash
# Copyright 2019 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
801d31135b3fa2ce65f64a1e8a937d20d61f4cbfdc6fdc6220add83b7510cbe1 | Shell | 7,302 | 192 | #!/usr/bin/env bash
# Copyright 2010-2011 Microsoft Corporation
# 2012-2013 Johns Hopkins University (Author: Daniel Povey)
# Apache 2.0
# This script operates on a data directory, such as in data/train/.
# See http://kaldi-asr.org/doc/data_prep.html#data_prep_data
# for what these directories contain.
#... |
7911441b40b59cf9e76b56dedebedaf78bbbce97018d01a2adc2c08703200010 | Shell | 7,412 | 54 | set -ex
#python train.py --dataroot ./datasets/edges2handbags --name edges2handbags --model pix2pix --netG resnet_9blocks --direction AtoB --lambda_L1 100 --dataset_mode aligned --norm batch --pool_size 0
#python train.py --dataroot ./datasets/stroke_ct --name stroke_ct --model pix2pix --netG resnet_9blocks --direction... |
fbd988905af0e018bc7605b1e2867e3b633e87e75de05145dd8ea5b97c06785a | Shell | 7,448 | 282 | #!/bin/sh
set -x
#mingw='yes'
mingw='no'
nrnpy='yes'
#nrnpy='yes'
#nrnpy='no'
#nrnjvm='yes'
nrnjvm='no'
#nrnmpi='yes'
NPYVER=
#NPYONLY='yes'
NPYONLY='no'
if test mingw = 'yes' ; then
ltlibs=
else
ltlibs=
fi
if test "$NPYONLY" = "no" ; then
#all the .o files
find .. -name \*.o -print | sed '
/\/modlunit\//d
/... |
3ca14381c5f853df2be1142a04578e212401f87209c466206b181b123f065e2c | Shell | 7,492 | 186 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
bd3cc80d85dcc3436f2b0e3c3ceb6ae4a88eadca20c58bba2e645bc65a6ada7d | Shell | 7,681 | 188 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
8dd701c545ecff68c758ce21a0d6aafc35ed063f2879a770394f685ad2ecc881 | Shell | 7,684 | 188 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=-1 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n_gpus=1 # number of gpus in traini... |
9d1d8db40606772673288d6ae79e5ce5608d99b5381edb26eba333e4c60daf37 | Shell | 7,785 | 190 | #!/bin/bash
# Copyright 2020 Tomoki Hayashi, Adapted in 2022 Gunnar Thor Örnólfsson
# MIT License (https://opensource.org/licenses/MIT)
. ./cmd.sh || exit 1;
. ./path.sh || exit 1;
# basic settings
stage=0 # stage to start
stop_stage=100 # stage to stop
verbose=1 # verbosity level (lower is less info)
n... |
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