sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
506e8348c1da21dfc2a3b1bbfaeb5e32912025a10e2c37dcaaa18157cb99c097 | Shell | 1,027 | 29 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
epoch_count=$1
audio_sample_rate=$2
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi... |
1256e9c93796c8893d2c97270fd0791c668dd7dd2fdcce64899be4e5c40e1532 | Shell | 1,029 | 42 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
8f28423b8dfd361d6cdd35610292d02e2a7f5257d83d9c9d3a839dba7b3be905 | Shell | 1,029 | 31 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi;
# Force only one visible device be... |
96fadf1133f5f5b331a612e2151b843dd7fdd6af453e70997f1ac5d9b1636935 | Shell | 1,032 | 35 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_ir
train_path=../data/ir/train.csv
val_path=../data/ir/val.csv
test_path=../data/ir/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type spectra \
--data_p... |
d65bc0bb18e3ce72f891fba91560133d1c69ff3836399f79a5f86905827d8ef5 | Shell | 1,033 | 36 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_pcqm4mv2
train_path=../data/pcqm4mv2/train.csv
val_path=../data/pcqm4mv2/val.csv
test_path=../data/pcqm4mv2/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset... |
d22fb5b442c16804e73f77b25ec70e8be6db25d29170eccba235214581a3e606 | Shell | 1,035 | 37 | To add sinusoidal fit lines on top of a scatterplot using `ggplot2` in R, you can follow these steps:
1. Load the necessary packages:
```R
library(ggplot2)
library(dplyr)
```
2. Create a scatterplot using `ggplot` with your data:
```R
# Assuming you have a data frame called 'df' with x and y values
scatterplot <- ggp... |
ecaaad1819c3828cd18d45b617ab5d613e833b2491273c6efe32c50f1f6ada3a | Shell | 1,036 | 28 | #!/bin/bash
#SBATCH --job-name=null_alexnet
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add openmind/minic... |
fc6072335e103c842c5d1a48cd77c2b9a989037592db47b150df7e33513f3ca9 | Shell | 1,037 | 29 | #!/bin/bash
#SBATCH --job-name=null_alexnet
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add openmind/minic... |
f8a687a0d4f191b8b9e32b0d5e047a8bf09bb9930f59aa07bd75a50fd886a1a4 | Shell | 1,039 | 29 | #!/bin/bash
#SBATCH --job-name=null_alexnetRA
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add openmind/min... |
ca493e7e631a1f02282eb2ea59e387e22923dc0572962a93393fd49ac7dbf941 | Shell | 1,040 | 31 | #!/bin/bash
# created by Meng-Yun
# 03-Aug-2022
# clean the data with FIX on mutisubjects with FSL
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/Pre_processing
cd $filepath
for sub in `cat ./subjList.txt`; do
for ses_name in `cat ./$sub/sesList.txt`; do
echo ">>>>start to clean the data w... |
4d656d6583e249b0dd4575b181a00db4d5036337caeac705a56e8f3afe45c612 | Shell | 1,042 | 36 | #!/bin/bash
cd $(dirname $0)
cd ..
train_pcqm(){
mkdir -p log/$exp_name model/$exp_name
python -m paddle.distributed.launch --log_dir log/$exp_name train_gem2.py \
--distributed \
--batch_size=$batch_size \
--num_workers=10 \
--max_epoch=150 \
--dataset_config=$dataset_... |
a58cebecf31a3c57d47c953ea273b1d205e305ef24bb23d68e12ed100dd6af39 | Shell | 1,046 | 44 | #!/usr/bin/env bash
# script for generating documentation for NMODL
set -eu
if [ $# -lt 1 ]
then
echo "Usage: $(basename "$0") output_dir [python_exe]"
exit 1
fi
# the dir where we put the temporary build and the docs
output_dir="$1"
# path to the Python executable
python_exe="${2:-"$(command -v python3)"}"... |
e4f4f696f07dd120c9a5c861b939e8ba78febc15134703a16ad26e15a59a72b4 | Shell | 1,046 | 39 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
gunzip -c r... |
e86d8257814f6f2b5e3602cb4eb1a9fb97aa39e1015a12e2cecaae2ae3963b5d | Shell | 1,046 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add ... |
ec4bb32e949f5eb4488150af750b786cea875b99a3a10840fa71b1b1399fd30f | Shell | 1,046 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add ... |
3f26338655f0cdac3bb1058ea965b54d95852a779456741c3841b7bfbdcd938a | Shell | 1,047 | 41 | #!/bin/bash
# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
#
# PREREQUISITES:
# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
# - Virtual environment activated
# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
#
# USAGE:
# ./start_gunicorn.sh
... |
b3d8107c19af7bfbdeac7ae12f667f6cd099bca09d2fdfb5576f5f04ac745ccc | Shell | 1,047 | 41 | #!/bin/bash
QUEUE_NAME="my-quorum-queue"
VHOST="/"
remove_existing_queue() {
docker exec -it rabbit1 rabbitmqctl delete_queue $QUEUE_NAME
}
create_quorum_queue() {
docker exec -it rabbit1 rabbitmqadmin declare queue name=$QUEUE_NAME durable=true arguments='{"x-queue-type":"quorum"}'
}
verify_quorum_queue() {
... |
51f7076be0e383c2b4566ed7ade4d662af4d61465c7951a54748eabf9f758527 | Shell | 1,048 | 29 | #!/bin/bash
#SBATCH --job-name=null_resl2
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module ad... |
db1a7bb177ca33dc268e6c335297b6b570742b2dc7b599c459f913f62caad7d3 | Shell | 1,048 | 29 | #!/bin/bash
#SBATCH --job-name=null_resl2
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module ad... |
3bddfcd2288139d2c94876a01e9ae18885b68ca6d6fa46410d5306659330e271 | Shell | 1,049 | 37 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_qm9_multitask
train_path=../data/qm9/train.csv
val_path=../data/qm9/val.csv
test_path=../data/qm9/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type regr... |
3cef6081d5bc22c509407411e477c075e86e998516cee6aa3c2290a3c2b35e9b | Shell | 1,051 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add ... |
902020709175abcaa4f05d0393f31cfaebc4525a048932509eae41862bfc16a6 | Shell | 1,051 | 24 | #==========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/l... |
a907c14ae87c25ae50c7646fca8a430e73b2d734e0d85f8470a32f9eb461e69b | Shell | 1,051 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add ... |
d5ef5921bebd5114c8e401cfa1bea1d956072868af13aed95b3edeb493c483f8 | Shell | 1,051 | 36 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/adnetworksppg/Project_1_Huang/NK01/tmp/log/
#$ -e /gladstone/bioinformatics/adnetworksppg/Project_1_Huang/NK01/tmp/log/
#$ -pe smp 4
#$ -l mem_free=40G
#$ -l scratch=50G
#$ -l h_rt=08:00:00
#$ -j yes
#set the paths
base_dir=/gladstone/bioinformatics/adnetworksppg/Pro... |
4b8fa5ca450bf7878d2bb5353da4c8a139a07bad17fe8f73a98cfc404f3f1c36 | Shell | 1,052 | 28 | #!/bin/bash
#SBATCH --job-name=null_resl2
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module ad... |
680b4f39b2261f9248bc5934f6ed9015ccca67253bc6a503717899e0903c19e9 | Shell | 1,053 | 29 | #!/bin/bash
#SBATCH --job-name=null_resl2
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module ad... |
a6c3469609274f1bff1c1af1dc33a1df273f3841d5cdea921e96dd5c93e3200c | Shell | 1,053 | 34 | #!/bin/sh
set -e
# This script updates the pinned requirements for linting.
# The lint requirements are split from the other ones since they often have
# incompatible dependencies.
THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
if command -v uv >/dev/null; then
VENV_CMD="$(command -v uv) venv --pyt... |
c9909da2b160aa7835ed8d24997197ade04156913392a790aa9a2cddd57b3a66 | Shell | 1,057 | 37 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_pcba_random
train_path=../data/pcba_random/train.csv
val_path=../data/pcba_random/val.csv
test_path=../data/pcba_random/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py... |
2d62177f15091c10d67a295a9c86f8b2e5bf206286eba4e57bbbacaad2fc2e90 | Shell | 1,058 | 30 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi;
# Force only one visible device be... |
b68e2a9ce32e2912f53c77744d0f15ed7cf6e1a185eeb22947272ac25ee1f31a | Shell | 1,058 | 52 | #!/bin/bash
#SBATCH -J ace_fin
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3700
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/10.2.0
module load Python/3.8.6
source ~/ace_pot2/bin/a... |
7e2eb52b34d5074ee270171ada19d6798b29672111a450f92a1c12f16d1f1726 | Shell | 1,059 | 31 | #!/usr/bin env bash
sudo apt install -y git
rm -rf score_install
mkdir score_install
cd score_install/
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b
. ~/miniconda3/etc/profile.d/conda.sh
export PATH=~/miniconda3/bin:$PATH
echo "export PATH=~/min... |
81abaa4b1591845beec074fe313e46b0bb72010a3ee19509fd9330006d105ea8 | Shell | 1,060 | 30 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
epoch_count=$1
audio_sample_rate=$2
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi... |
d7c2f9c45d6d52231112977aa4b48e836ef5e1dbabee8e5db6a2b26bfe6ada1e | Shell | 1,061 | 31 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi;
# Force only one visible device be... |
ea05bbf3ee9bdac1a5e0423ab59cc5f3b297599a275b9d9ec0073b73760a4e16 | Shell | 1,063 | 40 | #!/bin/bash
# exit when any command fails
set -e
# load modules on HPC
module load fsl
module load R/4.0.2
# subject
subj=$1
## APPLY FIX
echo "APPLY FIX: subject: " ${subj}
# paths and parameters
fix_path='/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/data/derivatives/fix/'
fix_cmd='/software/fix/fix-1.... |
9ae9edb145c3d621c5c81489ffe4e5865e446b2e9788c5f0d60daf76ed1a7e62 | Shell | 1,065 | 37 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_pcba_scaffold
train_path=../data/pcba_scaffold/train.csv
val_path=../data/pcba_scaffold/val.csv
test_path=../data/pcba_scaffold/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimiz... |
5cb073be93b98e8d9f617f43a0922b1f5a680f57545547ac54398f42e5cd0477 | Shell | 1,067 | 48 | #!/bin/bash
ROOT="."
MRIVOL="$ROOT/mri/crop/mri.crop.mgz"
MRIGM="$ROOT/mri/crop2/gray.crop.nii"
MRIWM="$ROOT/mri/crop2/white.crop.nii"
MRIVSL="$ROOT/mri/crop/vessels.manual.crop.mgz"
OCTVOL="$ROOT/oct/pool3x3x3/oct.win33.nii"
OCTMSK="$ROOT/oct/pool3x3x3/mask.nii"
OCTGM="$ROOT/oct/gray.lowres.mgz"
OCTWM="$ROOT/oct/wh... |
663484ae6679e08935ad1140dd7f6dffd9d0566dfcd1faa58305c6abd00f6cdf | Shell | 1,068 | 36 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
c26ad61eb878b3d62e2c28de8bf384f8f8259ab60c3ecef68e534f9dd40d9f59 | Shell | 1,068 | 32 | # start from splash path:
# usage: single_atlas_dice.sh $1 $2
# $1 Test atlas folder
# $2 Source atlas folder
ROOT_DIR=$(pwd)
# echo "Bash version ${BASH_VERSION}"
ATLAS=$(basename $2)
export QSUB_CMD="qsub -l h_rt=1:00:00 -l h_vmem=9.9G -l tmem=9.9G -l s_stack=128M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_err... |
efb97ea9ff1ce9120202b79e47c0f6c3a89644a9bde3e76ff0673a028d379c27 | Shell | 1,069 | 36 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
audio_sample_rate=$1
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi;
# Force only... |
ddd1ba1aaa3541ca2bf36ca37d033957244e915a2f281764d8cea849f427cce4 | Shell | 1,071 | 30 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --time=72:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses star/2.7.0e to align polished reads
module pur... |
4fc5ddc3ad745055a7427f7ef3600cb48db72394294a9cb7aabd6b7b0cc6e0c9 | Shell | 1,072 | 30 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
cf72c0a5b188899b6d5154dcdd31a98fa7a4cac7ea39985680b608478ef1483a | Shell | 1,072 | 30 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --time=72:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses star/2.7.0e to align polished reads
module pur... |
5dbc8c096cdcb542130d9863c9645d4e8df4c27c0f52bf6de20eeba95ceb2e02 | Shell | 1,073 | 30 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --time=72:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses star/2.7.0e to align polished reads
module pur... |
87393299c6745f02a78551489c79fd950e1c7fd4601798a1efc8d5586b041114 | Shell | 1,073 | 47 | #!/bin/bash
usage="$(basename "$0") [-h] [-f configfile] -- \
Run multiple stitch_well.sh submissions in parallel \
based on wells specified in config file.
where:
-h show this help text
-f path to config file
"
##Parse arguments
while [ "$#" -gt 0 ]; do
case "$1" in
-f) configfile="$2"; shift 2;;
... |
977efc239a12f0159d19575c4582c79321a06ee39043e4969985f4b37b1ec4ab | Shell | 1,073 | 30 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --time=72:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses star/2.7.0e to align polished reads
module pur... |
3d73f58d48f8f81466bd3771dc8242b1ccbcc5e447a6f707ff740cfe5cfc7736 | Shell | 1,075 | 37 | #!/bin/bash
python recalc_overfit.py cox_aids
python recalc_overfit.py cox_gbcs
python recalc_overfit.py cox_pbc
python recalc_overfit.py cox_veteran
python recalc_overfit.py cox_whas
python recalc_overfit.py deepsurv_aids
python recalc_overfit.py deepsurv_gbcs
python recalc_overfit.py deepsurv_pbc
python recalc_over... |
78e9effded50c5ce15fa9aabb6fb597f33fb33b980f02cd9cb42dfecff67de4b | Shell | 1,075 | 30 | #!/bin/bash
#SBATCH --job-name=null_2
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
#SBATCH --exclude=node093,node094... |
9856a5d24907b3df931be9d33517987066d0ccd6809e341ac8b8580646ec7af0 | Shell | 1,075 | 47 | #!/bin/bash
usage="$(basename "$0") [-h] [-f configfile] -- \
Run multiple stitch_well.sh submissions in parallel \
based on wells specified in config file.
where:
-h show this help text
-f path to config file
"
##Parse arguments
while [ "$#" -gt 0 ]; do
case "$1" in
-f) configfile="$2"; shift 2;;
... |
a2b658e70b70f7f0aef2e1bd5a89fc8d6c3e798ca08e94e9a8789ca3bae7e33b | Shell | 1,075 | 30 | #!/bin/bash
#SBATCH --job-name=null_1
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
#SBATCH --exclude=node093,node094... |
096aa2f65ff3fbf6c56d89559a4422c3a7b8a3585250e11dc13c4f94d18c8a6e | Shell | 1,076 | 38 | #!/bin/sh
### step 1: feature decoding
PARAM1="./feature-decoding/config/deeprecon-fmd-mscoco_fmriprep_500voxel_caffe_bvlc_reference_caffenet_allunits_fastl2lir_alpha100.yaml"
PARAM2="./feature-decoding/config/deepreconS6-fmd-mscoco_fmriprep_500voxel_caffe_bvlc_reference_caffenet_allunits_fastl2lir_alpha100.yaml"
#... |
428ebf689306de646d99491839c92471e8b7c38803a77a60fffddf4c23624021 | Shell | 1,077 | 37 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_pcba_random_nans
train_path=../data/pcba_random_nans/train.csv
val_path=../data/pcba_random_nans/val.csv
test_path=../data/pcba_random_nans/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparam... |
737233391ed3438ff30dac34eee2aef6b46c3e8f97f9f9ed6e586a9e68d07873 | Shell | 1,080 | 30 | #!/bin/bash
#SBATCH --job-name=null_3
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
#SBATCH --exclude=node093,node094... |
7bcca54f90af08d4dd1b7b6267a50fdff39dcff217f70b7099ce055c16e8881b | Shell | 1,080 | 30 | #!/bin/bash
#SBATCH --job-name=null_4
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
#SBATCH --exclude=node093,node094... |
f6e8544f6bbb1d246b701e8ad751326746eab47d2fb6ac1277ae639f72209b27 | Shell | 1,080 | 21 | #!/usr/bin/env bash
set -ex
SCRIPTDIR=$(dirname "${BASH_SOURCE[0]}")
kubectl apply -f "$SCRIPTDIR/deployment.yaml"
kubectl expose deployment testing --type=LoadBalancer --name=testing-service
# Wait for the postgres + rabbitmq pod to actually be Ready before letting
# tests run. The Service ClusterIP is reserved as s... |
eb2a0627503e27779cc7d5557a80c9fa79cbdb1d327113d23cca0311063c00c8 | Shell | 1,081 | 49 | #! /usr/bin/bash
#SBATCH -o /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/out/%A_%a_%x.out
#SBATCH -e /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/err/%A_%a_%x.err
#SBATCH -p carter-compute
#SBATCH -J profile_mem_load
#SBATCH -a 0-5
#SBATCH -c 2
#SBATCH --mem 64G
echo Starting
date
wdir=/... |
a4c5b3614c882c4752a3e7dbe8ad2dedd5033ee8641da550db1d9d70242409af | Shell | 1,083 | 44 | #!/bin/bash -l
cd $HOME
if [ -d ${HOME}/miniconda3 ] ; then
echo "miniconda installed in $HOME "
echo " ... continuing "
else
echo "miniconda not found in $HOME "
echo " ... installing "
# download latest miniconda3 env to home directory
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_6... |
d754ef1e58f68bb0a7b3e68410243e4aad815b0f5710f259e3582fbccfbb01c9 | Shell | 1,084 | 24 | #!/bin/bash
#SBATCH --job-name=spectemp
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=16000
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --partition=mcdermott
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node... |
fa329040a0fb91811d1765926d4547e8c419b8b585c804fe75c79f7aeb7322d2 | Shell | 1,085 | 31 | #!/bin/bash
export MRTRIX_NTHREADS=$1
#Subjects bblids
mapfile -t pnc < /work/scripts/MRtrix_recon/subject_lists/ltn_bblids.csv;
#Log FC and FDC
mkdir /work/data/MRtrix_recon/template/log_fc_10_new
mkdir /work/data/MRtrix_recon/template/fdc_10_new
cp /work/data/MRtrix_recon/template/fc_10_new/index.mif /work/data/MR... |
5c4fff37d0b6ceec14d3ed8a4cd4fa19e15e73d069812391213499692765581b | Shell | 1,086 | 27 | #!/bin/bash
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
echo "-----------------------------------------------------------------------"
echo "SRCDIR=${SRCDIR}, BDIR=${BDIR}"
echo "----------------------------------------------------... |
77e22aa7bbcda2eca1365b9096168a16d3ff474732d79c31402a863b6fd4f96d | Shell | 1,087 | 23 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
e3d7a5ec0515d99c72f5346e0e02a24087d50c9e8eb726796b1af5f60a0fb3e6 | Shell | 1,087 | 27 | #!/bin/bash
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
echo "-----------------------------------------------------------------------"
echo "SRCDIR=${SRCDIR}, BDIR=${BDIR}"
echo "----------------------------------------------------... |
8b6f733b1b5ff62e6a0fd4936e52063b04abb53b9547f8eadca732835d7ce65c | Shell | 1,088 | 39 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_qm9_gap
train_path=../data/qm9/train.csv
val_path=../data/qm9/val.csv
test_path=../data/qm9/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type regression... |
e33bcb0f04845780f1e613b14d48ecd0d4585c2e467b1c4347fc3b8647f1411f | Shell | 1,089 | 42 | #!/bin/bash
date
echo "Args: $@"
env
echo "jobId: $AWS_BATCH_JOB_ID"
echo "jobQueue: $AWS_BATCH_JQ_NAME"
echo "computeEnvironment: $AWS_BATCH_CE_NAME"
SOURCE_REF=$1
WORK_DIR=$2
COMMAND=$3
SAVED_OUTPUT=$4
SAVE_PATH=$5
REMOTE=$6
DEVICE=${7:-gpu}
if [ ! -z $REMOTE ]; then
git remote set-url origin $REMOTE
fi;
git f... |
f1628a0b3de3af69eb182e668b8a1cdb75eb806402ffc91ce03b4df3165e5e21 | Shell | 1,089 | 39 | #!/bin/bash
#SBATCH -p gpu_2l
#SBATCH -c 5
#SBATCH -N 1
#SBATCH -J ATAC_ONLY
#SBATCH --gres=gpu:1
#SBATCH -o corigami_atac_only.%j.out
#SBATCH -e corigami_atac_only.%j.err
#SBATCH -A tangfuchou_g1
#SBATCH --qos=Tangfuchoug2c
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd ... |
9759c776d0b1bde857e3858049c00d20f22230211f684d1bfd4b7a90ad91df2f | Shell | 1,097 | 39 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_qm9_u0
train_path=../data/qm9/train.csv
val_path=../data/qm9/val.csv
test_path=../data/qm9/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type regression ... |
82a38eaf9270da440af7d00e430725ea0548d2dca8e6b7eb3f76ecc506014135 | Shell | 1,098 | 33 | #!/usr/bin/env bash
##############################################################################
#
# Initialize the environment for the ./Tomcat/catalina-macapp.sh command
#
# Environment variables:
# GENEPATTERN_HOME
# CATALINA_HOME
###########################################################################... |
272ec1b9112299772685aec4d5284dc066c50204d01de165cda8e18feaf8a832 | Shell | 1,101 | 39 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -pe smp 4
#$ -l mem_free=40G
#$ -l scratch=50G
#$ -l h_rt=08:00:00
#$ -j yes
#$ -N cellra... |
d6beda183263aea70717ac8cc48dc65d5a12287a35aeee4c2c51aa11292e469c | Shell | 1,104 | 15 | bash ablation.sh experimental experimental3 50 4 20 && bash ablation_nophi.sh lines lines_nophi3 50 && bash ablation.sh grf grf3 50 8 20
bash ablation.sh experimental experimental3 50 4 20 && bash ablation_nophi.sh lines lines_nophi3 50 && bash ablation.sh grf grf3 50 8 20
bash ablation.sh experimental experimental3... |
4c856603e00d1c3b04d9fb50473185bc518bfd990c6269ed066fd63b038bf053 | Shell | 1,107 | 32 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/HLA_I_all_match/test/test_pos.csv \
--hla_class HLA_I \
... |
7f8cfa779845e3564324211e9eb144aeb83bd77016fb89ed9c4a39ef1e3b613a | Shell | 1,109 | 33 | #!/usr/bin/env bash
# Updates the documentation strings in the JSON files from the ITK Doxygen.
#
# Configuration for directories need to be manually done in the
# config_vars.sh file. The ITK Doxygen XML will automatically be
# downloaded if needed.
#
# Usage: JSONDocUpdate.sh Code/BasicFilters/json/SomeFilter.json
#... |
531848c8a22d38cea710c225d17407341b5a76e2692efa580d925ec63a3b2f61 | Shell | 1,110 | 32 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/HLA_I_full_mcpas/test/test_pos.csv \
--hla_class HLA_I \
... |
6e895a4049f551d7cee47436bcc041dab405708c263e8e7b2cfed766bbc11792 | Shell | 1,110 | 41 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_barriers_rgd1
train_path=../data/barriers_rgd1/train.csv
val_path=../data/barriers_rgd1/val.csv
test_path=../data/barriers_rgd1/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimiz... |
d84adaad04c23c2d6e0525ec08b5633e12d6fe2deb6f7059c296b1a89db22a4c | Shell | 1,110 | 41 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_barriers_rdb7
train_path=../data/barriers_rdb7/train.csv
val_path=../data/barriers_rdb7/val.csv
test_path=../data/barriers_rdb7/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimiz... |
e5b45d619e82e631bac2673c27989903589c07ed5543d292fa7c8cdbccb568e4 | Shell | 1,110 | 39 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
node --version
npm --version
npm install node-gyp@6.x
export PATH=$HOME/node_modules/.bin/:$PATH
devDir=$DS_ROOT_TASK/node-gyp-cache/
nodejsDevDir=${devDir}/nodejs/
electronjsDevDir=${devDir}/electronjs/
mkdir -p ${nodejsDevDir} ${electronjsDevDir}
no... |
64e806cbcbae03c426cf574ab6debe98b99a1afee2d6f518655bb772b854baab | Shell | 1,111 | 39 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_multi_molecule
train_path=../data/multi_molecule/train.csv
val_path=../data/multi_molecule/val.csv
test_path=../data/multi_molecule/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_opt... |
0b2c9acd3093288dad9c279aadb544667c74916a637b3cda2285e56e7edc0d7c | Shell | 1,112 | 29 | #!/bin/bash
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
DePTH predict --test_file data/HLA_I_all_match/train_valid/valid_pos.csv \
--hla_class HLA_I \
--output_dir... |
54ecad2ab91af429b716ba1131abd88fa1ab3d22a14d218331ed9b3e67d386b0 | Shell | 1,114 | 44 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/SEG_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/template/fd_10_new/sub-${subject}.mif
if [ -f ${OUTPUT_PROOF} ];
then
echo... |
fb1423b8ce721eb024823556a9fe74bfca18dc8925638d134b6c0ba4dc28ff63 | Shell | 1,114 | 35 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
# echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
# echo $0 \<deployedMCRroo... |
ebea0046350c8526fa889637f2dfae46f8227ded685d607e4613bd9a6c308da4 | Shell | 1,115 | 37 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# to test parameters used for MLSTEPS
# usage: ./STEPS_optimisation.sh $1 $2
# $1: atlas (in_vivo ex_vivo)
# $2: sample number
# echo "Bash version ${BASH_VERSION}"
export QSUB_CMD="qsub -l h_rt=10:00:00 -l h_vmem=3.5G -... |
de72636df6f28c23eb2623598ccd51f72880e81b990050626a34dee99c61e1e9 | Shell | 1,117 | 31 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
# outdir=${celltype}_ame_out_w... |
385f268f98dd259bc7f0ef5dd73f206042e36dc491918ea103b348a0aa1fa246 | Shell | 1,118 | 22 | #!/bin/sh
model="ResNet50multitask"
randnetw="False"
layers="layer1 layer3"
#layers="input_after_preproc relu0 maxpool0 relu1 maxpool1 relu2 relu3 relu4 avgpool relufc final"
#layers="input_after_preproc conv1_relu1 maxpool1 layer1 layer2 layer3 layer4 avgpool final"
#layers="GRU_1 GRU_2 GRU_3 GRU_4 Linear"
#layers="Re... |
bd3e1b6cd895849e5fc810a905cef95c0dfc0f026e76d48442e4c3f483523a0e | Shell | 1,118 | 32 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
# outdir=${celltype}_ame_out_w... |
d8f3d44ded0ae53f0d46fb46c1d8c41e225c728e36f7611a85bb40c0a6bc2f15 | Shell | 1,118 | 44 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/FOD_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/sub-${subject}/ses-PNC1/dwi/sub-${subject}_wmfod_new.mif
if [ -f ${OUTPUT_PROOF} ] ;
t... |
805dbdb81b03266896eb2a59f2e0036df3afa6de849661bdb5690af46d093384 | Shell | 1,120 | 32 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/HLA_II_all_match/test/test_pos.csv \
--hla_class HLA_II \
... |
a60e2ff5cf1b586fe255c264322a9a17b0df79de8aab8e247f31ad2d27b3203d | Shell | 1,121 | 31 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
# outdir=${celltype}_ame_out_w... |
34b95319937e49e2de2c037031bea3078c6d1b350f2ea4a982937ce8e6d138f9 | Shell | 1,122 | 29 | #!/bin/bash
#SBATCH --job-name=null_hmax
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=32000
#SBATCH --cpus-per-task=6
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=9,12,15,18,21,24
#SBATCH --exclude=node093,node040,node097,node098,node094,node037
#SBATCH --co... |
4eb8a6b60b1a6309e86931f1125fe7df7d03964a0eb85f7dc508538b6f50ac9c | Shell | 1,122 | 41 | #!/bin/bash
module purge
### Run fmriprep for specific sub
subj=$1
# fmriprep container
fmrip_con=/mnt/lustre/working/lab_lucac/shared/x_fmriprep_versions/fmriprep-20.2.1.simg
# paths
project_dir=/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/
bids_dir=${project_dir}data/derivatives/bids-fix/
out_dir=${pr... |
54dba181fab9f41be589bc5f1d534396ee338f5c1850c63a7b50479e3aa1981c | Shell | 1,122 | 45 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/RF_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/template/sub-${subject}/sub-${subject}_response_csf.txt
if [ -f ${OUTPUT_PROOF} ];
the... |
eca53efb17bbea08b26487fe4760e0bb0e1191a5f0aa86fc1e33599ace0d9821 | Shell | 1,122 | 32 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
# outdir=${celltype}_ame_out_w... |
2300b6e403139dedfe0cd27682e951fee580266e5127b36c4c4eba1cdeb1a9c7 | Shell | 1,124 | 37 | #!/bin/sh
### step 1: feature decoding
PARAM1="./feature-decoding/config/deeprecon-fmd-mscoco_fmriprep_500voxel_caffe_bvlc_reference_caffenet_allunits_fastl2lir_alpha100_quick_test.yaml"
PARAM2="./feature-decoding/config/deepreconS6-fmd-mscoco_fmriprep_500voxel_caffe_bvlc_reference_caffenet_allunits_fastl2lir_alpha1... |
ae5fba800d9751cb0bb301561756508cd9d11675f0de2134c5aafdf9127ff50d | Shell | 1,124 | 46 | #!/bin/bash -l
cd $HOME
if [ -d ${HOME}/miniconda3 ] ; then
echo "miniconda installed in $HOME "
echo " ... continuing "
else
echo "miniconda not found in $HOME "
echo " ... installing "
# download latest miniconda3 env to home directory
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_6... |
96c6834eb2627956476ce25ccb0f0fa5b93462d0e59659ab01e66562a80c5a9d | Shell | 1,127 | 32 | # start from splash path:
# usage: single_atlas_dice.sh $1 $2
# $1 Test atlas folder
# $2 Source atlas folder
ROOT_DIR=$(pwd)
# echo "Bash version ${BASH_VERSION}"
ATLAS=$(basename $2)
export QSUB_CMD="qsub -l h_rt=1:00:00 -l h_vmem=9.9G -l tmem=9.9G -l s_stack=128M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_err... |
94cef48f2363075f890c2f165dd8faccf6fb0652a57f4e95dbdee052fa610a7d | Shell | 1,134 | 23 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
9610e897469e39e54df53dcf89f432544a9c1b134e0f49610f696637234ab6f5 | Shell | 1,134 | 23 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
26056e9909bd38cd6ae594bfbdf769b869491edd14b27d0771cedc02bce53fba | Shell | 1,138 | 39 | #!/usr/bin/env bash
# Run all tests for the ethoscope device package
# This script runs unit tests, integration tests, and generates coverage reports
set -e # Exit on any error
echo "Running Ethoscope Device Package Tests"
echo "======================================"
# Change to the device package directory
cd "$... |
9badb96d33f753041700679daf9d67c3c7cd84440a156c2a444ec0e737fadee1 | Shell | 1,138 | 44 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/nii2mif_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/sub-${subject}/ses-PNC1/dwi/sub-${subject}_ses-PNC1.mif
if [ -f ${OUTPUT_PROOF} ];
... |
6da4d7c1314431e26c03d642950214348ebb78f3206a6981c55ca96a59b84657 | Shell | 1,144 | 41 | #!/bin/bash
#SBATCH --job-name=reann_init_925K_1
#SBATCH --time=06:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=12
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/11.3.0 Pyt... |
75d4b05041e3eaaadc5a5cb4cc7f5ba98fe61e49a9df0ad88e4ac5ae8f864a51 | Shell | 1,146 | 45 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/FODreg_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/sub-${subject}/ses-PNC1/dwi/sub-${subject}_fod_temp_NR_new.mif
if [ -f ${OUTPUT_PROOF} ... |
91a7114559443529b2a3c0d939ece94d582e720fcdee2f286721ffa376cd8c87 | Shell | 1,148 | 32 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/HLA_I_all_match/test/test_pos.csv \
--hla_class HLA_I \
... |
09737f352c9e621bd0b16e45ad2e399b98063c23f7b9e5031900efa884e137d6 | Shell | 1,151 | 37 | # set -ex
# models
RESULTS_DIR='Image_translation_codes/BicycleGAN/results/combined_SEN1_2_20%_summer'
# dataset
CLASS='combined_SEN1_2_20%_summer_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels ... |
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