sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5fc41c99a2717da1925e222e5872dabbe4a97745340c6b071b4280cc6f915428 | Shell | 1,156 | 25 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: REMOVE DUPLICATES AFTER RUNNING HEUDICONV
# PROJECT NAME: SFGPI
# WRITTEN BY LENNART WITTKUHN, ADAPTED BY SAM ... |
0372843885d67af5c427e624fd47f95f1cb16a2abbb07775edf869a77c1a986a | Shell | 1,159 | 29 | #!/bin/sh
mkdir ORI
# Download genome
wget http://agambiae.vectorbase.org/downloads/public_data/organism_data/agambiae/Genome/agambiae.CHROMOSOMES-PEST.AgamP3.fa.gz
wget http://agambiae.vectorbase.org/downloads/public_data/organism_data/agambiae/Geneset/agambiae.PEPTIDES-AgamP3.7.fa.gz
wget http://agambiae.vectorbase... |
b48c1e4d5a2746af3d0845fa8144e7cf838e0420f6786da63298bb09d1f22fe8 | Shell | 1,159 | 36 | #! /bin/bash
#SBATCH --nodes=1
#SBATCH -J mednist_train
#SBATCH -c 4
#SBATCH --gres=gpu:2
#SBATCH --time=2:00:00
#SBATCH -p big
set -v
# change this if run submitted from a different directory
export BUNDLE="$(pwd)/.."
# have to set PYTHONPATH to find MONAI and GenerativeModels as well as the bundle's script directo... |
d92b8b3ee9446926edb9e5635c91ba3e178579cab50da6d08c2881d9bfb0ddaf | Shell | 1,166 | 50 | #!/bin/sh -e
# Genes to use
#cat GPCRs.txt | grep -v "$^" | tr "\n" "," > genes.txt
cat t2d_genes.txt | grep -v "$^" | tr "\n" "," | tr -d " \t" > genes.txt
#---
# Prepare GTEx IDs file
#---
rm -vf gtex.ids || true
touch gtex.ids
for tissue in Brain Liver Pancreas Skeletal Subcutaneous Visceral
do
tis=`echo $tis... |
07a72eb06f662f772711e490df4141f62a49e646640ee88c8ac7bb2356ae8d90 | Shell | 1,168 | 44 | #!/bin/sh
# Download from NCBI
for num in 406684590 406684589 406684588 406684587 406684586 406684585 406684584 406684583 406684582 406684581 406684580 406684579 406684578 406684577 406684576 406684575 406684574 406684573 406684572 406684571 406684570 406684569 406684568 406684567 406684566 406684565 406684564
do
wg... |
1ec0d7bf0552f95cccea657ff9338a3d872fa3aa0e6f1cd19537d9c6a31d971d | Shell | 1,173 | 34 | #!/bin/bash
#
# Copyright 2024 AlQuraishi Laboratory
#
# 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 ... |
9f7636c718880e2d33ac6251ad007766b7ca5e06004856373a2f376b8d50d46f | Shell | 1,174 | 34 | #!/bin/bash
#
# Copyright 2024 AlQuraishi Laboratory
#
# 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 ... |
d673e5be523b9669305c7494a6d1016e56cb83f3e8678727221028db0ccaa32e | Shell | 1,177 | 27 | #!/bin/bash
#SBATCH -J dsets # Job name
#SBATCH -o dsets.%A.out # File to which stdout will be written
#SBATCH -N 1
#SBATCH -n 3 # number of ranks
#SBATCH -c 2
#SBATCH -t 0-08:00:00 # Runtime in DD-HH:MM
#SBATCH... |
3d9b46e1f43338d2d0a53a09863843d226ffc31a08f7fdb347829703af72ff5d | Shell | 1,179 | 49 | #!/bin/bash
set -e
if [[ $# != 6 ]]; then
echo "usecase: mode range precision type op input_file"
exit 1
else
MODE=$1
RANGE=$2
PRECISION=$3
TYPE=$4
OP=$5
INPUT_FILE=$6
fi
declare -A precision_option
precision_option["float"]=--precision-binary32
precision_option["double"]=--precision-binary64
declar... |
2c7c140810161958dba67799da663c772b6af79ca0ae438b50283f7d10b2392a | Shell | 1,184 | 63 | #!/bin/bash
Check_status() {
if [[ $? != 0 ]]; then
echo "error: test failed"
exit 1
fi
}
Check_difference() {
ret=$(diff -q $1 $2)
if [[ $ret == 0 ]]; then
echo "error: files must be different"
exit 1
else
echo
fi
}
Check_similarity() {
diff -s $1 $2
if [[ $? == 1 ]]; then
echo "error: files mus... |
3e206eda80baa28dd87dc8622e88b47f40522cf2b1a7c19ed3f33fdcb30884bc | Shell | 1,186 | 41 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_unknown cora_unknown.csv -v &
varKoder query --include-probs --model /Volumes/Ynes_Mexia/Corall/cora_model_cgr/trained_model.pkl --images /Volumes/Ynes_Mexia/Corall/cgr_unknown query_cora_cgr_try1
pid=$!
# Create a log file in the home director... |
d097e6fc203bacd163907f025da80ac34769de9e91893659210bf21079b4f667 | Shell | 1,188 | 49 | #!/bin/bash
. $INSTALLPATH/env.sh
modelist="ob ib full"
#modelist="ob"
typeList="float double"
nbSample=
inc=1
runListFile="parallelInput"
echo "" > ${runListFile}
for mode in ${modelist} ;
do
for realType in ${typeList};
do
if [ ${realType} = "float" ]
then
bit=32
rangelist=`seq 4 ${inc} 8`
p... |
26abb408a9b15447f01167029f992d277bad3965654057991284252d0759cf7f | Shell | 1,199 | 50 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User settings
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# * DATA: Path to the directory containing
# the data (see variable DATA below).
#
# * Input data:
# - Must be in raw/nrrd format. To create
# raw/nrrd files from the tif files, see
# the... |
9949f4d398457f3adb519e3cb9c7ce8c9fbc9ae3653f5f9afdf345bb4f4c5e6b | Shell | 1,199 | 43 | #! /bin/bash
salmon_path="/public/workspace/liyan/rna_data/clean_data/salmon-0.11.3-linux_x86_64/bin/salmon"
index_path="/public/workspace/liyan/rna_data/clean_data/salmon-0.11.3-linux_x86_64/bin/Mm.GRCm39.Hs.GRCh38.ensembl.cdna_salmon_index"
data_dir="/public/workspace/liyan/rna_data/clean_data2/RNAseq_H_J"
output... |
228f7196a3e0dff804e70acc76900b4e8f916993fff6f4009db6ce5a5dee0070 | Shell | 1,202 | 62 | set -e
TIME=/usr/bin/time
#results files
MINI_OUT=minimds_10kb_times.txt
MMDS_OUT=mmds_10kb_times.txt
CMDS_OUT=cmds_10kb_times.txt
MOGEN_OUT=mogen_10kb_times.txt
#reset
if [ -e $MINI_OUT ]
then
rm $MINI_OUT
fi
if [ -e $MMDS_OUT ]
then
rm $MMDS_OUT
fi
if [ -e $CMDS_OUT ]
then
rm $CMDS_OUT
fi
if [ -e $MOGE... |
3c5598f02da38fe398db9a7f01ef0d13906fa7f0b284679d81f445bbfce8db90 | Shell | 1,205 | 47 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=dedup-gigaverbo
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lustre/... |
e90ee2abace6703aadf11d9c2e5d20c4bdd9efd660e3e81ff2d0f3ff700f25fd | Shell | 1,211 | 67 | #!/bin/bash
name=tests_CGCNN
mkdir -p out_${name}
cat <<EOF > out_${name}/config.yml
property: [4]
target: [5]
max_size: 25
# type_list: [C, S, Si, O, H, N, Se] #cep
# bonding: [4, 2, 4, 2, 1, 3, 2] #cep
type_list: [H, C, N, O, F] #qm9
bonding: [1, 4, 3, 2, 1] #qm9
extra_features: [n_valence] # atomic_weight, atom... |
0b438054beb3deefce25d727790f0c281a105c6270c67527d6c18d0dbe07a6cf | Shell | 1,212 | 67 | #!/bin/bash
name=tests_GAT
mkdir -p out_${name}
cat <<EOF > out_${name}/config.yml
property: [4]
target: [5]
max_size: 25
# type_list: [C, S, Si, O, H, N, Se] #cep
# bonding: [4, 2, 4, 2, 1, 3, 2] #cep
type_list: [H, C, N, O, F] #qm9
bonding: [1, 4, 3, 2, 1] #qm9
extra_features: [n_valence] # atomic_weight, atomic... |
858ecbeb1f592e2f7d1cc1a357f68f1fe0185dea9e51ada6651a705d95c8a374 | Shell | 1,213 | 67 | #!/bin/bash
name=tests_GCN
mkdir -p out_${name}
cat <<EOF > out_${name}/config.yml
property: [4]
target: [5]
max_size: 25
# type_list: [C, S, Si, O, H, N, Se] #cep
# bonding: [4, 2, 4, 2, 1, 3, 2] #cep
type_list: [H, C, N, O, F] #qm9
bonding: [1, 4, 3, 2, 1] #qm9
extra_features: [n_valence] # atomic_weight, atomic... |
a37c5e1561857bf963b30dbb18a3597365a1c8f7604801e0f9bd082255acb460 | Shell | 1,213 | 44 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=shuffle-gigaverbo
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lustr... |
cd8a541c486c6b62baa38f559f49c9797627a9f30e111be3030a691fa88df463 | Shell | 1,213 | 67 | #!/bin/bash
name=tests_GIN
mkdir -p out_${name}
cat <<EOF > out_${name}/config.yml
property: [4]
target: [5]
max_size: 25
# type_list: [C, S, Si, O, H, N, Se] #cep
# bonding: [4, 2, 4, 2, 1, 3, 2] #cep
type_list: [H, C, N, O, F] #qm9
bonding: [1, 4, 3, 2, 1] #qm9
extra_features: [n_valence] # atomic_weight, atomic... |
c5d09ee5878c878454ce46adb5f2475629003f908785a5fedd37468f8dcf6902 | Shell | 1,217 | 45 |
set -e
set -o pipefail
# Use the OpenPBTA bucket as the default.
URL=${PBTA_URL:-https://s3.amazonaws.com/d3b-openaccess-us-east-1-prd-pbta/pbta-ancestry}
RELEASE=${PBTA_RELEASE:-v2}
PREVIOUS=${PBTA_RELEASE:-v1}
# Remove old symlinks in data
find data -type l -delete
# The md5sum file provides our single point of t... |
19f4f67edd8c55fed34c9b7100aedc4f94d1cd02a9200acbc2ddfefe33c737d0 | Shell | 1,220 | 52 | #!/bin/bash
cd ..
#source ~/.bashrc
#source ./scripts/utils.sh
#source /GPUFS/paratera/scripts/cn-module.sh
#module load CUDA/10.2 compiler/CUDA/10.2
#module load anaconda/2020.11
#module load nccl/2.9.6-1_cuda10.2
#module load cudnn/7.6.5.32_cuda10.2
module load cuda/11.3
source activate paddlehelix
export PYTHONUN... |
2d4645de492317893553390398e44c52f070e117acffef79fbbcf2fc6b01afed | Shell | 1,221 | 33 | #!/bin/bash
# This script includes examples using the cuBNM CLI.
# Usage:
# source ./cli_examples.sh
# This will load the test functions into the current shell. E.g.:
# cubnm_run_grid
cubnm_example_grid () {
cubnm grid \
--model rWW --sc example --emp_bold example \
--out_dir ./grid_cli \
-... |
43cfa1e4cb94a1a6713917aaa7f05bf642c714057c5c1d49fb52ba1ee255464c | Shell | 1,221 | 23 | salloc -p gpu_test -t 0-06:00 --mem 90000 --gres=gpu:3
module load python/3.10.12-fasrc01
source activate varKoder_cgr1
cd /n/holyscratch01/davis_lab/pflynn/soil
varKoder train --overwrite -b 300 -r 0.1 --single-label -e 30 -z 0 cgr_images varkoder_trained_model_SL1_images_cgr_FINAL
val_samples=$(grep -E 'True$' var... |
b76f4739746eceeb63874dd96c334cb5369c87b6f60938fba3f6c1b942bf13aa | Shell | 1,224 | 43 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=sgpu_long
#SBATCH --job-name=Tucano-sft
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=4
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=32
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a100:4
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/m... |
fa06959e267095612c73cb91bd585e3f66c0e02b02fb7a24984f66c9e3712c95 | Shell | 1,225 | 67 | #!/bin/bash
name=tests_GraphSAGE
mkdir -p out_${name}
cat <<EOF > out_${name}/config.yml
property: [4]
target: [5]
max_size: 25
# type_list: [C, S, Si, O, H, N, Se] #cep
# bonding: [4, 2, 4, 2, 1, 3, 2] #cep
type_list: [H, C, N, O, F] #qm9
bonding: [1, 4, 3, 2, 1] #qm9
extra_features: [n_valence] # atomic_weight, ... |
fde140cb064acaa8cd8fde39b893e099c5d6cc80a2318c620fa1f21995722145 | Shell | 1,225 | 46 | #!/bin/bash
#SBATCH -n 1 # 1 core
#SBATCH -t 0-05:00:00 # 5 hours
#SBATCH -J ms # sensible name for the job
#SBATCH --output=logs/tensorboard%j.log # Standard output and error log
#SBATCH -p sched_mit_ccoley
#SBATCH --mem 20G
#SBATCH -w node1238
##SBATCH -w node1238
##SBATCH --mem=20000 # 10 gb
##SBATCH ... |
e2f0d055c8c1ed2f43d88f315439da483e97622a6eff6e031807459a2b882e9f | Shell | 1,226 | 44 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=bpe-sentencepiece-training
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
sour... |
2ddb80ec10fff103e3ea59292b3cd3d34d8ddf88cb29c9f6f967ed9c22146154 | Shell | 1,228 | 35 | #!/bin/bash
#need to download sratoolkit.2.11.0-mac64
#set path
export PATH=$PATH:/path/to/sratoolkit.2.11.0-mac64/bin/
#Make id lists from Supplemental table
mkdir ../data/1_ids/
#Paired reads
awk '{print $1 FS $5 FS $6}' ../data/Adult_Table.txt | grep "Pair" | awk '{print $3}' > ../data/1_ids/paired_ids.txt
#Single ... |
78f9c6ea538cbda0454d1d2bcfe389c3142b2bdaf0aaccb8cb58999750304533 | Shell | 1,230 | 43 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=sgpu_long
#SBATCH --job-name=Tucano-training
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=4
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=32
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a100:4
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tuca... |
07c7e666b879cdcdbc69453106a77fed90b85756274a0a93f735234003c21e78 | Shell | 1,237 | 28 | #!/bin/bash -x
#To trim these sequences and merge them:
#pushd .. && make clean && make && popd
../SeqPrep -6 \
-f ./data/multiplex_bad_contam_1.fq.gz \
-r ./data/multiplex_bad_contam_2.fq.gz \
-A GATCGGAAGAGCACACGTCT \
-B AGATCGGAAGAGCGTCGT \
-1 ./out/pe_bad_contam_merged_1.fastq.gz \
-2 ./out/pe_bad_contam_merged_2.f... |
4ca878bddb956b7a779ee7c23e7544ffc8f3bb58d2434065d546ab6d96553e2a | Shell | 1,237 | 43 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# DATA PATHS
# - DATA: Folder containing input data
# - OUTDIR: Folder to store output
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DATA="data"
OUTDIR="data/out_filter647_01"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SAMPLES
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~... |
8c19e6ad1da1e1ddd7c9f641a9995e45952fe5b7f802076c9ef3ca9dd01bdfbf | Shell | 1,238 | 45 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=tokenize-gigaverbo
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lust... |
21e8c683525961776f0ae6e72b1bd0784c5f4d65f6d3d66d3399961b6cbf3315 | Shell | 1,241 | 34 | #!/bin/bash
if [ $# -lt 2 ] ; then
cat << EOF
Usage: mp_diffpow24 regparam.dat diffregparam.dat
Creates file with 24 columns; the first 6 are the motion
parameters, the next 6 are the square of the motion
parameters, the next 6 are the temporal difference of motion parameters,
and the next 6 are the square of the... |
cded60432f15be6cbbdf87e167f528db90b246a9e31386eeca501ca9c8c2ea34 | Shell | 1,241 | 47 | #!/bin/bash -x
#SBATCH --time=72:00:00
#SBATCH --account=def-misic176
#SBATCH --job-name=pyspi-hcp
#SBATCH --output=logs/%x-%A-%a.out
#SBATCH --error=logs/%x-%A-%a.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=64G
# Save some useful information to the "output" file
echo "==========... |
454fcfb04f628211e9c43a0aa2beaeb69830ad1afa8740a4ca34161dfe902b60 | Shell | 1,242 | 52 | #!/bin/sh -e
# These variables need to be updated with every version
base="dbNSFP4.0a" # Database version
dbZip="$base.zip" # Zip file name
db="$base.txt.gz" # Output file
# Check dbNSFP
if [ ! -e "$dbZip" ]
then
echo "ERRO... |
52d303fae29ce3c423a814451fb4b5a7afb15d00aa5e29a23a300188265293d2 | Shell | 1,242 | 50 | #!/bin/sh -e
#---
# Download
#---
for chr in LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11 LG12 LG13 LG14 LG15 LG16 MT
do
echo "Download chromosome $chr"
# Download GFF file
#wget "http://biomirror.aarnet.edu.au/biomirror/ncbigenomes/Apis_mellifera/special_requests/gff/ame_ref_Amel_4.5_chr$chr.gff3.gz"
# Downloa... |
033e34b6c4f98517005faee8611cb5f70697f6b7408267a7df10b999de683544 | Shell | 1,257 | 34 | #!/bin/bash
#
# This script is a quick workaround for the consistent failure of first_mult_bcorr in 01_proc-struc_volumetric.sh
# see first_run_all (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide)
#
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#--------------------------------------------... |
5dcbc8a0f363bb8da3471d743d20263915b70532ac00a4a66b4654c9236c8432 | Shell | 1,261 | 44 | # Sample script to finetune RAG using Ray for distributed retrieval.
# Add parent directory to python path to access lightning_base.py
export PYTHONPATH="../":"${PYTHONPATH}"
# Start a single-node Ray cluster.
ray start --head
# A sample finetuning run, you need to specify data_dir, output_dir and model_name_or_path... |
5389a2092c804a41e4fec029f78a148b9920ff0af4c7e9d4dc9066bd4cd25518 | Shell | 1,264 | 61 | #!/bin/bash
cd $(dirname $0)
cd ..
############
# config
############
runs=3
root="data"
config="model_configs/unsupervised_pretrain_config.json"
############
# use ctrl+c to kill parallel exec
############
trap killgroup SIGINT
killgroup(){
echo killing...
kill -9 0
}
train() {
local dataset=$1
local m... |
8c3816de680b79bd4233933e1901d933ac27f1102b79a7f8a4e41ccaf87db38c | Shell | 1,265 | 45 | #!/bin/bash
visualization=false
linear_model=false
grad_cam=false
causal=false
act_max=false
while getopts "vlgca" opt; do
case $opt in
v) visualization=true ;;
l) linear_model=true ;;
g) grad_cam=true ;;
c) causal=true ;;
a) act_max=true ;;
\?) echo "Invalid option -$OPTARG" >&2 ;;
esac
d... |
18ec3f7f8d553faee63c70d8692256f5bd79cdcc58dff9e07ae2d66bd140d819 | Shell | 1,267 | 49 | #!/bin/bash
#: Title : test_imgformat
#: Date : 2018-10-24
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgformat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
aa75f011fe61b0fb103831416588240f3b09281a4f48c705df403633c3d000fe | Shell | 1,267 | 31 | #!/usr/bin/env bash
# This script should be run from the repository root.
set -euo pipefail
source scripts/linux-target.sh
NUM_JOBS_MAKE=${CMAKE_BUILD_PARALLEL_LEVEL:-${CPU_COUNT:-8}}
while getopts ":j:" opt; do
case $opt in
j) NUM_JOBS_MAKE=$OPTARG ;;
\?) echo "Invalid option: -$OPTARG" >&2; exit 1 ;;
... |
620ade86e968df42ec8553e0f25e70ff2f187ab512e4eb3e5fb62bac29b40842 | Shell | 1,269 | 52 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$OMPI_COMM_WORLD_SIZE
# For weak scaling, adjust the number of reps accordingly
if [ "$1" == "strong" ]; then
script="strong_scaling.lmp"
logg="strong"
elif [ "$1" == "weak" ]; then
script="weak_scaling.lmp"
logg="weak"
else
echo "Invalid mode. Pl... |
0af0425517654b4214323f17c5b2566f450566f924c170180fb683fdc8ad9983 | Shell | 1,272 | 32 | #!/bin/bash
#
# Removes processed func files from subs with poor registration
#
#
# INPUTS:
# $1 : subject directory
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------------------
# Settings
ID=$1
SES=$2
subdir="/data_/t... |
ae7cb774c1b4814e5319002f24150d5a5a0eaa3c34ca53543ad35f5a1c7ea04d | Shell | 1,272 | 49 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_long
#SBATCH --job-name=Alpaca-Eval
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a40:1
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/... |
8685777aea7f5b0ca526335369e2823d46df03f580a418162be998e091d205f6 | Shell | 1,274 | 47 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_long
#SBATCH --job-name=mntp-simcse-eval
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a40:1
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tuc... |
e533a4a1c16925f95ea34d50883225162abaffd083fee92b3bfc3148597cb44d | Shell | 1,275 | 44 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=sgpu_long
#SBATCH --job-name=Tucano-mntp-simcse
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=32
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a100:1
#SBATCH --exclusive
source /lustre/mlnvme/data/the_t... |
162cb199224dc41358fcc24f20111266803ccc7cdf4be3c70a5094c74b929a61 | Shell | 1,277 | 36 | #!/bin/bash
#SBATCH --job-name=fs_reconall
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=5
#SBATCH --time=10:00:00
#SBATCH --qos=prio
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
echo omp num threads: $OMP_NUM_THREADS
# set subject id
SUBJECTS=('sub-01' 'sub-02' 's... |
fc9c0006cd98d515927689e8aeeed4642439edf0413b966ebef9ee7f6b639f96 | Shell | 1,277 | 23 | salloc -p gpu_test -t 0-06:00 --mem 90000 --gres=gpu:3
module load python/3.10.12-fasrc01
source activate varKoder_cgr1
cd /n/holyscratch01/davis_lab/pflynn/soil
varKoder train --overwrite -b 300 -r 0.1 --single-label -e 30 -z 0 images_VarKode varkoder_trained_model_SL1_images_VarKode_FINAL
val_samples=$(grep -E 'Tr... |
4f09271a33a908fa3748578a807cfa65ebf87d4b56c8135e5207c26d3327a6bb | Shell | 1,282 | 41 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_unknown_Xantho_attempt2 Xantho_unknown.csv -v
varKoder image --kmer-mapping cgr -k 7 -o cgr_unknown_Xantho_38 Xantho_unknown1.csv -v
varKoder query --include-probs --model /Volumes/Ynes_Mexia/Corall/cora_model_cgr/trained_model.pkl --images /Volu... |
d48b637bc520691ddafb419e7110a87d42610c543b65a327bc9be19b969a4f6e | Shell | 1,283 | 52 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$OMPI_COMM_WORLD_SIZE
# For weak scaling_million_atoms, adjust the number of reps accordingly
if [ "$1" == "strong" ]; then
script="strong_scaling.lmp"
logg="strong"
elif [ "$1" == "weak" ]; then
script="weak_scaling.lmp"
logg="weak"
else
echo "In... |
09ead6d9ea4c81ec541ca4f390487f32545e30842185a0c31104f278e6e34a87 | Shell | 1,285 | 48 | #!/bin/bash
#
# Manually changes individual bvals to desired value
#
# INPUTS:
# $1 : bvals file
# $2 : Target b values (array)
#
# OUTPUTS:
# Modified bvals file saved in same dir as original
#
#
# Mark C Nelson (2021), McConnell Brain Imaging Centre, MNI, McGill University
#-----------------------------------------... |
b4debfc0bf294c55f429b72008978968c57b2667aa365ba3eaae892136c2e01f | Shell | 1,289 | 40 | #!/bin/sh
# no sbatch, computations done in FMNH cluster with linus screen
conda activate varKoder
export CUDA_VISIBLE_DEVICES=1
export VARKODER_PATH=../varKoder/varKoder.py
mkdir -p vit_results
echo ARCHITECTURE vit_large_patch32_224, equal weight
#list all samples
export samples=$(find ./images -name '*.png' -ex... |
3df2279f92ae6ba113a6c6bbf09e9560436d650ce25751459e2a6b77a6c8837c | Shell | 1,295 | 35 | #!/bin/bash
set -e
verificarlo-c --ddebug -O0 test.c -o test
rm -f operations.txt operations2.txt
# Generation run
VFC_BACKENDS="libinterflop_ieee.so --debug" VFC_DDEBUG_GEN="operations.txt" ./test
noperations=$(wc -l <operations.txt)
# Test that exclusion works in filter mode
# Exclude the first two operations (in ... |
25ab9069e1c7888b8649ec32fe7f34070a1bbe91ba78839ff4224faabc2755c9 | Shell | 1,299 | 58 | #!/bin/bash
# This script builds the genomecomb extension using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build in (default ~/build/tcl$arch)
# -v|-tclversion|--tclversion: tcl version (default 8.5.19)
# -d|-debug|--debug:... |
cb87891f067cbaee8b40bedd4fe561c9bf82388749d7cbff36ca5d760d523b36 | Shell | 1,302 | 39 | # Sourced by every recipe: `flavor <ieee|prism>` sets the compilers and flags
# of one build. Both builds use the same LLVM front ends (verificarlo-c runs
# clang, then the PRISM pass, then clang again, with the caller's flags), the
# same -march and the same options, so the only difference between them is
# PRISM's ro... |
8d4aa80efa1ef4e5b4b179f193f5c4c5f4e2842c521c3d072fe8abd8480794ef | Shell | 1,303 | 28 | #!/bin/bash
module load homer/4.10
sample="93"
res="0.001"
mkdir ${sample}
cp ../${sample}v35CR_${res}/${sample}v35CR.diffloop1.bedpe ${sample}/${sample}v35CR.diffloop1.bedpe
cp ../${sample}v70CR_${res}/${sample}v70CR.diffloop1.bedpe ${sample}/${sample}v70CR.diffloop1.bedpe
cp ../${sample}v77CR_${res}/${sample}v77C... |
b1ac087542c8504edba7e1c95a74c0c03af7f3e9be831156ecc1a3f724b12c2d | Shell | 1,305 | 28 | ml load fmriprep/24.1.0
subj=${1##*-}
work=/home/repo/grieg/work
unset ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
#export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=6 # specify the number of threads you want to use
fmriprep /home/repo/grieg/neurogrieg_defaced /home/repo/grieg/neurogrieg_defaced/derivatives/fmriprep participant \... |
99edda52607a9f4159f1ee052b7e26fea1ed34250faef4776e7e08649ee6398c | Shell | 1,308 | 28 | #!/bin/bash
module load homer/4.10
sample="NCI"
res="0.001"
mkdir ${sample}
cp ../${sample}v35CR_${res}/${sample}v35CR.diffloop1.bedpe ${sample}/${sample}v35CR.diffloop1.bedpe
cp ../${sample}v70CR_${res}/${sample}v70CR.diffloop1.bedpe ${sample}/${sample}v70CR.diffloop1.bedpe
cp ../${sample}v77CR_${res}/${sample}v77... |
a39f10764a74b3b905d246103f6b7e242c097aa676dbfc376a7ab3e60f6d99ac | Shell | 1,309 | 13 | #!/bin/bash
# $1 : path to folder containing bioname == sim_folder
# $2 : regions to synth axons (eg "['MOp']" or "['Isocortex', 'SPVI']")
# $3 : mtype to synth axons (eg "PC")
# $4 : path to axon-synth config file
# $5 : path to axonal-projection output (eg "/gpfs/bbp.cscs.ch/project/proj82/home/petkantc/axon/axonal-p... |
f1a87505a96a4d113dfc61066dae50f97b8f0b8fd754bd1e297717369301244b | Shell | 1,309 | 43 | function exec_() {
local vm_root=/home/$USER/work
local host_proj=$1
local subprojs=$2
local projnam=$3
local cfgnam=$4
local exe=$5
local debug=$6
echo exec: $exe 1>&2
echo cfg : $host_proj/$subprojs/$projnam/test_config_$cfgnam.ini 1>&2
if [[ ! -f $host_proj/$subprojs/$projnam... |
9e55bd083e8490894213dc853de6182509973d4966dcc6b3e9f08b0aa4d243df | Shell | 1,311 | 60 | #!/bin/bash
dropbox=../../../dropbox
data_name=$1
tpl_name=default
gm=mean_field
act=relu
msg_dim=128
embed_dim=256
neg_size=64
lv=3
tpl_enc=deepset
subg_enc=mean_field
graph_agg=max
retro=True
bn=True
gen=weighted
gnn_out=last
neg_sample=all
att_type=bilinear
save_dir=$HOME/scratch/results/gln/$data_name/tpl-$tpl_na... |
271c19e63512742e4ae94038bf34fadb937350664770fc2cf7a64898b08288fd | Shell | 1,313 | 28 | #!/bin/bash
module load homer/4.10
sample="1451"
res="0.001"
mkdir ${sample}
cp ../${sample}v35CR_${res}/${sample}v35CR.diffloop1.bedpe ${sample}/${sample}v35CR.diffloop1.bedpe
cp ../${sample}v70CR_${res}/${sample}v70CR.diffloop1.bedpe ${sample}/${sample}v70CR.diffloop1.bedpe
cp ../${sample}v77CR_${res}/${sample}v7... |
7240ba800c5543afa99e0623f8ddc2fa57ad00c464eefe8076f5c43024ca54d9 | Shell | 1,313 | 28 | #!/bin/bash
module load homer/4.10
sample="1452"
res="0.001"
mkdir ${sample}
cp ../${sample}v35CR_${res}/${sample}v35CR.diffloop1.bedpe ${sample}/${sample}v35CR.diffloop1.bedpe
cp ../${sample}v70CR_${res}/${sample}v70CR.diffloop1.bedpe ${sample}/${sample}v70CR.diffloop1.bedpe
cp ../${sample}v77CR_${res}/${sample}v7... |
da2fe4c182f7c7cdc5d6574842c1d5f2cdf3cf7fd48524fca61ee14b5aaa2bf2 | Shell | 1,318 | 51 | TIMIT=$1
HTK=$2
PATH=$PATH:$HTK/HTKTools
WORK=work
cd $WORK
cat <<"EOF" > fbankconfig
SOURCEKIND = WAVEFORM
NATURALWRITEORDER = T
SOURCEFORMAT = NIST
SAVECOMPRESSED = FALSE
SAVEWITHCRC = FALSE
TARGETKIND = FBANK_E_D_A
TARGETRATE = 100000.0
WINDOWSIZE = 250000.0
PREEMCOEF = 0.97
ZMEANSOURCE ... |
1ab7aed9100caa964398927835678db2eff0afd4522c5c7efb16426a1ca024f6 | Shell | 1,321 | 6 | #paste in order of phylogeny, unsure if need but was nervous
paste ortho.cap.hypot.tpm.tsv ortho.ovi.hypot.tpm.tsv ortho.bos.hypot.tpm.tsv ortho.sus.hypot.tpm.tsv ortho.sor.hypot.tpm.tsv ortho.cav.hypot.tpm.tsv ortho.het.hypot.tpm.tsv ortho.fuk.hypot.tpm.tsv ortho.per.hypot.tpm.tsv ortho.mic.hypot.tpm.tsv ortho.mus.hyp... |
e04c238a2d33b5b953a0856a4b60ece533adae5065b0630038a7cc10c1c68b39 | Shell | 1,321 | 43 | BED_PATH=$1
MAT_PATH=$2
INTER_RES_KB=$3
INTRA_RES_KB=$4
INTER_RES=$((INTER_RES_KB*1000))
INTRA_RES=$((INTRA_RES_KB*1000))
BEDPE_PATH=all.bed
test ! -s $BEDPE_PATH && (python3 hicpro_to_bedpe.py $BED_PATH $MAT_PATH $BEDPE_PATH)
PREFIX=${MAT_PATH%.matrix}
CHROMS=(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 ... |
faf3f8e2623a23dd64c1f1bff3a35e8c779bea5e5bbeb3a2f16a2f221c0010fd | Shell | 1,321 | 46 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_short
#SBATCH --job-name=Tucano-eval-multilingual-harness
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=8:00:00
#SBATCH --gres=gpu:a40:1
#SBATCH --exclusive
source /lustre/mlnvm... |
f617cf49e2e8fb65c16c38130d994b5795cec9d1d7fad39b8d08db344634b091 | Shell | 1,329 | 61 | #!/bin/bash
set -e
# Test for the --debug-binary option
check_success() {
if [[ $? != 0 ]]; then
echo "Test failed"
exit 1
fi
}
check_executable() {
if [[ ! -f $1 ]]; then
echo "Executable $1 not found"
exit 1
fi
}
run() {
TYPE=$1
if [[ $# == 2 ]]; then
... |
2d62265b4339a7208aed893a18c0efca85e074347f0c67760b7a19c574d50330 | Shell | 1,332 | 53 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User inputs:
# - DATA: Folder containing autofluorescence data
# - OUTDIR: Folder to store output
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DATA="3D-microglia-netoglitazone/data/channel_520"
OUTDIR="3D-microglia-netoglitazone/data/segmentation"
#~~~~... |
95cb6cfbde1b565fa6ed97a34165b0c68fec04e9aff8b0eeb7f6585be2fd94d3 | Shell | 1,333 | 64 | set -e
#parameters
TIME=/usr/bin/time
DOMAIN_SIZE_PARAMETER=0.01
MIN_DOMAIN_SIZE=0.01
#results files
MINI_OUT=minimds_10kb_memory.txt
MMDS_OUT=mmds_10kb_memory.txt
CMDS_OUT=cmds_10kb_memory.txt
MOGEN_OUT=mogen_10kb_memory.txt
#reset
if [ -e $MINI_OUT ]
then
rm $MINI_OUT
fi
if [ -e $MMDS_OUT ]
then
rm $MMDS_OU... |
23527d6a152f73276c24e19b091e3665d13409ef4858dccf948b912d49d2b84b | Shell | 1,334 | 55 | #!/bin/bash
#: Title : test_siflist
#: Date : 2017-06-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../siflist
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
67b6cff91a6017f3846c8f293df2be0dac3d3272317448e9744d720d99da912c | Shell | 1,335 | 49 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=bpe-tokenizer-training
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /... |
d9a285ef01378473865b917322ddadbe7b003e1249a4c4a0c536434dfd6a7fac | Shell | 1,346 | 46 | #!/bin/bash
# Define the base directory
base_dir="varKodes/"
# Find all accessions with 00010000K reads and store them in an associative array
declare -A accessions_map
while IFS= read -r file; do
accession=$(basename "$file" | cut -d'@' -f1)
accessions_map["$accession"]=1
done < <(find "$base_dir" -type f -n... |
dffea1abfeac6b233887c463b6f342e300384a9deb215c669c84b32f2a1489c2 | Shell | 1,346 | 46 | #!/bin/bash
cd $(dirname $0)
cd ..
source ~/.bashrc
source ./scripts/utils.sh
root_path="$(pwd)/../../.."
export FLAGS_fraction_of_gpu_memory_to_use=0.6
export PYTHONPATH="$root_path/":$PYTHONPATH
pretrain_attrmask() {
compound_encoder_config="model_configs/pregnn_paper.json"
# compound_encoder_config="model_confi... |
5f6644339675938ab91cf8bbf19049fa9b661f67fc4777a63d493b1aeb2fab51 | Shell | 1,363 | 44 | #!/bin/bash
#
# Often used to move connectomes around
#
# Inputs:
# $1 : source directory
# $2 : target directory
#
# note: files should conform to expected naming structure i.e.
# subjectid_nstreamline_filter_segmentation_parcellation_weight.txt e.g.
# "HC001_5M_unfiltered_full_glasser-360_median-fa.txt"
# "HC... |
73403ab7e4a07fbb11b150003072a5a55e5bd46d14c785227ab2fbd88b69f868 | Shell | 1,363 | 50 | #!/usr/bin/env bash
set -e
# List of available graph convolution methods.
# schnet test is skipped, since it takes long time to preprocess...
methods=(nfp ggnn weavenet rsgcn relgcn relgat gin gnnfilm megnet nfp_gwm ggnn_gwm rsgcn_gwm gin_gwm relgcn_sparse gin_sparse megnet)
# device identifier; set it to -1 to trai... |
c26b65dc7fbb4b184291c68434bae30444f6b1d2dd908455f916a59e0a4bca7c | Shell | 1,367 | 54 | #!/bin/bash
# Two test two color tracking
case "$1" in
run)
## view data, & means runs in background
#oat view RAW &
#
## look at mask overlaid on video to make sure it's ok
#oat view FINAL &
#
#oat framefilt bsub RAW SUB &
# decorate
sleep ... |
d632db71f326baf36cbf40f7a39597772cfeb9f56efc81896a890b64f27ecabc | Shell | 1,370 | 46 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_short
#SBATCH --job-name=Tucano-eval-pt-harness
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=8:00:00
#SBATCH --gres=gpu:a40:1
#SBATCH --exclusive
source /lustre/mlnvme/data/the... |
532c5e9151283d69ff8a3553af69ce8ff254b3676ee0cb0f800c5cb329187476 | Shell | 1,372 | 47 | #!/bin/bash
# This is a pre-commit hook that ensures attempts to commit files that are
# larger than $limit to your _local_ repo fail, with a helpful error message.
# Maximum file size limit in bytes
limit=$(( 2200000 )) # 2,2MB
limitInMB=$(( $limit / 2**20 ))
# Move to the repo root so git files paths make sense
re... |
7f5289eb0e2974e27e3c42fdf2d703b4609ff2b34361d3e2494a89ee99792fdf | Shell | 1,383 | 23 | dataset=nist20
python data_scripts/make_splits.py --data-dir data/spec_datasets/$dataset/ --label-file data/spec_datasets/$dataset/labels.tsv --seed 1 --split-type scaffold --split-name scaffold_1.tsv --greedy-pack
python data_scripts/make_splits.py --data-dir data/spec_datasets/$dataset/ --label-file data/spec_datas... |
d4ad7c08e2461cd73e81fe53566de2df72ee8a457bf22a7198b28a1e676cb487 | Shell | 1,384 | 14 | #!/bin/bash
# $1 : path to folder containing bioname == sim_folder
# $2 : region to synth axons (eg "MOp")
# $3 : mtype to synth axons (eg "PC")
# $4 : path to axon-synth config file
# $5 : path to axonal-projection output (eg "/gpfs/bbp.cscs.ch/project/proj135/home/petkantc/axon/axonal-projection/axon_projection/out_M... |
58bee6e6746f85909a5d162153204170676a07ea306c6787d1ef38631a734e6a | Shell | 1,385 | 38 | #!/bin/bash
# Line 1 of this file must not be altered as it indicates how the command line interpreter should handle this script
# grab the files, and export it so the 'child' sbatch jobs can access it
# Directory where trimmed fastq files are located
# These files should not be gzipped
FQDIR=/data/hodges_lab/NPCdiff... |
f8d697efad75a3b9cd9c7b9fc494537b92dfb9ea155809eeaf9507d9e3ebe2b5 | Shell | 1,387 | 36 | # MaskRCNN
# Debug:
# ../configs/skin/skin_config.py --work_dir ../work_dirs/skin_config_debug
# train.sh:
CUDA_VISIBLE_DEVICES=0 python tools/train.py configs/skin/skin_config.py --work_dir ./work_dirs/trainnwd
# faster_rcnn
# Debug:
# ../configs/faster_rcnn/skin_faster_rcnn_r50_fpn_2x_coco.py.py --work_dir ./work_di... |
4b1092ced83a145962011c1cef9ac6cdfd3caccf44653847e74b818db4ba5fbf | Shell | 1,394 | 41 | #!/bin/bash
#
# Copyright 2021 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 applica... |
faa80e5d2d0d212354e1d209b147b340571dd63737342258fe25fd0fea61813b | Shell | 1,396 | 38 | #!/bin/bash
# Original script from https://github.com/gregvw/amd_sdk/
# Location from which get nonce and file name from
URL="http://developer.amd.com/tools-and-sdks/opencl-zone/opencl-tools-sdks/amd-accelerated-parallel-processing-app-sdk/"
URLDOWN="http://developer.amd.com/amd-license-agreement-appsdk/"
NONCE1_STR... |
ab5a664678798debf4ffd4179dfd864315e38bb7c7c68673460d087afb1c181c | Shell | 1,397 | 49 | #!/bin/bash
# Test that vector operations wider than the target vector registers are
# passed to the MCA wrappers following the target calling convention: with
# the IEEE backend, comparisons (--inst-fcmp) and arithmetic must give exactly
# the native results, for every ISA target the host can run.
source ../paths.sh
... |
23e6f4402140eba621b18924dc7b7be05d31b3beef211db52bae05406735a76e | Shell | 1,400 | 56 | #!/bin/sh
# this will delete all temporary data on the box
# e.g. all custom tracks, user session data etc
# and all temp files
# clean docs
find /usr/share/doc -depth -type f | xargs rm -f || true
rm -rf /usr/share/man /usr/share/groff /usr/share/info /usr/share/lintian
# clean package repo
rm -rf /var/lib/apt/list... |
d7a660cd85a154778c16c1c964bda03d396cdb0912bdebddd0b812ae627798d5 | Shell | 1,401 | 39 | #!/bin/bash
# Line 1 of this script must not be altered so that the shell interpreter knows what to do
# grab the files, and export it so the 'child' sbatch jobs can access it
# Set directory to where fastq files are located
FQDIR=/data/hodges_lab/NPCdiff_ATACme/raw_reads
# Export read1 files
export FILESR1=($(ls -1 ... |
ab32b214cff35a564157865e472f801acb7046d4bfa2ba81f3b39ac8abea4fbd | Shell | 1,402 | 49 | #!/bin/bash
#
# Quick function to QC T1w-dwi registrations
#
# Inputs:
# $1 : subject ID (01..30)
# $2 : Session number (1 or 2)
# $3 : Mode ("original"=main pipeline, "ants"=ANTs test, "flirt"=flirt test)
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#--------------------------------------... |
6fb1c6fec1740a9b1fa2d80ce557da5bb51d6f98bc12d2060ebf7b3165977134 | Shell | 1,403 | 41 | #!/bin/bash
#
# Copyright 2021 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 applica... |
06835101efa4f2086d5c8d37c40da51cfea69fb55c894c3f62444d49ed1d1e5d | Shell | 1,406 | 49 | #!/bin/bash
#
# Use to get the number of ICs for each subject prior to manual labeling (post-melodic, pre-fix)
#
#
# INPUTS:
# $1 : subject directory
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------------------
# Settings
d... |
8f083efd6279346da3f05fe73b160a686616bfae1330c3fe10f362ca9dc68fd9 | Shell | 1,407 | 35 | # Copyright 2020 The HuggingFace Team. 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 required by applicabl... |
a7112aa83014f3a482dcb5a1a6aca9a1216bad6e3afe1cc6257d1898370ae573 | Shell | 1,407 | 40 | #/bin/bash
#
# Produces FIX training file
#
# $1: subject directory
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
# Setup
source /data_/tardiflab/mwc/mwcpipe/ta... |
632fcb07b58e543a3a7ddac26a568e336c9d694e43fc761133708b38741ffd4a | Shell | 1,411 | 23 | set -ex
FILE=$1
if [[ $FILE != "ae_photos" && $FILE != "apple2orange" && $FILE != "summer2winter_yosemite" && $FILE != "horse2zebra" && $FILE != "monet2photo" && $FILE != "cezanne2photo" && $FILE != "ukiyoe2photo" && $FILE != "vangogh2photo" && $FILE != "maps" && $FILE != "cityscapes" && $FILE != "facades" && $FILE ... |
07d42c2e57feb93c6a7409d5ed116e79326693137dbea3535e674e6adee6d965 | Shell | 1,419 | 44 | #!/bin/bash
# Clones the HCP SC output dataset. The source dataset is currently stored on a
# local cluster and is not accessible publicly. Therefore this script can only be
# run by maintainers who have access to the cluster.
# The SC output was created by running https://jugit.fz-juelich.de/inm7/public/vbc-mri-pipeli... |
7587a2476788d24cdaf5a7c4f901f206a0a66694fc02f531a19c28c2cab2c19c | Shell | 1,424 | 49 | #!/bin/bash
#
# Quick function to QC T1w-dwi NONLINEAR SyN registrations
#
# Inputs:
# $1 : subject ID (01..30)
# $2 : Session number (1 or 2)
# $3 : Mode ("original"=main pipeline, "ants"=ANTs test, "flirt"=flirt test)
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------... |
20dc399f334d6431048d065d4df3a0af997069a04e3caffee32df91bc1131d52 | Shell | 1,427 | 40 | #!/bin/bash
# Line 1 of this file must not be altered as it indicates how the command line interpreter should handle this script
# grab the files, and export it so the 'child' sbatch jobs can access it
# Directory where trimmed fastq files are located
# These files should not be gzipped
FQDIR=/data/hodges_lab/NPCdiff... |
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