sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
499010c8b23c2444c78e906e3623765ce1e9c8d97c1b86ab2f722ec596dd5ae0 | Shell | 941 | 26 | dataset=nist20 # nist20
ppm_diff=20
workers=64
python data_scripts/forms/01_assign_subformulae.py \
--data-dir data/spec_datasets/$dataset/ \
--labels-file data/spec_datasets/$dataset/labels.tsv \
--use-all \
--output-dir no_subform.hdf5 \
--num-workers $workers
python data_scripts/forms/01_assig... |
39cf900232a44abacbcd26a1a163a2158b0a6f1c158d5c918fba137bb2472254 | Shell | 950 | 30 | #!/bin/sh
# Download FASTA
#wget ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.4_release/S_lycopersicum_chromosomes.2.50.fa.gz
#wget ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.4_release/ITAG2.4_cds.fasta
#wget ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.4_release/ITAG2.4_proteins... |
3777bf5c3af9c23fccc1e2a8bb9f59b113a5ecbfd905ca8de8d2151cde3f71f5 | Shell | 952 | 29 | #!/bin/bash
# grab the files, and export it so the 'child' sbatch jobs can access it
# Directory where mapped sam file output from WALT is located
BAMDIR=/data/hodges_lab/NPCdiff_ATACme/data/mapped_reads
export FILES_rep1=($(ls -1 ${BAMDIR}/NPCdiffATACme*_rep1_filtered.bam))
export FILES_rep2=($(ls -1 ${BAMDIR}/NPCdi... |
72a86a092882f007ee609759f40dc6470eed368cce489063c0bc42a2beb4bd88 | Shell | 952 | 45 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$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... |
ab921e5515f0ee6e796288a47b074c3bb086651e7b8fd329b9f00c4f7c9b2461 | Shell | 952 | 34 | #!/bin/bash
#: Title : test_tacmatch
#: Date : 2014-10-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmatch
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
3a1eb3505a0c684e3e21e10fc051bb1919726b51af6d256d4215ec1182be9a13 | Shell | 953 | 45 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$OMPI_COMM_WORLD_SIZE
# For weak scaling, adjust the number of reps accordingly
if [ "$1" == "strong" ]; then
script="strong_scaling.lmp"
logg="strong"
elif [ "$1" == "weak" ]; then
script="weak_scaling.lmp"
logg="weak"
else
echo "Invalid mode. Pl... |
d1bcdddc67db0035d5ecc20fc966d724b82ccada4caf4af5114c82566a2283bb | Shell | 953 | 45 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$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... |
f954d306e284f23c8676b713950099fa091269e591b4bdc4fb2832f66bc073e6 | Shell | 954 | 25 |
# Create direcotry for genome reference files
cd ~/snpEff
mkdir -p data/puccinia_striiformis_pst-78/ORI
cd data/puccinia_striiformis_pst-78/ORI
mv ~/Downloads/puccinia_striiformis_pst-78_1_* .
# Uncompress
unzip puccinia_striiformis_pst-78_1_data.zip
unzip puccinia_striiformis_pst-78_1_transcripts.gtf.zip
unzip pucci... |
ce7d3b06ca73d1933dabb039e16c2c498f1a31783be6e164406b5445d3d8f54f | Shell | 956 | 33 | #!/bin/bash
# Conduct sample preprocessing and background removal using cellranger and cellbender
# Sample ID
sample=$1
# FASTQ directory
fastq_path=$2
# Path to reference genome
ref_genome=$3
# Run cellranger
cellranger count --id=${sample} \
--transcriptome=${ref_genome} \
--fas... |
cced59a39262006f3deabac2f03a197116e95f7019d17007c1b7425efa80a6b4 | Shell | 959 | 15 | #!/usr/bin/env bash
DOWNLOAD_DIR=$1
DATA_ROOT=$2
unzip $DOWNLOAD_DIR/OpenDataLab___COCO_2017/raw/Images/val2017.zip -d $DATA_ROOT
unzip $DOWNLOAD_DIR/OpenDataLab___COCO_2017/raw/Images/train2017.zip -d $DATA_ROOT
unzip $DOWNLOAD_DIR/OpenDataLab___COCO_2017/raw/Images/test2017.zip -d $DATA_ROOT/
unzip $DOWNLOAD_DIR/Op... |
385157d50d05414ec23c10609e0e46be8545dc4e34d4fbdb37fe77a225aa980e | Shell | 962 | 34 | #! /bin/bash
#SBATCH --nodes=1
#SBATCH -J mednist_train
#SBATCH -c 4
#SBATCH --gres=gpu:1
#SBATCH --time=2:00:00
#SBATCH -p small
set -v
# change this if run submitted from a different directory
export BUNDLE="$(pwd)/.."
# have to set PYTHONPATH to find MONAI and GenerativeModels as well as the bundle's script direc... |
d9e413235cafa855f6f18f0c26bd9a206241c8a0932e2736349e7fb3b4b4ed6f | Shell | 963 | 39 | #!/bin/bash
set -e
source ../paths.sh
# ${LLVM_BINDIR}/clang -Wall -Wextra -O3 -march=native print.c operation.c test.c -g -o test-clang -I.
# ${GCC_PATH} -Wall -Wextra -O3 -march=native print.c operation.c test.c -g -o test-gcc -I.
# verificarlo-c -Wall -Wextra -O3 -march=native print.c operation... |
76cb84a79f1ea8069a04dd1943f041c48971f59f3376069c908ffb354230ff13 | Shell | 969 | 20 | mkdir -p out_synthesis_example && \
# first create a CellCollection that contains the morphologies for which we want synthesized axons
python create_collection.py && \
# and then synthesize the axons for the cells
axon-synthesis \
--no-debug \
--log-level info \
-c config_synthesis_example.cfg \
synthesize \
--morpholo... |
68a11a2074b57d1bd49de8c06fde616c18d87b6362033300d263672d73475be3 | Shell | 975 | 58 | #!/bin/sh -e
#---
# Create ref sequence
#---
echo "Creating reference fasta"
rm -vf $HOME/snpEff/data/genomes/canFam3.103.fa
for fa in $HOME/snpEff/data/genomes/canFam3.103/chr*.fa
do
chr=`basename $fa .fa`
echo " Chromosome $chr"
cat $fa \
| sed "s/^>gi|[0-9]*|ref|\(.*\)|.*/>\1/" \
>> $HOME/snpEff/data/g... |
b477315982f38c120528025a63e1d706555063e952011fd3a4cc24de54f78bd1 | Shell | 975 | 38 | #!/usr/bin/env bash
set -e
# List of available graph convolution methods.
methods=(nfp ggnn schnet weavenet rsgcn relgcn relgat megnet)
# device identifier; set it to -1 to train on the CPU (default).
device=${1:--1}
# Number of training epochs (default: 1).
epoch=${2:-1}
for method in ${methods[@]}
do
# Train ... |
f528efc6319b1cf15ba04a3b951405d07a07ef04e03c60e4882bf3d10c7f8205 | Shell | 976 | 30 | SUB="$1"
HEMI="$2h"
SUBJECT_ID="sub-0$SUB"
SUBJECT_ID_2="sub0$SUB"
# Convert labels from surface space to volume space
echo "Converting manually-defined ROI labels to niftis in functional space for subject $SUBJECT_ID"
# Define directories
PROJECT_DIR=../relational_neural_control/in_vivo_validation/in_vivo_fmri_data... |
39691d91e356acc03f8eeb4ad88e3bc996e8be0f14c7b74e536964e9f32b8a67 | Shell | 979 | 16 | #!/bin/bash
rm datasets/edges2shoes -rf
mkdir datasets/edges2shoes -p
axel -n 1 https://people.eecs.berkeley.edu/~tinghuiz/projects/pix2pix/datasets/edges2shoes.tar.gz --output=datasets/edges2shoes/edges2shoes.tar.gz
tar -zxvf datasets/edges2shoes/edges2shoes.tar.gz -C datasets
mkdir datasets/edges2shoes/train1 -p
mkdi... |
8590bb4dcafbeda08e7314948c1d990da5ec6f375ccd8f3ab1cca2cc89ddce94 | Shell | 979 | 24 | # 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... |
46ca2ba1d871612cf23de39265025dccd585de22010f9ecd35ed7a4d82f7f3db | Shell | 981 | 24 | #!/bin/bash
# Download folding resources
wget -N --no-check-certificate -P openfold/resources \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
# Certain tests need access to this file
mkdir -p tests/test_data/alphafo... |
660594c0e4c81a6558e7278e83953659bf5908f138ac50101df363ab8eb50e6c | Shell | 981 | 35 | #!/usr/bin/env bash
set -e
# List of available datasets.
# TODO: Investigate why training on `clearance` fails.
datasets=(bace_Class bace_pIC50 bbbp clintox delaney HIV hopv lipo \
muv nci pcba ppb qm7 qm8 qm9 SAMPL sider tox21 toxcast)
methods=(relgcn)
# device identifier; set it to -1 to train on the CPU ... |
cc2d08da806580d0524c3c0a7e853fb224c07d7a536c83d9d4fd4bf4b3621556 | Shell | 990 | 20 | #!/bin/bash
docker run --rm repronim/neurodocker:latest generate docker \
--pkg-manager apt \
--base-image ubuntu:20.04 \
--env "DEBIAN_FRONTEND=noninteractive" \
--run "chmod 777 /tmp" \
--install build-essential git ca-certificates netbase\
--miniconda \
version="py311_24.4.0-0" \
con... |
dcaee88a5ae61774fcb48cf23781445f65bd3462800e35af3f60f24f68d954be | Shell | 990 | 24 | set -ex
FILE=$1
if [[ $FILE != "cityscapes" && $FILE != "night2day" && $FILE != "edges2handbags" && $FILE != "edges2shoes" && $FILE != "facades" && $FILE != "maps" ]]; then
echo "Available datasets are cityscapes, night2day, edges2handbags, edges2shoes, facades, maps"
exit 1
fi
if [[ $FILE == "cityscapes" ]]; th... |
78de4d71d67b7131ecfe1348c507e8f8d8927f2b3049cd14b7b7c22e37c97b6a | Shell | 993 | 37 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_short
#SBATCH --job-name=train-xgboost
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=8:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lustre/mlnv... |
dac79d4fd3a9a45a93c1db2ca461b76fcdfb3f1937aa418ada539d527a37c71f | Shell | 994 | 23 | #!/bin/bash
set -e
TRANSCRIPT=$1
PFDOMAIN=$2
START=$3
END=$4
CONTAINER=$5
DATA=$6
TRANSCRIPTS_FILE=$7
range1=`singularity run -c -B ${DATA}:/data ${CONTAINER} panno --ensembl -i $TRANSCRIPT:$START | tail -n+2 | cut -f5 | cut -d'/' -f1 | sed 's/\:g\./_/g' | tr '_' '\t'`
range2=`singularity run -c -B ${DATA}:/data ${CO... |
42968ada9fc51f49ebc4a707b835285e8976e91b431691a71c2f5c199f5f9411 | Shell | 1,008 | 40 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_Cora Cora.csv -v &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
rm -f "$logfile"
fi
... |
0424040279ced5d16fe37ca5ec0ba4973702a65e52a262200078445f5b5bac62 | Shell | 1,010 | 18 | ######################
# The following script will only run for split_1_rnd1 (random split, seed=1), which is suitable if you want to train
# your own ICEBERG for applications.
######################
# If you want to replicate the reported result with random + scaffold splits and 3 random seeds, please uncomment
# all ... |
a13f3b42e87513b7fdb041f76b9fa6c37d2daccd32f3a445a640061d54b38dbc | Shell | 1,010 | 18 | ######################
# The following script will only run for split_1_rnd1 (random split, seed=1), which is suitable if you want to train
# your own ICEBERG for applications.
######################
# If you want to replicate the reported result with random + scaffold splits and 3 random seeds, please uncomment
# all ... |
56beacd65cff97ef2993fc2661ac120236ae51783f05ac963ab4f46f79c69dd6 | Shell | 1,013 | 39 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_Myco Myco_model.csv -v &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
rm -f "$logfile"
... |
433b599e42c4f398c6b0444212531d562be11b851609611deee238d68571ac4b | Shell | 1,014 | 6 | #!/bin/bash
module load samtools
module load deeptools
computeMatrix reference-point --referencePoint center --missingDataAsZero -S m1043.bw m1044.bw m1131_added.bw m1377_1378.bw m1379.bw -R m1043vsm1044_m1043only.bed m1043vsm1044_shared.bed m1043vsm1044_m1044only.bed -a 2000 -b 2000 -o m1043vsm1044_in_m1043_m1044_m11... |
d85e3706cd4a1883e001f5c4f1433e937f04bba1cd4feec42c6c6402de067eef | Shell | 1,014 | 19 | Rscript step2_SPAtests.R \
--vcfFile=./input/seedNumLow_126001_seedNumHigh_127000_nfam_1000_nindep_0.sav \
--vcfFileIndex=./input/seedNumLow_126001_seedNumHigh_127000_nfam_1000_nindep_0.sav.s1r \
--vcfField=DS \
--chrom=chr1 \
--minMAF=0 \
--minMAC=0.5 \
--maxMAFf... |
0a8c564f948966e3a52d8b9971144525005efd154d41f08d01cf110769a5036a | Shell | 1,017 | 39 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_Xantho Xantho_model.csv -v &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
rm -f "$logfile"... |
c37c7974bdbe8068229c286dd3357dab6a8c367343d1012ce0a41abb266981ef | Shell | 1,021 | 34 | #!/bin/bash
submit_file=all_FLANKER.submit # submit file for condor
cdir=`pwd` # get the path to current working directory
if [ ! -d $cdir/log ] # create directory for condor log files
then
mkdir $cdir/log
fi
# create header for the condor submit file
echo "Executable = /usr/bin/matlab
Universe = vani... |
eb85cc53b83e1477eb1398bb3153351b4fcdecc66d9db73baf033d0c6c3a5620 | Shell | 1,022 | 37 | if ! [ -f ./dev.txt ]; then
echo "Download dev dataset...."
curl -L -o ./dev.txt 'https://github.com/UniversalDependencies/UD_English-EWT/raw/master/en_ewt-ud-dev.conllu'
fi
if ! [ -f ./test.txt ]; then
echo "Download test dataset...."
curl -L -o ./test.txt 'https://github.com/UniversalDependencies/UD_English-... |
2126264e4fcdada3814295f74f547cb81d73987898f95d8c07f0ce9c2096a6d0 | Shell | 1,024 | 33 | #!/bin/sh
#-------------------------------------------------------------------------------
# Convert the gene names in order to be used in an R script
#
# Usage: cat snpEff_genes.txt | ./scripts/genesTxtColumnNames.sh > genes.txt
#
# Once in R, you can:
# - Load this table:
# data <- read.csv("genes.txt", sep= "\t",... |
7b20b8ba51e690405e6a601ce0a4540f115695a09c9332669c61e9f16a2c52c9 | Shell | 1,024 | 24 | #!/bin/bash
#SBATCH -n 1
#SBATCH --ntasks-per-node=1
#SBATCH -p pi_gerstein
#SBATCH --job-name=hg19
#SBATCH --time=120:00:00
#SBATCH --mem-per-cpu 10G
#SBATCH --cpus-per-task=1
### Credit: Flynn Chen ###
raw_input="/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/LDSC/unique_peaks/peaks"
processed_output="/gpfs/gib... |
94c538379137e6ce5b60a0324d039b19cb0d061d733673d0647519a6467b727e | Shell | 1,024 | 39 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_Bemb_final Bembidion_multi.csv -v &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
rm -f "$l... |
c8bea2268f2f49e036b551e778d4989c8c0d190e3524029561eb803990fdb4fa | Shell | 1,024 | 40 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o cgr_unknown_Myco Myco_unknown.csv -v &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
rm -f "$l... |
d91fd65ff40ce15fe9e8abb9f21abb38e1ae235ecd1e4b0153cde60403e56ec0 | Shell | 1,024 | 37 | if ! [ -f ./dev.txt ]; then
echo "Downloading CONLL2003 dev dataset...."
curl -L -o ./dev.txt 'https://github.com/davidsbatista/NER-datasets/raw/master/CONLL2003/valid.txt'
fi
if ! [ -f ./test.txt ]; then
echo "Downloading CONLL2003 test dataset...."
curl -L -o ./test.txt 'https://github.com/davidsbatista/NER-... |
f960842f3299aea60d5815867c6b1f079e537d61e27f1af01a97bc756150524c | Shell | 1,026 | 26 | # Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
025e662ce444231e634c1f1c7dbd55b85d6930cea0febf57192a85a94dc8926d | Shell | 1,032 | 34 | # arguments
while getopts "a:t:i:o:p:f:" var
do
case "$var" in
a) ANTS_PATH=${OPTARG};;
t) TEMPLATE=${OPTARG};;
i) INPUT_IMG=${OPTARG};;
o) OUT_PATH=${OPTARG};;
p) PRETRAINED_MAP=${OPTARG};;
f) FINETUNED_MAP=${OPTARG};;
esac
done
# setup
ID=$(basename ${INPUT_IMG} .nii.g... |
aea30563ab40b034650be7496ae234f8587a9ede5f36d3c1645ef87beb6e1bae | Shell | 1,034 | 31 | # split targets.interval_list to run with stage4_2
srun --nodes=1 --ntasks-per-node=1 --pty bash -i
# --- set paths
sif=/data/dcibioinformatics/sifs/dcibioinformaticsHTS-v0.8.sif
wd=/data/dcibioinformatics/Anders/MelBrM_rerun/Annotation
ref=/data/dcibioinformatics/Annotation/GATK/hg38
tmp=/data/dcibioinformatics/Ander... |
b08e72295965b6b2e671f222637df49f3863378efa4d20de5af54b01e2ecaa6c | Shell | 1,035 | 19 | #!/bin/bash
# Finishes FS recon-all -autorecon3 with some adjustments from FS 7.3
fp=${1}
fun=${2}
sub=${3}
recon-all -autorecon3 -subjid ${sub} -expert ${fun}/expert.opts # use expert options to cause recon-all to crash at Pial Surface step
mris_make_surfaces -grad_dir 1 -intensity .3 -output .tmp -pial_offset .... |
f0956411837580c688bc528db3a4e4eacd02ac340bbf90988c3346e58a25f416 | Shell | 1,036 | 34 | # Add parent directory to python path to access lightning_base.py
export PYTHONPATH="../":"${PYTHONPATH}"
# A sample finetuning run, you need to specify data_dir, output_dir and model_name_or_path
# run ./examples/rag/finetune_rag.sh --help to see all the possible options
python examples/rag/finetune_rag.py \
--d... |
989815c0fe432fa403d4f1400cfefb18212b37d4d87f655757c1de3cbe660ff9 | Shell | 1,037 | 34 | #!/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_con... |
57d5410e31f73f9df61a0a93d4d3c6651fc2cb6fad0f6d713c07b44df12aa272 | Shell | 1,041 | 40 | #!/usr/bin/env bash
set -e
# Start the process in the background and capture its PID
varKoder train cgr_Myco Myco_model_cgr &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
... |
639d7b83193cb79c24449c34493d550f51b2b3b745dc35da3ea6b3a683bf79db | Shell | 1,041 | 40 | #!/usr/bin/env bash
set -e
# Start the process in the background and capture its PID
varKoder train cgr_Cora cora_model_cgr &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; then
... |
c3532f96ef58ca9d2cf0cf014efea3ee7a109045aa77d0727199897dd53a2344 | Shell | 1,041 | 40 | #!/bin/bash
set -beEu -o pipefail
if [ $# -ne 1 ]; then
printf "usage: rebuild.sh makeItSo\n" 1>&2
exit 255
fi
if [ "$1" != "makeItSo" ]; then
printf "usage: rebuild.sh makeItSo\n" 1>&2
exit 255
fi
export srcDir="$HOME/kent/src/hg/gar"
export dateStamp=`date "+%F"`
export workDir="/hive/data/outside/ncbi/ge... |
b2e784a571ec237f44b0691580d944bfd992ced5fc0f3dea7b135b22eefa8ec5 | Shell | 1,042 | 23 | #!/bin/bash
#move this to results folder for branch shift then run it
#example inputs bash hypothal.output.converter -f BSThetaTestLRTsadult_hypothal_BS2ALV.res -s 16 -g genelist -o result
while getopts f:s:g:o: flag
do
case "${flag}" in
f) filename=${OPTARG};;
s) species_num=${OPTARG};;
g)... |
fc22e4a1dc0636f9305b511977fb1237be3204388e68e0bbf3dba8a141925a6b | Shell | 1,042 | 24 | sortBed -i End.peaks.bed > End.peaks.sort.bed
sortBed -i Exc.peaks.bed > Exc.peaks.sort.bed
sortBed -i Inh.peaks.bed > Inh.peaks.sort.bed
sortBed -i Mic.peaks.bed > Mic.peaks.sort.bed
sortBed -i Oli.peaks.bed > Oli.peaks.sort.bed
sortBed -i OPC.peaks.bed > Opc.peaks.sort.bed
thresh=(0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9... |
dcec3949203edcf44ab1ba4cd8216290fbe3ccd1d4e9199b7f0ff0848bd2b627 | Shell | 1,044 | 31 | #!/bin/bash
# This script gets the smooth pial files (runs the first four steps from the localGI command in Freesurfer).
# Requires a tab delimited txt file that lists the subject IDs in a row (subjects.txt).
# Require FreeSurfer and Matlab to be installed.
# manually load and source FreeSurfer
export FREESURFER_... |
751d25062c24c41cc146b03d4f614ced64630e4a4de277151108011a27432032 | Shell | 1,045 | 40 | #!/usr/bin/env bash
set -e
# Start the process in the background and capture its PID
varKoder train cgr_Xantho xantho_model_cgr &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]; t... |
5ac86b1540af49e46c25d6c110a8b0ebeba8809bb385a9d84a5292fb4325a399 | Shell | 1,048 | 40 | #!/usr/bin/env bash
set -e
# Start the process in the background and capture its PID
varKoder train cgr_Bemb_final Bemb_model_cgr1 &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +%s)
# Function to clean up in case of an error
cleanup() {
if [[ -n "$logfile" ]]... |
63a17adb74370c744d3e2324a2a7ba85298e0bf2fa9b5fe8da01077654e1a1b5 | Shell | 1,049 | 57 | #!/bin/sh -e
export VERSION=5.4
# Separate version-subversion by '_'
# E.g.: '4_1' (instead of '4.1')
export VERSION_UND=`echo $VERSION | tr '.' '_'`
#---
# Build SnpEff
#---
cd $HOME/workspace/SnpEff/
mvn clean compile assembly:single jar:jar
cp target/SnpEff-$VERSION-jar-with-dependencies.jar $HOME/snpEff/snpEf... |
713dfeb8af7705fa2c2e4343f4f589f51ab49e5e5506dbf4ad058c0e3acfb498 | Shell | 1,053 | 17 | #!/bin/bash
rm datasets/edges2handbags -rf
mkdir datasets/edges2handbags -p
axel -n 1 https://people.eecs.berkeley.edu/~tinghuiz/projects/pix2pix/datasets/edges2handbags.tar.gz --output=datasets/edges2handbags/edges2handbags.tar.gz
tar -zxvf datasets/edges2handbags/edges2handbags.tar.gz -C datasets/
mkdir datasets/edge... |
68000e9f47c6d01cae18366ef1d77ad8b9e00629db35147ae3f0f4f3a4159a50 | Shell | 1,054 | 17 | export slurmscript=$OAK/projects/astrock/2021_common/scripts/slurm
alias sourcenv='[ -f ./environment.sh ] && { source ./environment.sh; echo "Starting project $PROJECT_NAME"; } || { echo "Setup your environment before running."; }'
export flag1c='-c 1 -p normal,menon'
export flag8c='-c 8 -p normal,menon'
export flag1g... |
29ea4edef957cc4108f4350de8c31bc5d4d2027f902412830ba890d499eb7374 | Shell | 1,059 | 37 | #!/bin/bash
#
# Quick function to QC func OR t1w brain masks
#
# Inputs:
# $1 : subject ID (01..30)
# $2 : Session number (1 or 2)
# $3 : Space (func, t1w)
#
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------------------
# Setti... |
c11193fefa7488e52e61d42906936eb34a867c15cc87d6d925c93f3fbb81199f | Shell | 1,062 | 10 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --time=1:00:00
#SBATCH --mem-per-cpu=20GB
#SBATCH --account=bbenayou_34
module purge
module load gcc/8.3.0
/project/bbenayou_34/mcgill/subread-2.0.2-source/bin/featureCounts -O -p -M -a /project/bbenayou_34/mcgill/mm39_refGene.gtf -o EMA... |
31dad617b384f11b71a5e9285daff171fa690d1ab82d31b7bfb28da715c9a5a4 | Shell | 1,063 | 32 | # split targets.interval_list to run with stage4_2
srun --nodes=1 --ntasks-per-node=1 --pty bash -i
# --- set paths
sif=/data/dcibioinformatics/sifs/dcibioinformaticsHTS-v0.8.sif
wd=/data/dcibioinformatics/Anders/MelBrM_rerun/Annotation
ref=/data/dcibioinformatics/Annotation/GATK/hg38
tmp=/data/dcibioinformatics/Ande... |
e1b86cc173b2d75bc4240ce8fa5d19dae65adf07bcc030bfd18307b190ca56a7 | Shell | 1,067 | 47 | #!/usr/bin/env bash
set -e
CDS=$1
VEP_CONTAINER=$2
VEP_CACHE_DIR=$3
OUT=$4
CORES=$5
tmpdir=`mktemp -d`
echo $tmpdir
SCRIPT_FOLDER="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
python ${SCRIPT_FOLDER}/mutations.py -r ${CDS} -o ${tmpdir}/mutations.tsv
sort -k1,1 -k2n,2 -k3n,3 ${tmpdir}/mutations.tsv... |
d8fbf710217075828f310fb179e38e662ce690e49a227647f39efa02048143b4 | Shell | 1,070 | 39 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_short
#SBATCH --job-name=train-xgboost
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=8:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lustre/mlnv... |
2690390b4776330d4d68353b55aa875c76e81cbae19c71544f562dd55d91d15f | Shell | 1,071 | 44 | #!/bin/bash
set -e
source ../paths.sh
# Clean up previous coverage files
rm -f *.gcno *.gcda *.gcov
# To use verificarlo-c with branch coverage we add the --coverage cli option
verificarlo-c --coverage unst_branch.c -o unst_branch --save-temps
gcov_report() {
# Clean up previous coverage files
rm -f *.gcda *.g... |
61cd7bd6f473d7f1da2110ed9b81f6b5bc4af687137aec32a596ce10f56712c2 | Shell | 1,072 | 34 | # Openframe
# BEADS_DIR="/home/miguel/Projects/data/11042024_beads4Miguel/11042024_beads4Miguel_beads/";
# OUTDIR="/home/miguel/Projects/smlm_z/autofocus/VIT_autofocus2";
# PX_SIZE=86;
# ZSTEP=10;
# Zeiss
BEADS_DIR="/home/miguel/Projects/data/20240415_beads_AF_Miguel/stack_before_1/";
OUTDIR="/home/miguel/Projects/sm... |
163db59c1cf20ff9e3166c21ff551a44d54e7f24b147e2a7170b161696843624 | Shell | 1,073 | 51 | #!/bin/sh -e
#-------------------------------------------------------------------------------
#
# Download a GenBank file form NCBI and build the corresponding SnpEff database
#
# Note: It is assumed to be run form SnpEff's directory and that
# the 'data' directory is 'data'
#
# Usage example:
# $ cd ~/snpE... |
33086309981e630954b12fd17b380c1b6502f96ca239d4694606e162d20b2aa1 | Shell | 1,079 | 38 | #!/bin/bash
#
# Runs ANTs SyN registration for the whole cohort on the batch
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
rootdir=/data_/tardiflab/mwc/bids/de... |
02f2682f487aa9370042060ab7c957923a8870a5e9886ee8f625123921483a40 | Shell | 1,083 | 37 | #!/bin/sh
# Fully static executables have no RUNPATH; dlopen() needs the install lib dir.
. "$(dirname "$0")/../paths.sh"
export LD_LIBRARY_PATH="${INTERFLOP_LIBDIR}${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
# Mark this test as expected to fail (exit 88)
# static mode fails with
# * libinterflop_ieee.so
# due to libqua... |
bb7ffc9730fb8e7eb26f756ea3a5866d4d6c84857cc2b806dad340bce71665c0 | Shell | 1,083 | 34 | #!/bin/bash
#SBATCH -p NOParalela
#SBATCH -J Hagen_model_simulations
#SBATCH -t 120:00:00
#SBATCH --array=0-79%40
#SBATCH --cpus-per-task=56
#SBATCH --output=/dev/null
#SBATCH --error=/dev/null
SCRATCH_ROOT="/SCRATCH/TIC117/pablomc/Hagen_model_simulations"
# --- move to your project directory ---
cd /LUSTRE/home/TIC1... |
bf1ea42d3232b440141bd582a69b6e6209094805d756e347840c0f22a6e6bbc9 | Shell | 1,086 | 31 | set -e
bash install_mogen.sh
bash get_gm12878.sh 100000 0
bash get_gm12878.sh 10000 0
for CHROM in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
do
BEDPATH="hic_data/GM12878_combined_"$CHROM"_10kb.bed"
python ../minimds.py -o "hic_data/GM12878_combined_"$CHROM"_10kb_mmds_coords.tsv" $BEDPATH
python .... |
5762ad4b551904953c2964b7847f326651c3c6f9e21a96b8044188e29277c1f1 | Shell | 1,089 | 44 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p normal
#SBATCH -n 1
#SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_mustache_93
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate mustache
pt2="0.001"
samples=("35CR" "147" "70CR" "7... |
a3cdbce342b31fcd76dc9f1cc0ba68253044e3d7b6bd501f86af2f481cb085d6 | Shell | 1,089 | 43 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_short
#SBATCH --job-name=Tucano-eval-calame-pt
#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_... |
0b1c355bc166ffa0189b8d4c9bd392bbac8e658d42c4298524438be982d6a151 | Shell | 1,091 | 43 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_short
#SBATCH --job-name=Tucano-eval-lambada-pt
#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... |
8a41f2b417baa461ffd26b5bd23a699fc77bfad73e003dcb52cd84a2fab05772 | Shell | 1,091 | 44 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p normal
#SBATCH -n 1
#SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_mustache_93
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate mustache
pt2="0.001"
samples=("35CR" "147" "70CR" "7... |
fa6e9de2d66595d19bf3a5827241e859bfd2f5542bd3a065c7e669bba6a2f555 | Shell | 1,091 | 34 | #!/bin/bash
#
# Slices connectomes according to a give look up table (using the BIC batch)
# Should be happening in ${MICAPIPE}/functions/03_SC.sh, but sometimes needs to be repeated...
#
# Inputs:
# $1 : sub ID
# $2 : FUNC_ID (DEPRECATED!)
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------... |
8f69ea67881d3787ab997ed88e2424a933f2f76d7ac4613c1ed884d967d289be | Shell | 1,093 | 33 | #!/bin/bash
#mass create kallisto indexes
#while read j; do
# gunzip "../data/0_refs/"$j".gz"
# HEAD=$(echo $j | sed 's/fa//g')
# REF=../data/0_refs/$j
# IDX="../data/0_refs/"$HEAD"idx"
# kallisto index -i $IDX $REF
# gzip ../data/0_refs/$j
#done<../data/0_refs/cDNAList.txt
#make output directory for kallisto
#mkdir ... |
e9d5ee67275c151b1a46c8c0593a6a0697b6f0a50d4fb034f0699eee18368a8b | Shell | 1,093 | 19 | #!/usr/bin/env bash
# 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 r... |
ca0cde8cc3b793cfb1956d8ca995645b6b8331aadce986f51ae14cca07490b27 | Shell | 1,094 | 44 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p normal
#SBATCH -n 1
#SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_mustache_93
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate mustache
pt2="0.001"
samples=("35CR" "147" "70CR" "7... |
edc55de2a9f902deca86d746af38839ca1431eb6af740048c112ea0b08c453e3 | Shell | 1,094 | 44 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p normal
#SBATCH -n 1
#SBATCH --mem=40G
#SBATCH -t 48:00:00
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_mustache_93
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate mustache
pt2="0.001"
samples=("35CR" "147" "70CR" "7... |
88457f9d44237abb9c0efaf0f4bb7ff7cda132ce2a0e4acd0cacaf9302b014cd | Shell | 1,095 | 52 | #!/bin/sh
REF=hg19
#---
# Download latest datasets
#---
# # Genome sequence
# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/bigZips/chromFa.tar.gz
#
# # Protein sequences
# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz
#
# # CDS sequences
# wget ftp://ftp.ncbi.nlm.nih.gov/re... |
73a68c6a451653625e9525d8d6252f2ff68de0903f86dfb2bc250fc6a90b28a9 | Shell | 1,096 | 50 | #! /bin/bash
# Infer the number of GPUs from the rank size
D=$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... |
7ff67f34bbb29e4f2976f1832b3a10236949a690d855cda770932a52d171edf3 | Shell | 1,099 | 34 | #!/bin/bash
#SBATCH -p NOParalela
#SBATCH -J Cavallari_model_simulations
#SBATCH -t 300:00:00
#SBATCH --array=0-79%40
#SBATCH --cpus-per-task=56
#SBATCH --output=/dev/null
#SBATCH --error=/dev/null
SCRATCH_ROOT="/SCRATCH/TIC117/pablomc/Cavallari_model_simulations"
# --- move to your project directory ---
cd /LUSTRE/h... |
f478cf0af35daa5371fae24770bad8165b79e23c0c21a52b6a20a88e8f84851d | Shell | 1,099 | 41 | #!/bin/bash
set -e
verificarlo-c --ddebug -g -O0 test.c -o test
run_with_timeout() {
local timeout_s="$1"
shift
"$@" &
local pid=$!
local waited=0
while kill -0 "$pid" 2>/dev/null; do
if [ "$waited" -ge "$timeout_s" ]; then
kill "$pid" 2>/dev/null || true
wait "$pid" 2>/dev/null || true
... |
4fac32f9be58ae9351ba41f858042dbf372ebd7f8b0f3d917ec95a227684e7e3 | Shell | 1,100 | 25 | #!/bin/bash
#
# exit on any error at any time
set -beEu -o pipefail
# rm -f /usr/local/apache/userdata/cleaner.pid
# rm -f /var/tmp/trashSizeMonitor.pid
echo "running two commands to test the cleaner."
echo "There should be no output to your terminal from the two commands."
echo "There should be some files created in... |
5be6e2df6905fd5fc9962d571c2199cf84db2e620698019665e346e1cb01b1d6 | Shell | 1,104 | 42 | #!/usr/bin/env bash
#simple script to pack up a precompiled binary package
if [[ -z "$1" ]]; then
echo -e "Usage:\n./make_bin.sh <binary_package_name> [<boost_prefix>]"
echo " <binary_package_name> cannot be a full path, but only a file name"
echo " e.g.: tophat-2.1.0.Linux_x86_64"
exit 1
fi
#echo "packing up $1... |
e0f60528ef0bbe802c94aeacf02d6d67d15fc3c5a307bbc4ba1a449ebac3325f | Shell | 1,104 | 28 | #!/bin/bash
conda activate skmer
# In a first run, we got this error:
#Coverage of 8522+SRR16117178@00003994K is too low, not able to estimate it; no correction applied
#Coverage of 7100+ERR4094845@00003940K is too low, not able to estimate it; no correction applied
#Coverage of 8522+SRR16117178@00003994K is too low, ... |
2113daaaa9c1386524d3de7cbacaebcfddd456ff0e406283e16054ab1c1fa375 | Shell | 1,109 | 26 | #!/bin/bash
# Script to compute metrics reloaded across spinal cord segmentation models
# Run MetricsReloaded
metrics_to_compute="dsc nsd rel_vol_error"
# methods_to_compare="monai_v2.0 nnunet_2d propseg deepseg_2d deepseg_3d"
methods_to_compare="monai_v2.5 monai_v2.6 propseg deepseg_2d"
PATH_RESULTS="/home/GRAMES.PO... |
31165091e17ae39e49298c29fc41044725c17c6f3abe1c4c9fe9df4a2ffaadea | Shell | 1,110 | 42 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=vlm_long
#SBATCH --job-name=split-gigaverbo
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
source /lustre/... |
a8944100fa73057b24ee05bcf82fd4a0431903e148212393353865d82243f55d | Shell | 1,112 | 39 | #!/usr/bin/env bash
if ! [ -f ./dev.txt ]; then
echo "Download dev dataset...."
curl -L -o ./dev.txt 'https://github.com/UniversalDependencies/UD_English-EWT/raw/master/en_ewt-ud-dev.conllu'
fi
if ! [ -f ./test.txt ]; then
echo "Download test dataset...."
curl -L -o ./test.txt 'https://github.com/UniversalDepe... |
b96ae42a281b3b9e5174e635d9bb3de18ab2830af15f4511c5f11da29bd1e7be | Shell | 1,114 | 64 | #/bin/bash
if [ "$#" -eq 0 ]; then
echo "A directory argument is required"
fi
cd $1
diffList=$(find . -name "*std*.diff" -o -name "*post.diff")
testCasList=${diffList//.stdout.diff/}
testCasList=${testCasList//.stderr.diff/}
testCasList=${testCasList//.post.diff/}
testCasList=$(echo $testCasList |uniq)
echo "te... |
262918473a738a62e6a876dde6c4073ad82e4a2e2e13980d01de0ee5aea742b4 | Shell | 1,115 | 33 | # ------------------
# PROJECT VARS
# ------------------
export PROJECT_NAME=2021_md_excitability_nn_model_redo_clean
export PROJECT_LEAD=astrock
# ------------------
# PROJECT PATHS
# ------------------
export PROJECT_OAK=$OAK/projects/$PROJECT_LEAD/$PROJECT_NAME
export PROJECT_GROUP_SCRATCH=$GROUP_SCRATCH/projects/$... |
a6bd3a145489eaccd761eb9c694aec1ea70ef842b0d540f6d8fa62cdb44592c6 | Shell | 1,117 | 48 | #!/bin/bash
# base name of this script (without extension)
scriptname=$(basename $0 .sh)
echo -e "\n*** Running batch script '"$scriptname"' ***\n"
# path to Matlab code directory
codedir=$LOCALREPO/matlab/DI_opt_02
# current directory (the directory this script is run in - log files will go here)
currdir=$(pwd -P)... |
dbe6e597e742278869ad5fda6b9ed80705c889572013d16bffe9003360f769ee | Shell | 1,118 | 20 | while getopts f:s:g:o: flag
do
case "${flag}" in
f) filename=${OPTARG};;
s) species_num=${OPTARG};;
g) genelist=${OPTARG};;
o) output=${OPTARG};;
esac
done
var=1
header=$(($species_num+$var))
#how to convert the output
# take all of the spaces of LRT file and turn them into linebreaks, then s... |
94c81924b61ad698d6eab6d2bf588e52e4f1d4fb4090744503b8d26f94fcc4ce | Shell | 1,124 | 20 | while getopts f:s:g:o: flag
do
case "${flag}" in
f) filename=${OPTARG};;
s) species_num=${OPTARG};;
g) genelist=${OPTARG};;
o) output=${OPTARG};;
esac
done
var=1
header=$(($species_num+$var))
#how to convert the output
# take all of the spaces of LRT file and turn them into linebreaks, then s... |
7adf0af7194e3df6b92a82bfe9fb46423cff98a235d6ced62b0fb6be64aa44c2 | Shell | 1,126 | 35 | #!/bin/bash
#
# Slices connectomes according to a give look up table
# Should be happening in ${MICAPIPE}/functions/03_SC.sh, but sometimes needs to be repeated...
#
# Inputs:
# $1 : target dir (needs to be adjusted for dir structure
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#----------------... |
f0b2160bed66125e693042e06a06692b5d71dd08ec7e4406af6cefafbfdd9bfd | Shell | 1,130 | 19 | # install pytorch (CPU only)
pip install torch==1.8.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
pip install torch_geometric==1.7.0
# install prerequisites for torch geometric - torch_{sparse|scatter|cluster|spline_conv}
wget https://data.pyg.org/whl/torch-1.8.0%2Bcpu/torch_scatter-2.0.8-cp38-cp38-linux_... |
423997f01a0efacb165e0bbb29ec69d05c0445bd0a3e8d1ad6caa2f8dff51a0f | Shell | 1,131 | 11 | python graph_pde.py --edge_features full --train_wdn Hanoi --train_demand_mode random --train_pattern spike random
python graph_pde.py --edge_features full --train_wdn Hanoi --train_demand_mode random --train_pattern spike
python graph_pde.py --edge_features full --train_wdn Hanoi --train_demand_mode normal random --tr... |
5aa418fc3b9c5fdc17cd9f7a5c1d6fe0ac27a967cdd51a24596bd63c7754d2ec | Shell | 1,132 | 20 | #!/usr/bin/env python
import argparse as ap
from pipeline import main
parser = ap.ArgumentParser()
parser.add_argument('recipe', type=str, help='plan file')
parser.add_argument('-S', '--samples', type=str, help='data file descriptions')
parser.add_argument('-P', '--settings', type=str, help="miscellaneous settings")
... |
739ff387c2ec11c6d212a822c7ff3bf764e73ddb1933cd0a84fbfbd9a5a32d43 | Shell | 1,134 | 40 | #!/usr/bin/env bash
set -e
varKoder image --kmer-mapping cgr -k 7 -o Bembidion_unknown Bemb_unknown.csv -v &
varKoder query --include-probs --model bemb_model/trained_model.pkl Bembidion_unknown Query_Bembidion_image &
pid=$!
# Create a log file in the home directory
logfile=$(mktemp ~/memory.log.XXXX)
start=$(date +... |
98f8ca7eb5146a92f4fb0b59c42d6db270b73ae17a208219c33d0cef9ebbb45e | Shell | 1,138 | 43 | set -e
RES=$1
mkdir -p hic_data
cd hic_data
if [ ! -e GSE63525_GM12878_combined_interchromosomal_contact_matrices.tar.gz ]
then
curl ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_combined_interchromosomal_contact_matrices.tar.gz -o GSE65325_GM12878_combined_interchromosomal_conta... |
887a7062ef08118f1797aaf0c24af10a07403e561600eaccb989430d7e52d4a6 | Shell | 1,140 | 30 | #!/bin/bash
# Reference BLAS, CBLAS and LAPACK, one build:
#
# recipes/lapack/build.sh <ieee|prism>
#
# Installs into $FUZZY_ROOT/lib/lapack/<version>/<build>. Both builds have the
# same sonames (libblas.so.3, libcblas.so.3, liblapack.so.3), so `fuzzy use
# lapack=...` switches every program and Python package linke... |
ce8df8bbf8b6bc88e40473a2c43521bdc8482fc73c257490c8ace7b1c1bce7b6 | Shell | 1,145 | 35 | #!/bin/sh
# #---
# # Download sequences
# #---
#
# wget http://rapdb.dna.affrc.go.jp/download/archive/irgsp1/IRGSP-1.0_genome.fasta.gz
# wget http://rapdb.dna.affrc.go.jp/download/archive/irgsp1/IRGSP-1.0_representative_2013-04-24.tar.gz
# wget http://rapdb.dna.affrc.go.jp/download/archive/irgsp1/IRGSP-1.0_protein_201... |
905882b7e043ec9e384d4895cd97309b67fe7eb7f11dadfca65e8037537afb44 | Shell | 1,146 | 11 | python eval.py -model_name trfeplus -load_path "./run/trfe-plus/fold0/trfe-plus_best.pth" -fold 0 -gpu 0
python eval.py -model_name trfeplus -load_path "./run/trfe-plus/fold1/trfe-plus_best.pth" -fold 1 -gpu 0
python eval.py -model_name trfeplus -load_path "./run/trfe-plus/fold2/trfe-plus_best.pth" -fold 2 -gpu 0
pytho... |
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