sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
28c77a4441e71e08dd967f255f422e8695e04284c4240d9f619b4c623d727314 | Shell | 566 | 23 | #!/bin/bash
#SBATCH --job-name=ndl-pytest
#SBATCH --time=0-00:20:00 # days-hh:mm
#
#SBATCH --cpus-per-task=6 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=32000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arrayi... |
6964c0d253764d30e11cec3b33ad0bc2364bf9256c6f363fbf546df2f1d55300 | Shell | 572 | 9 | #!/bin/bash
# rmf 2.13.2020, last modified 3.6.2021
for f in ../../promoters/ELC*_transcriptList.txt; do echo $f >> fileList.transcriptLists.txt; done
for f in ../../promoters/RLC*_transcriptList.txt; do echo $f >> fileList.transcriptLists.txt; done
for f in ../../promoters/LLC*_transcriptList.txt; do echo $f >> file... |
92b9cea70fd1585e8307d33501bc715ee39ce3cf6d7e0f150dfd9e5ab6eccb00 | Shell | 572 | 6 | #!/bin/bash
# rmf 12.8.2020, last modified 4.15.2021
# usage <binding site file> <GOI list file> <promoter loc file> <xscale> <yscale> <secondaryIDs file>
for f in bindingSiteInfo*DAVID*.txt; do filebase=$(echo $f | sed 's/_FDR.*txt//' | sed 's/_p[0-9].*txt//'); outbase=${filebase##bindingSiteInfo_}; GOIfile="../../.... |
ef8af45178e22df849e9edb5cbeb3d32cfaf4cc5be26ce41a40494db315795ea | Shell | 576 | 10 | #!/usr/bin/env bash
faceforensics_script=$1
python $faceforensics_script datasets/T_deepfake -d original -c raw -t videos -n 200
python $faceforensics_script datasets/T_deepfake -d Deepfakes -c raw -t videos -n 50
python $faceforensics_script datasets/T_deepfake -d Face2Face -c raw -t videos -n 50
python $face... |
5aca022e83923710c1abc4e386df572c352cbc9a0517eaf527738e3c102f0f9a | Shell | 577 | 21 | modelname="gpt2"
savename="gpt2"
mode=history
dataset=/home/jitianbo/Workspace/driver_simulator_kvret/data/data_for_clm_ablation/$mode
num_epochs=50
python run_clm.py \
--model_name_or_path $modelname \
--dataset_dir $dataset \
--per_device_train_batch_size 4 \
--per_device_eval_batch_size 4 \
--nu... |
9c98ce2cbaac70f44ebecb7c1a50b792bf8c341367a898c2589dd06e6bb786a7 | Shell | 577 | 21 | modelname="gpt2"
savename="gpt2"
mode=profile
dataset=/home/jitianbo/Workspace/driver_simulator_kvret/data/data_for_clm_ablation/$mode
num_epochs=50
python run_clm.py \
--model_name_or_path $modelname \
--dataset_dir $dataset \
--per_device_train_batch_size 4 \
--per_device_eval_batch_size 4 \
--nu... |
f7fe4e79e1454bba8c16df5c3089269795b2f2a29fc11b11270733e96ebc652d | Shell | 577 | 12 | #!/bin/bash
# must be run from a virtualenv with...
# https://github.com/koxudaxi/datamodel-code-generator
base_url="https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master"
for domain in description_domain error_domain execution_domain io_domain parametric_domain provenance_domain usability_domain
do
... |
17a2f9277d1e38b31b82e0d559a8a8a88482b48daefb820de28179935737a0fe | Shell | 581 | 21 | #!/bin/bash
#SBATCH -c 4
#SBATCH --array=0-7
#SBATCH --job-name=training
#SBATCH --mem=25GB
#SBATCH -t 24:00:00
#SBATCH --gres=gpu:1
#SBATCH --constraint=any-gpu
#SBATCH --partition=cbmm
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/
hostname
export CUDA_VISIBLE_DEVICES=0
/om2/user/jakubk/miniconda3/envs/torch... |
59ed0efd7c1481d7a1c7d0f09664677f3a78f11f57239233800dce38c277a557 | Shell | 583 | 13 | #! /bin/zsh
#install docker, adapted from here: https://docs.docker.com/desktop/install/mac-install/
#NOTE this assumes you don't have docker installed already. If it's already there, it might get overwritten!
curl https://desktop.docker.com/mac/main/amd64/Docker.dmg --output ./Docker.dmg
sudo hdiutil attach Docker.... |
40c41aa91349a0ff7e5754864b4d5132e1f91ca4589fc7feb9b1ffbc454fbab4 | Shell | 585 | 22 | #$ -l tmem=16G
#$ -l h_rt=9:0:0
#$ -l gpu=true
#$ -S /bin/bash
#$ -j y
#$ -N gpu_worker50
#$ -t 1-50
#$ -tc 4
#$ -o /home/vauvelle/doctor_signature/jobs/logs
hostname
date
PROJECT_DIR='/home/vauvelle/doctor_signature/'
export PYTHONPATH=$PYTHONPATH:$PROJECT_DIR
cd $PROJECT_DIR || exit
source /share/apps/source_files/p... |
81cd97e0514bf70ed040d1631651d56b92cf5fcbe819d16af34f26dcab40a013 | Shell | 587 | 21 | modelname="gpt2"
savename="gpt2"
mode="history-profile"
dataset=/home/jitianbo/Workspace/driver_simulator_kvret/data/data_for_clm_ablation/$mode
num_epochs=50
python run_clm.py \
--model_name_or_path $modelname \
--dataset_dir $dataset \
--per_device_train_batch_size 4 \
--per_device_eval_batch_size 4 ... |
323cb6702bd46a4b1b42e893b473a6e99aadd565869961e0e9ac1721ab721d4a | Shell | 590 | 18 | Rscript prepare_features.R
#output stored in datasets/
# Benchmark the following models:
# B: basic general regional features - 8 features
# BE: basic+codon
# BP: basic+kmers(in 5'UTR regions)
# BR: basic+kmers(in ORF regions)
# BM: basic+kmers(in 3'UTR regions)
# Be: basic+codon+kmers(in ORF regions)
# BER: basic+kme... |
090e648adcd3bf1aeb516ea5b3947c76718be1e916c1567cf35e086f6442c1dc | Shell | 592 | 19 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(... |
fcd6899d175a53df8a5e515dcb5edf72a82c9c93cd431285c998bf58a184eb60 | Shell | 592 | 25 | #!/bin/sh
cd /Users/szhang32/Desktop/INTACT6/bivalency
annotation="/Users/szhang32/ref/mm10/gencode_vM23_name_conversion.txt"
### A2a
geneExpression="ribo_D2_FPKM.txt"
outHigh="A2a_high_gene.bed"
outMedium="A2a_medium_gene.bed"
outLow="A2a_low_gene.bed"
python3 scripts/categorize_gene_expression.py $geneExpression... |
cafcacf4b42e615d3f25cc4d54ebb5a8bbda9c941185e8e269f89f0d8cfa2f6e | Shell | 595 | 37 | #!/bin/bash
HOMFAM="../../data/homfam/train/*.fasta"
BALIFAM100="../../data/balifam100/train/*.fasta"
BALIFAM1000="../../data/balifam1000/train/*.fasta"
BALIFAM10000="../../data/balifam10000/train/*.fasta"
BALIFRAG="../../data/balifrag/train/*.fasta"
mkdir -p alignments
mkdir -p times
run () {
for f in $1
do... |
1039480cba7144ef4b221c532783f980db8e7e43c6355745f819349290602084 | Shell | 597 | 25 | #!/bin/sh
set -e
if [ $# != 1 ]; then
echo "Usage: $(basename $0) version" >&2
exit 1
fi
version="$1"
# Linux and Darwin builds.
for arch in i686 x86_64; do
for target in apple-darwin unknown-linux-musl; do
url="https://github.com/10xDev/subset-bam/releases/download/$version/subset-bam-$version-$arch-$targ... |
19d12c30abab64ffd7b7d49aee38fa3f4679f0ffdb9163784ac001c013dea9c6 | Shell | 597 | 33 | dataset=$1
device=$2
[ -z "${dataset}" ] && dataset="ppi"
[ -z "${device}" ] && device=-1
python main_inductive.py \
--device $device \
--dataset $dataset \
--mask_rate 0.5 \
--encoder "gat" \
--decoder "gat" \
--in_drop 0.2 \
--attn_drop 0.1 \
--num_layers 3 \
--num_hidden 2048 \
--num_heads 4 \
--max_ep... |
54e344ecc009cdb6ebe6dd2ab12edd862ae5468cc9969c6c226325f658268d68 | Shell | 600 | 17 | #!/bin/bash -l
#PBS -N MLP_Region67_Validation_6
#PBS -q gpu
#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l mem=32G
#PBS -l walltime=48:00:00
cd $PBS_O_WORKDIR
module load pytorch/1.5.0-conda3.7-GPU
source PaperDescriptiveEnvHPF/bin/activate
python3 Model_MultilayerPerceptron_Validation_CoronalSagittalSampling.py --labels r... |
a738f583ef627d748cc5a9a0f059ff8539209f83ea5083981f60d340d40f1c48 | Shell | 604 | 17 | #!/bin/bash -l
#PBS -N MLP_Region67_Validation
#PBS -q gpu
#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l mem=32G
#PBS -l walltime=48:00:00
cd $PBS_O_WORKDIR
module load pytorch/1.5.0-conda3.7-GPU
source PaperDescriptiveEnvHPF/bin/activate
python3 Model_MultilayerPerceptron_Validation_CoronalSagittalSampling.py --labels reg... |
ec4ea2f579d84ee98613f1be5ee0a3e03c09cbb04777b648b64bc81cc83aff71 | Shell | 607 | 14 | #!/bin/bash
#SBATCH --job-name=bilin_pfam # Job name
#SBATCH --nodes=1 # Run all processes on a single node
#SBATCH --ntasks=1 # Run a single task
#SBATCH --cpus-per-task=32 # Number of CPU cores per task
#SBATCH --mem=2000gb # Job memory request
#... |
f6bef96159719978a367f1645f7be6bd6ea82523a6fbfb0db80159d36e879878 | Shell | 610 | 28 | # Clear dist/ directory
#rm -R dist/*
# Install requirements
python3 -m pip install setuptools wheel twine
# Build source distribution
python3 setup.py submodule_update test sdist
# Build wheel
python3 setup.py bdist_wheel
# Test install the wheel (replace 'xyz' by the actual description of the latest wheel)
#pytho... |
38c8b52cd2a4e15ba8cdac69bd085269616555c2f30223507bbc808009a8f196 | Shell | 611 | 18 | Rscript prepare_features.R
#output stored in datasets/
# Benchmark the following models:
# B: basic general regional features - 8 features
# BE: basic+codon
# BP: basic+kmers(in 5'UTR regions)
# BR: basic+kmers(in ORF regions)
# BM: basic+kmers(in 3'UTR regions)
# Be: basic+codon+kmers(in ORF regions)
# BER: basic+kme... |
1788e538304ac5c3163e72ab470066dabb0cdb3ac485533eb953d3733965eac4 | Shell | 612 | 17 | #!/usr/bin/env bash
# Reproduce every result and figure of the manuscript (approx. 45-60 min on 2 CPU cores).
set -euo pipefail
cd "$(dirname "$0")"
bash scripts/00_fetch_data.sh
python3 scripts/01_omics_psychencode.py
python3 scripts/02_omics_splicing.py
python3 scripts/03_genetic_anchoring.py
python3 scripts/04_calib... |
aeb80424083364dafd5b417ca37fc3593c4fd0cfb6d3f2d9417ba4990c45e879 | Shell | 620 | 31 | #!/bin/bash
# build, test and generate docs in this phase
set -ex
. "$(dirname $0)/utils.sh"
main() {
# Test a normal debug build.
cargo build --target "$TARGET" --verbose --all
# Show the output of the most recent build.rs stderr.
set +x
stderr="$(find "target/$TARGET/debug" -name stderr -prin... |
a7e07b78a0747287ed1a21b97458ffa8b6bcbf9c22864e044815436fa22e9e7c | Shell | 621 | 22 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 5-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
662955bfa493fee56323bf00e335e86be5e785c76c154dc8dacd1310ed7731ad | Shell | 631 | 19 | #!/bin/bash
################################################# Get into edbo environment
eval "$(conda shell.bash hook)"
conda activate edbo
################################################# Install pytest
pip install pytest
################################################# Tests
pytest acquisition_functions_gp.py... |
f35d2e0397a4b41bd7ca3121646a36be5026d6056d596f85b94b844d971280b7 | Shell | 634 | 30 | #!/bin/bash
PROCESS_ID_FILE="$1"
LOG_FILE="$2"
OUTPUT_FILE="${PROCESS_ID_FILE}.tmp"
: > "$OUTPUT_FILE"
COUNT=0
while IFS= read -r PROCESS_SPECIFIER; do
IFS=':' read -r -a PARTS <<< "$PROCESS_SPECIFIER" ; unset IFS
PROCESS_ID="${PARTS[0]}"
PROCESS_PATH="${PARTS[1]}"
if ps -p "$PROCESS_... |
0b45a78109a1db89236ce89d6f5c4a059c24c2428daa90fbfd3e4e2285c43bed | Shell | 638 | 17 | # Install Docker, you can ignore the warning from Docker about using WSL
curl -fsSL https://get.docker.com -o get-docker.sh
sudo sh get-docker.sh
# Add your user to the Docker group
sudo usermod -aG docker $USER
# Install Docker Compose v2
sudo apt-get update && sudo apt-get install docker-compose-plugin
#... |
3da91b22a3fdbd86593cc485a5f8bcebb7adb6ff9e502a26613beb796b2b04f1 | Shell | 641 | 15 | #!/bin/sh
cd /Users/szhang32/Desktop/INTACT6/bivalency
annotation="/Users/szhang32/ref/mm10/gencode_vM23_name_conversion.txt"
K4="/Users/szhang32/Desktop/INTACT7/peak/A2a_H3K4me3_peaks.narrowPeak"
K27="/Users/szhang32/Desktop/INTACT6/peak/A2a_27me3_Active_merged-W200-G600-FDR0.01-island.bed"
geneExpression="/Users/sz... |
3637ab754996dbf6f89597da1fe959c69563863fb7fa199f75ea8bff57209ea1 | Shell | 644 | 26 | #!/bin/bash
#SBATCH -c 2
#SBATCH --array=90
#SBATCH --job-name=lstm_train
#SBATCH --mem=12GB
#SBATCH --gres=gpu:1
#SBATCH --constraint=any-gpu
#SBATCH --partition=cbmm
#SBATCH -t 20:00:00
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/
hostname
/om2/user/jakubk/miniconda3/envs/torch/bin/python -c 'import torch;... |
3b249e4ff64b18e2afa2b9a220991531f04d6ca667fcc8fcaeaa81736a39dab5 | Shell | 644 | 21 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 1-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
2d73d74e5ac45f3c9d2d0647521c2926baccf56a094c5602f9f3721208033c6b | Shell | 646 | 22 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 5-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
9586af4dad2139c9427bb57b37f9ab8682290bde801b872365ae811681c75f3f | Shell | 646 | 17 | #!/bin/bash
# 1 2 4 8 16 32 64
for ntiles in 1 2 4 8 16 32 64 128; do
CMD="mprof run -o ramlogs/mem_2d_${ntiles}_\"$1\"_\"$2\".out timings.py --ntiles ${ntiles} --alg \"$1\" > ramlogs/log_2d_${ntiles}_\"$1\"_\"$2\".out"
echo "$CMD"
eval "$CMD"
done
for ntiles in 1 2 4 6 8; do
CMD="mprof run -o ra... |
1125fab88d3748109aa694ecf622101c36b6b95cfe01380f1d084e22d0001de8 | Shell | 649 | 10 | #!/bin/bash
# rmf 3.25.2020, last modified 12.9.2020
grep MOTIF fly_factor_survey.meme | cut -d ' ' -f2,3 > memeMapFile.txt
grep MOTIF JASPAR2020_CORE_insects_non-redundant_pfms_meme.txt | cut -d ' ' -f2,3 >> memeMapFile.txt
grep ^MOTIF ../memeChip/ERR649814_cnc_memeChip/meme_out/meme_renamedMotifs.txt | cut -d ' ' ... |
70b5a336526a5bc4359c4b40d6c45c9c66161a562e3e0d5167d9fe8c02a8fc65 | Shell | 649 | 23 | #!/bin/bash
#SBATCH -c 2
#SBATCH --array=1-90
#SBATCH --job-name=LSTMTrain
#SBATCH --mem=16GB
#SBATCH -t 100:00:00
#SBATCH --gres=gpu:tesla-k80:1
#SBATCH --partition=cbmm
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/
/om2/user/jakubk/miniconda3/envs/torch/bin/python -c 'import torch; print(torch.rand(2,3).cuda... |
2c696184de26510d237489d437b1d456f17ba20eef72f89e8e0b16d46d7bd7f0 | Shell | 657 | 38 | #!/bin/bash
HOMFAM="../../data/homfam/train/*.fasta"
BALIFAM100="../../data/balifam100/train/*.fasta"
BALIFAM1000="../../data/balifam1000/train/*.fasta"
BALIFAM10000="../../data/balifam10000/train/*.fasta"
BALIFRAG="../../data/balifrag/train/*.fasta"
run () {
for f in $1
do
filename=$(basename "$f")
#slow a... |
6719bdbf5bf62639a59f91397bde259b7b679903efe6d907be2f26c645bd42ef | Shell | 658 | 34 | dataset=$1
device=$2
[ -z "${dataset}" ] && dataset="cora"
[ -z "${device}" ] && device=-1
python main_transductive.py \
--device $device \
--dataset $dataset \
--mask_rate 0.5 \
--encoder "gat" \
--decoder "gat" \
--in_drop 0.2 \
--attn_drop 0.1 \
--num_layers 2 \
--num_hidden 512 \
--num_heads 4 \
--max... |
be6811de86d5bb8dd2b41545daf9399e2068fce8468d5f695ba2516d714fc3f8 | Shell | 658 | 17 | #!/bin/sh
cd /Users/szhang32/Desktop/INTACT6/bivalency
annotation="/Users/szhang32/ref/mm10/gencode_vM23_name_conversion.txt"
D1_gene="D1_upregulated_genes.txt"
D1_K4="/Users/szhang32/Desktop/INTACT5/peak/D1_H3K4me3_peaks.narrowPeak"
D1_K27="/Users/szhang32/Desktop/INTACT6/peak/D1_27me3_Active_merged-W200-G600-FDR0.0... |
3f95d6ffdfb22648c686aff5ddab65358623aaa1d3973abb80ccc12d1160e194 | Shell | 676 | 24 | #!/bin/bash
#SBATCH -c 2
#SBATCH --array=1-54
#SBATCH --job-name=Dilated
#SBATCH --mem=60GB
#SBATCH --gres=gpu:1
#SBATCH --constraint=any-gpu
#SBATCH --partition=normal
#SBATCH -t 5:00:00
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/
hostname
/om2/user/jakubk/miniconda3/envs/torch/bin/python -c 'import torch;... |
7e23ff28447593407a03795f35ec2a2b96599f57dfad28208a09ceeedb68f126 | Shell | 676 | 15 | #!/bin/bash
# rmf 9.23.2020, last modified 4.19.2021
# only plots if the pval thresh is met
# RP24
for f in results_RP24*txt; do python ../../../../scripts/graphBoxPlot_compareSiteSignificance.py $f 0.05 RP24; done
# expression
for f in results*medianExpression*.txt; do python ../../../../scripts/graphBoxPlot_compa... |
01e8ac3bdaaebad37c33002b78ad32e124a1a8e7abfc484c8d005978ec1ae07a | Shell | 678 | 18 |
sudo apt-get update -y
sudo apt-get install -y ca-certificates curl gnupg lsb-release unzip bzip2
#download + unpack Ilastik
mkdir ./Ilastik
wget -O ./Ilastik/Ilastik.tar.bz2 https://files.ilastik.org/ilastik-1.4.0rc2-Linux.tar.bz2
tar -xf ./Ilastik/Ilastik.tar.bz2
#download + unpack FIJI
mkdir ./Fiji
w... |
92b966cce413d9c8a9c00bb03d66357fd868b8201af6312b0ef4ca5ad35a2e8a | Shell | 678 | 23 | #!/bin/bash
#SBATCH -c 2
#SBATCH -n 1
#SBATCH --array=1-90
#SBATCH --job-name=LSTM
#SBATCH --mem=12GB
#SBATCH --gres=gpu:1
#SBATCH --constraint=any-gpu
#SBATCH --partition=cbmm
#SBATCH -t 5:00:00
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/
/om2/user/jakubk/miniconda3/envs/torch/bin/python -c 'import torch; p... |
bfe27ccabd4b8a3e0ef39d1b3fb3ffed0a1fadbe68227a1c4f54ce25175d766e | Shell | 679 | 10 | #!/bin/bash
# must be run from a virtualenv with...
# https://github.com/koxudaxi/datamodel-code-generator
for model in AccessMethod Checksum DrsObject Error AccessURL ContentsObject DrsService
do
datamodel-codegen --input-file-type openapi --output-model-type pydantic_v2.BaseModel --url "https://raw.githubusercon... |
ea9040e8a9d6037c31f230ecd84915252491013f0871f183da3dc47056f73989 | Shell | 687 | 36 | #!/bin/bash
echo "------------ start --------"
# config path:
data_path=/li_zhengdao/dataset
proj_path=/li_zhengdao/github/GGN
k=$1
if [ ! -n "$k" ];then
k="train"
fi
echo $k
pid=$(ps -ef | grep eeg_main | grep -v grep | awk '{print $2}')
if [ -n "$pid" ]; then
echo "running testing: $pid"
kill -9 $pid
... |
67c7ab22466a6211ed73a85e3abc23bd5e7816084e5d1d4397dab3995d899558 | Shell | 698 | 11 | #!/bin/bash
# rmf 2.13.2020, last modified 6.18.2021
for f in ../../../promoters/ELC*_transcriptList.txt; do echo $f >> fileList.transcriptLists.txt; done
for f in ../../../promoters/RLC*_transcriptList.txt; do echo $f >> fileList.transcriptLists.txt; done
for f in ../../../promoters/LLC*_transcriptList.txt; do echo ... |
0df9ba5024aa95abc5c6f1611813c9d2edf4d5e33febde0f5140a5547e09a1dd | Shell | 701 | 22 | #!/bin/bash
#SBATCH -c 4
#SBATCH --job-name=exp_set_1
#SBATCH --mem=25GB
#SBATCH -t 24:00:00
#SBATCH --gres=gpu:1
#SBATCH --constraint=any-gpu
#SBATCH --partition=cbmm
#SBATCH -D ./log/
cd /om/user/shobhita/src/symmetry/experiment_set_1
hostname
export CUDA_VISIBLE_DEVICES=0
/om2/user/jakubk/miniconda3/envs/torch/bi... |
d328685882ea97c43298f1b8e256f5fa92bc535f483064035e4014bbbbf3aadd | Shell | 708 | 15 | #!/bin/bash
## Download a standalone version of PROCHECK from https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
## Install Procheck on your local machine and provide the path of installation in next lne.
MODULE=<Absolute path to PROCHECK installation>
## Run this script in the directory containing the model str... |
bd428db8172410ac270cfdfec9254da954a922ed05d0dffb9740bca325c5b417 | Shell | 712 | 15 | #!/bin/sh
TEST=$(mktemp)
TEST_EXTRA_CLASSES=$(mktemp)
pytest --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST"
pytest -o python_classes='Test* *Test *TestCase' --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST_EXTRA_CLASSES"
n_tests=$(grep 'tests collected' "$TEST" | sed -... |
86770628c7eaed468da5231a6fc0a55d884c0ed48ea9b3f65bb0cfb218fc1296 | Shell | 717 | 14 | #!/bin/bash
# rmf 12.17.2020, last modified 6.18.2021
# cleaned up 3.1.2022
# usage: plotHorizontalHeatmapAndBarplot.py <summary file> <p-value threshold> <asterisk threshold> <FDR annotation (True or False)>
# horizontal heatmap
for f in motifEnrichmentSummary_*FPKM*.txt; do python ../../../scripts/plotHorizontalHea... |
c48c41c13ebf7824e3c57dc0d2e427276ff46e3f330439550218d72f5435504c | Shell | 724 | 16 | # rmf 5.28.2019, last modified 11.10.2020
# note that though the python script refers to peak expression, this is actually filtering on phase from the gene group files (output of rhythmicity analysis)
# ZTs are start-inclusive, end-exclusive (ie, phase==ZT12 is included, but phase==ZT24 is excluded from 12-24)
# ELCs... |
764837c4a926789850d55f327678a501e31f6db96b15b2d4b033e015193e84c0 | Shell | 734 | 14 | echo ""
echo "Empty cache, starting NEST v$NEST_VERSION installation."
echo ""
export MY_BEFORE_DIR=$PWD
cd /home/travis
wget https://github.com/nest/nest-simulator/archive/v$NEST_VERSION.tar.gz -O nest-simulator-$NEST_VERSION.tar.gz
tar -xzf nest-simulator-$NEST_VERSION.tar.gz
mkdir nest-simulator-$NEST_VERSION-build
... |
8654f3a618e6bea7d0920a2e51befa83f2e5490efa36bfaefad87355ef4c7c0e | Shell | 739 | 22 | data_dir=/Users/vkumar/Documents/col/self/cluster_munich/smith10_parcellation/smith10_parcellation/script/smith10/volume_smith
atlas_dir=/Users/vkumar/Documents/col/self/cluster_munich/smith10_parcellation/smith10_parcellation/script/win17_rsn/32k_ConteAtlas_v2
cd $data_dir
ls LEFT*.nii.gz | sort -V > list.txt
for j ... |
f5eba7bd241d2039e56a41aa81c4c512ebda9011f8ae3a9cd0ba68600e12411b | Shell | 748 | 15 | #!/bin/bash
# rmf 3.12.2019, last modified 3.6.2021
# gets just the transcript symbols from transcript group file
# NR>1 skips the header, print $2 prints the second column containing symbols
for f in ELCs*.txt; do base=${f%%.txt}; outfile=$base'_transcriptList.txt'; cat $f | awk 'NR>1{print $0 | "cut -f2"}' > $outf... |
c816d7338b03f68d7639aaa18098b7a980b91a96d169042e969783d1ae298427 | Shell | 753 | 18 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(echo "$line" | awk -F, '{... |
a9cfdfaf118aa7b07a0daa58836935578754ccedf534313a8536a54c636bb05d | Shell | 755 | 16 | #!/bin/sh
cd /Users/szhang32/Desktop/INTACT6/bivalency
annotation="/Users/szhang32/ref/mm10/gencode_vM23_name_conversion.txt"
K4="/Users/szhang32/Desktop/INTACT5/peak/D1_H3K4me3_peaks.narrowPeak"
#K27="/Users/szhang32/Desktop/INTACT6/peak/D1_27me3_Active_S45_duplicate_removed.sorted-W200-G600-FDR0.01-island.bed"
K27=... |
ea60337f5202da5a3a3d8da04c333b29dd7575e8cc2c7914b3d8db042e09366f | Shell | 758 | 37 | dataset=$1
device=$2
[ -z "${dataset}" ] && dataset="cora"
[ -z "${device}" ] && device=0
CUDA_VISIBLE_DEVICES=$device \
python main_full_batch.py \
--device 0 \
--dataset $dataset \
--mask_method "random" \
--remask_method "fixed" \
--mask_rate 0.5 \
--in_drop 0.2 \
--attn_drop 0.1 \
--num_layers 2 \
--... |
edff5103e50c6c4dcb572a8b218643eb6361f223973fea9449246935e086c8ca | Shell | 759 | 13 | #!/bin/bash
# rmf 3.12.2019, last modified 4.3.2020
# cleaned up 2.28.2022
# gets all the motif IDs from a meme file into one file
# resulting file is used as input for running FIMO on all motifs in a database meme file in parallel
grep MOTIF fly_factor_survey.meme | cut -d ' ' -f2 > motifList_fly_factor_survey.txt
... |
6f61cf1d66e0c9a3d9523d03e14c3e56fcfff4ac545b01fe422a04c1fa63633b | Shell | 764 | 21 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Re-dilating the snr-mean-416-erode
# Edit sphere size in mm or box size in voxels
# Edit dilation Mean -dilM versus Mode -dilD
cd /dhcp/scanner_positioning/resliced/
# Dilated first time:
fslmaths /... |
004244187d71767216e3a77fb9f4a2474be868addca3932bbbf2658ba58a81d5 | Shell | 766 | 18 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(echo "$line" | awk -F, '{... |
c4b5833fe471160d6a685c6966ec0f1aa55180c9d6229debf5f1e58a4e313007 | Shell | 767 | 18 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(echo "$line" | awk -F, '{... |
c09b1d8f6ba062e79dfb92ffadfc2497b471c66642d848999b04c2425fa8c18d | Shell | 777 | 20 | #!/bin/bash
#SBATCH -A C3SE2023-1-17 -p vera
#SBATCH -n 20
#SBATCH -t 2-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
b65b4d73aaaf6839e6bff1f5d95887f639a1a436a255cd49715881eb92a73629 | Shell | 778 | 27 | #!/bin/bash
#SBATCH --job-name=hpt
#SBATCH --time=0-12:00 # days-hh:mm
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:1 #Request GPU "generic resources"
#SBATCH --mem=32000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arrayidx.out
# se... |
fa9d5f1e00950e008a86f5f95151a70c99d5a6132c68b79fc1d91feb3643fc01 | Shell | 782 | 25 | #!/bin/bash
#SBATCH --job-name=hpt
#SBATCH --time=0-16:00 # days-hh:mm
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:1 #Request GPU "generic resources"
#SBATCH --mem=32000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arrayidx.out
# se... |
bdab2b3ef6eea0b2312e491b0a089ae6a6d86fee4d62c268f022cdf25b35e576 | Shell | 791 | 28 | #!/bin/bash
#SBATCH --job-name=ablation
#SBATCH --time=0-23:00 # days-hh:mm
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=32000M
#
#SBATCH --output=./output/%x-%j.out # name-jobid-arrayidx.out
... |
ee90bcc6e76fc0bc52337ec20b5be3cdaf0c3f3b1e0d5960b27a5fe818b30c9a | Shell | 792 | 24 | #! /bin/bash
cpus=$(nproc)
sudo perf stat -o output.txt -e instructions -e task-clock sysbench --num-threads=$cpus --test=cpu run &> /dev/null
clock=$(cat output.txt | grep 'seconds time' |awk '{print $1;}'| while read spo; do echo $spo; done)
echo $clock
ioping -S64M -L -s4k -c 10 . > disk_read.txt
disk_read=$(cat... |
4594b17adb10536f1c393438af7f3d60873ff3878564040d9fd8e329d0499875 | Shell | 795 | 23 | #!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --mem=16GB
#SBATCH --cpus-per-task=8
#SBATCH -J fba_6
########## Make study-specific analysis mask in template space ##########
# Get variables from config
config=/PATH/TO/config
source $config
# Stop on error
set -eu
echo "CALCULATING INTERSECTION OF ALL SUBJECT MASKS TO... |
886799360044b44e3cf3ca6d7e00acd39f24693742cea58d7961f2431e7b3db6 | Shell | 795 | 34 |
#On MICe machines: Remove all modules
module purge
#If venv does not exist, create it
if [ ! -d ".venv" ]; then
echo "Initializing python virtual environment..."
#Create the venv
python3 -m venv .venv
echo "Installing python packages..."
#Activate the venv
source .venv/bin/activate
#Upgrade pip
echo "Upgr... |
eac77ae69efc49e37416f5e6ed7997d19861f6065ac55a2bc770de784cfea24f | Shell | 798 | 28 | #!/bin/bash
#SBATCH --job-name=c10ngn
#SBATCH --time=2-00:00 # days-hh:mm
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=128000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arrayidx.ou... |
dbdb3c56b6b91a4ee8356e64868ce8b9130a7000537c6e83fe49e9edb7bb51be | Shell | 800 | 31 | #!/bin/bash
HOMFAM="../../data/homfam/train/*.fasta"
BALIFAM100="../../data/balifam100/train/*.fasta"
BALIFAM1000="../../data/balifam1000/train/*.fasta"
BALIFAM10000="../../data/balifam10000/train/*.fasta"
BALIFRAG="../../data/balifrag/train/*.fasta"
LARGE="../../data/large/train/*.fasta"
OUT_DIR="./"
mkdir -p ${OUT... |
cd23fc75e1c122402083b0861669347ed3fdc2969caf3a1cd62dad3b315928a8 | Shell | 802 | 14 | # rsync code to cbica
rsync -avzh /Users/lindenmp/Google-Drive-Penn/work/research_projects/nct_hierarchy/src \
parkesl@cubic-login.uphs.upenn.edu:/cbica/home/parkesl/research_projects/nct_hierarchy/
rsync -avzh /Users/lindenmp/Google-Drive-Penn/work/research_projects/nct_hierarchy/scripts \
parkesl@cubic-login.uphs.upe... |
506918812a9c997035cd005616f4fbf3bbe7c8cc85512dbbbd5df766393fde80 | Shell | 805 | 22 | ## Download the pretraiend models and structure files from the github release
github_release="https://github.com/jlaw9/upper-bound-energy-gnn/releases/download/0.1"
f="fully_relaxed.json.gz"
echo "wget -O inputs/$f $github_release/$f"
wget -O inputs/$f $github_release/$f
f="volume_relaxed.json.gz"
echo "wget -O input... |
c5d6e800b8e75e4de16a5b2be54ae71eaba815cc7818360b526a97854fecdb00 | Shell | 805 | 22 | ## Download the pretraiend models and structure files from the github release
github_release="https://github.com/jlaw9/upper-bound-energy-gnn/releases/download/0.1"
f="fully_relaxed.json.gz"
echo "wget -O inputs/$f $github_release/$f"
wget -O inputs/$f $github_release/$f
f="volume_relaxed.json.gz"
echo "wget -O input... |
8f477d0e5c56217455d9b6ae433fce07102aaa9895237fdb985539fe4205b510 | Shell | 815 | 44 | #!/bin/bash
HOMFAM="../../data/homfam/train/*.fasta"
BALIFAM100="../../data/balifam100/train/*.fasta"
BALIFAM1000="../../data/balifam1000/train/*.fasta"
BALIFAM10000="../../data/balifam10000/train/*.fasta"
BALIFRAG="../../data/balifrag/train/*.fasta"
mkdir -p alignments
mkdir -p times
MAFFT_PATH=""
run () {
mkd... |
017271e62a09e8298b5523d65529e78a27a153bb88acc0bb21db994715aace08 | Shell | 817 | 22 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 2-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
73be8cbc06c990a6a4f91c85156123f4a2e99d21be15b05db4431f73e59130de | Shell | 818 | 28 | #!/bin/bash
#SBATCH --job-name=c10-noise
#SBATCH --time=0-09:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=128000M
#
#SBATCH --output=./output/%x-%j.out # name-jobid-arrayidx.o... |
eb57afb34ff228ee4c8a111fb0c52527b8687b461e9094ba59ce10f71172bb9e | Shell | 818 | 22 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 2-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
72bbfbec9259cab6a28cb462aa42bb665b41ada1c5e071e34113b73e26f50435 | Shell | 821 | 22 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 2-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
dbca7a5721431b540e8cb5fdec7a7d8eb74efc951168473af772708389af8a65 | Shell | 821 | 21 | #!/bin/bash
# Shelli Kesler 8/26/16
# Batch save screen capture of tractography results from TrackVis for quality check
# Requires GraphicsMagick (http://www.graphicsmagick.org)
export PATH=$PATH:/Applications/TrackVis.app/Contents/MacOS
SUBJS=$(cat /fullpath/Paths.txt) #txt file containing full path to each subject ... |
f5638175782087c35e2ff04c65d58af6787a673445e426ca396591ca7764130d | Shell | 822 | 18 | # clean up on cbica
rm -rf core.*
rm -rf ./sge/*
conda activate pfactor_gradients
# 1) pnc subjects, array job
# 793 (schaefer200) | 766 (schaefer400) | 792 (glasser360)
qsub -N subjects -l h_vmem=8G,s_vmem=8G -pe threaded 2 -j y -b y -o /cbica/home/parkesl/sge/ -e /cbica/home/parkesl/sge/ \
-t 1:793 \
/cbica/home/pa... |
1f8657ef933ac58ccf18a71470c7e8113250ecfd827521fd90a1f63401cb35b7 | Shell | 824 | 10 | # rmf 3.25.2020, last modified 6.18.2021
# cleaned up 3.1.2022
python ../../../scripts/writeSummaryFile.py fileList.hypergeomCorrectedResults.coreGroups.txt _coreGroups
python ../../../scripts/writeSummaryFile.py fileList.hypergeomCorrectedResults.upAndDown.txt _upAndDown
python ../../../scripts/writeSummaryFile.py fi... |
3ced99b4032a950ae7ff467475951632fb641d78ab5d2eb65fdd8cdd75344604 | Shell | 833 | 22 | #!/bin/bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); ... |
ca8c2a73f96e446d37031f50d393115ead039fdfb09c1e130da1839de85085c0 | Shell | 834 | 37 | #!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -l h_rt=100:0:0
#$ -l h_vmem=18G
#S -l mem_free=18G
#$ -pe smp 1
#SBATCH -o job.%j.out
#SBATCH -J image
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 2G
#SBATCH --time=99:99:99
set -oe pipefail
echo "Job started on `hostname` at `date`"
#export PATH=$HOME/miniconda... |
41ee67161b2001966ec2a6c5c0dbd05c817acebf6ecb106ed3085cf909786669 | Shell | 845 | 28 | #!/bin/bash
#SBATCH --job-name=compare_best
#SBATCH --time=1-08:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=128000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arra... |
d06644874e2835fbdfb58f1b131099e6f0b55d9aec33f18e7b96ed41e75ae991 | Shell | 847 | 27 | #!/bin/bash
#SBATCH --job-name=compare_best
#SBATCH --time=1-00:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=128000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arra... |
28b96a2fffdf4f34b9fe255ff3f27e507c0d3db86218f4a632f20792004263ef | Shell | 850 | 28 | #!/bin/bash
#SBATCH --job-name=compare_target
#SBATCH --time=0-20:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=32000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-jobid-arr... |
2293b1f6daf569007c0d2a217f7b1842a4754e460f39cce85de83876a242af1a | Shell | 858 | 20 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
b9c151e0a6acbdec924fb01f965ffc1c912d06deb8224d52c55fe2143af6930b | Shell | 861 | 38 | #!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -l h_rt=100:0:0
#$ -l h_vmem=18G
#S -l mem_free=18G
#$ -pe smp 1
#SBATCH -o job.%j.out
#SBATCH -J image
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 5G
#SBATCH --time=99:99:99
set -oe pipefail
echo "Job started on `hostname` at `date`"
#export PATH=$HOME/miniconda... |
fa1e585b959934666e52b1a921061e38834f7100af920d988e3c1563a73a1a8f | Shell | 865 | 28 | #!/bin/bash
#SBATCH --job-name=compare_regularization
#SBATCH --time=2-08:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=128000M
#
#SBATCH --output=./output/%x-%j-%a.out # name-... |
4b66b66e8bcfa5a7b2fce9ac77c4e9ca534d27065dcafe8452c482073571069d | Shell | 873 | 8 | #!/bin/bash
export PYTHONPATH="/home/zchayav/projects/syntheye/PerceptualSimilarity/"
path1=/home/zchayav/projects/syntheye/datasets/eye2gene_new_filepaths/all_baf_valid_50deg_filtered_train_0_edited.csv
path2=/home/zchayav/projects/syntheye/datasets/eye2gene_new_filepaths/all_baf_valid_50deg_filtered_train_0_edited.cs... |
da75c114d24e5fd1113ce2e0e2ddc4faec163ef16e1463627cd4aee3a72b7ce6 | Shell | 874 | 27 | #!/bin/sh
cd "$(dirname "$0")"/.. || exit
xsd_path="lib/galaxy/tool_util/xsd/galaxy.xsd"
# Lint the XSD, failing fast on a bad path or malformed schema
xmllint --noout "$xsd_path" || exit 1
test_tools_path='test/functional/tools'
# test all test tools except upload.xml which uses a non-standard conditional
# (withou... |
e5f28763dcb02b9c9c18c36800579178533e866657b9e1a375524b228a00c27b | Shell | 884 | 29 | #!/bin/bash
#SBATCH --job-name=excite
# #SBATCH --array=1-10%2 # job array, start-end%max_concurrent
#SBATCH --time=0-02:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem=1... |
d1f1cea3f8dcb8d1688c677c03866f5195e7439cd98dafea7e170c15bf9348b1 | Shell | 885 | 29 | #!/bin/bash
#SBATCH --job-name=template
# #SBATCH --array=1-10%2 # job array, start-end%max_concurrent
#SBATCH --time=0-01:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH --mem... |
a6ba4a297838ac6b702735f98b94a2daae3f8fa63f800e69f075b1bd402cf843 | Shell | 886 | 36 |
initTPRFile=wt_ca_domain.tpr
initXTCFile=all_combined.xtc
initNDXFile=wt_ca_domains.ndx
prefix=both_tmd
TPRFile=backbone.tpr
XTCFile=tetramer_backbone_combined.xtc
output=cov-domain-tetramer
selText=both_tmd
## = = Extract alpha-Carbons for quicker processing.
#echo "$selText $selText" | gmx trjconv \
#-s $initTPRFil... |
e8b35291427f41b553bf940e0eb45b9209e82dfcc6001f5c02b9441166aef6c3 | Shell | 890 | 27 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
# Use adult T1 to define space for reslicing
REF=/usr/local/fsl/data/standard/MNI152lin_T1_1mm.nii.gz
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
... |
478f7cd90cfda20271ef9cd90113102b6b2e0e8c5999075f3e9c302c994410fa | Shell | 891 | 18 | # ENZYMES
python -m train --datadir=data --bmname=ENZYMES --cuda=3 --max-nodes=100 --num-classes=6
# ENZYMES - Diffpool
python -m train --bmname=ENZYMES --assign-ratio=0.1 --hidden-dim=30 --output-dim=30 --cuda=1 --num-classes=6 --method=soft-assign
# DD
python -m train --datadir=data --bmname=DD --cuda=0 --max-nodes... |
46a46b2fb5cb26b0cf6f99ec57e7c5d698deba760f82397cc6cf0c6d0d65ccc5 | Shell | 898 | 23 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licen... |
f178178ca81bf69891ce5ac46c42865719c94e9e214970e1488f0d9f6afee97b | Shell | 900 | 29 | #!/bin/bash
#SBATCH --job-name=excite_control
# #SBATCH --array=1-10%2 # job array, start-end%max_concurrent
#SBATCH --time=0-02:30 # days-hh:mm
#
#SBATCH --cpus-per-task=16 # Cores per GPU: Cedar - 6, Graham - 16
#SBATCH --gres=gpu:t4:1 #Request GPU "generic resources"
#SBATCH... |
0beb4114329d57ce8cab10b14a00bff3432a48221d8a3139d23a9557fabb2d87 | Shell | 902 | 9 | python mouse2human.py GRCm38.81.P60Cerebellum_ALT_mouse.txt GRCm38.81.P60Cerebellum_ALT_human.txt
python mouse2human.py GRCm38.81.P60Cortex_noRep5_FRONTALonly_mouse.txt GRCm38.81.P60Cortex_noRep5_FRONTALonly_human.txt
python mouse2human.py GRCm38.81.P60Cortex_noRep5_POSTERIORonly_mouse.txt GRCm38.81.P60Cortex_noRep5_PO... |
976863ad20c68582f41d5d9f102f3cb4800c10263ad5996b7786b211fdd2d365 | Shell | 907 | 23 | #!/bin/bash
#SBATCH -A C3SE2022-1-16 -p vera
#SBATCH -n 20
#SBATCH -t 5-00:00:00
#SBATCH --mail-user=gustajo@chalmers.se
#SBATCH --mail-type=end # send mail when job ends
# instead of using the "SBATCH -o run_init-X.log" line here,
# include the flag "-o run_init-%A_%a.log" in the sbatch submission command:
# sbatch... |
11c9262f00382023715469589f5741199b8e04af40396907c0a717c4b9a14224 | Shell | 912 | 27 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(... |
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