sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4b93ed2c18d385521eac00af90da5d3dd328da3412f2330b03dec1696259de71 | Shell | 491 | 19 | #!/usr/bin/env bash
# definitions
workDir=/vols/Scratch
scriptDir=/vols/Scratch/comparative_scripts
mkdir -p $workDir/connectivity_maps_tracing
seedList="M1 ALM aM2 pM2"
template=$scriptDir/registrations/QBI_atlas_2mm_v6.nii
for seed in $seedList; do
echo "$seed"
fsl_sbca -i $scriptDir/registrations/tracer_m... |
6dd1376419f397f164ddeeda4bb4a9ddb19c53ca76991616f344eb0f227bc5e2 | Shell | 492 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'gprofiler_plotting'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module lo... |
aa2d0a63d9cf6a497d18fc226baf5d108360fccd52008ad2ab3b7a3424a46420 | Shell | 492 | 27 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N gsea_analysis
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
4c4779254dc40909acbb6b2b1c6d58e846fc175f2cb0385e73076df2da946cc5 | Shell | 495 | 21 | #Installations needed:
#pip install sphinx
#pip install sphinx_rtd_theme
# Remove old docs
rm -r source/* _build
# Auto-generate API docs:
sphinx-apidoc -M -o ./source ../pensa ../pensa/diffnets/
# Format the auto-generated API docs
sed -i 's/ package//g' source/*.rst
sed -i 's/ module//g' source/*.rst
sed -i -e '/S... |
e00d71f8db0dcff17472285b3e772f99cb06d493c5697b91ec7e900e139ce64e | Shell | 497 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=2.0G,h_vmem=20G,h_fsize=50G
#$ -N 'resid_interaction_eqtl'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module... |
e937f5d54c69ab693735b2904ca08fe1b24657e05d309f2c0451b0a0188cbca4 | Shell | 498 | 20 | ROOT_PATH=""
model_path="$ROOT_PATH/outputs/chipseq/train_inf_gpt_small_gm12878/checkpoints/val/sei.ckpt"
python -m train \
experiment=hg38/chipseq \
wandb.mode=online \
wandb.group=Chipseq \
wandb.name=gen_gpt_small_gm12878 \
hydra.run.dir="./outputs/chipseq/gen_gpt_small_gm12878" \
model.con... |
498b6df1cd57bc920b33d1d455f1a968c7bf4a9492a55fbc6e7ff0ee12dd4092 | Shell | 500 | 6 | # Before running, adjust folder names (/datafolder), segmentation task (retchat.task.*) and model (models\*)
for DATA in "/datafolder" ; do
rm "/home/fiona.muellner/faim-retina-chatbands/outputs/stacks_to_process.txt"
luigi --local-scheduler --module retchat.tasks.run_segmentation_d20 retina.ParallelChatbandPredicti... |
959c5df7ca6843f0b81a7ccddebffe51f2032138ec2fd2dfa41ab4061ae884e8 | Shell | 502 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'gprofiler_eqtl'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module load c... |
234311b5c0178a186f6672d592476c3571bd6d9f5f0a962f5afe941983ced55b | Shell | 503 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'semantic_plotting'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module loa... |
0d1f20d42c0d2feb65937ef3bd6555ae161530078ecc24c64005ee450f3ba650 | Shell | 504 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=50G,h_vmem=50G,h_fsize=50G
#$ -N prepare_mashr
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current module... |
87685fb43d69e050c5d660589b928c8fc27c795c2895bfe5739eaaca80812352 | Shell | 504 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=90G,h_vmem=90G,h_fsize=50G
#$ -N prepare_mashr
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current module... |
1e9fb39f2d6fc51e19c3acfa123e0d97fe0d163acf07a2230bbd963b0826470a | Shell | 506 | 29 | cd /project/4180000.19/multiRat/tmp_crop/ds50
ls ./ | while read line
do
echo $line
cd ${line}
ls ./ | while read ses
do
#ses='ses-1'
cd ${ses}/anat
nii=$(ls *.nii.gz)
mv $nii tmp.nii.gz
fslroi tmp.nii.gz $nii 40 170 0 -1 70 145
slicer $nii -a ../../../../$(remove_ext $nii).png
cd ../func
nii=$(ls *.nii.gz)
mv $nii ... |
5533ca5ba0791e65f5e5a1a1200c632471a4cfb60ce301fbad3aff5b4d42fb9a | Shell | 506 | 19 | #!/bin/bash
# Define variables
ENV_FILE="environment.yaml"
# Change to the script's directory or exit if unsuccessful
cd "$(dirname "$0")" || { echo "Unable to change directory. Exiting."; exit 1; }
# Get environment name
ENV_NAME=$(awk '/name:/ {print $2}' "$ENV_FILE")
# Create environment
conda env create --file ... |
e585e3175c1c4890c513b45e52d63ee2172091d37d5f2fe3e72bd97fa5301ca8 | Shell | 508 | 13 | #!/bin/bash
#
# This script finds the min & max values for all randomise output for comparisons between social & doors for ISTART 2022
# Jimmy Wyngaarden, May 2022
for model in 2 3 4 5; do
for type in "act" "nppi-dmn" "ppi_seed-VS_thr5"; do
for file in /data/projects/istart-socdoors/derivatives/fsl/L3_model-${model... |
037512c494124ae4ab44c77bd360e7e9e54f337c01d8896554576cf871c714e8 | Shell | 510 | 19 | #!/bin/bash
#SBATCH --job-name=gradients
#SBATCH --output=gradients_%a.log
#SBATCH --time=1-12:00:00
#SBATCH --mem=32GB
#SBATCH --cpus-per-task=1
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --exclude=node-12,dgx-2,dgx-5
module purge
module load cuDNN/7.6.4.38-gcccuda-2019b
module load CUDA/10.1.243-GCC-8.3.0
... |
0fc6647782fbc9a61f3ef59e031514eec348812b538608ae04c8aa2122ee2df6 | Shell | 510 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=80G,h_vmem=80G,h_fsize=50G
#$ -N prepare_mashr
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current module... |
39b986792d96cd9fe36056893e3d9cfae39c3421d3f2d58e7e5e21cae19d5a48 | Shell | 510 | 16 | #!/bin/bash
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/Utah_analysis/CBIG2016_preproc_ALL
output_DIR=/fslgroup/grp_proc/compute/Utah_analysis/CBIG2016_preproc_FS6
##Change this first line to your code_DIR pointing to the subjids file
for subj in `cat $code_DIR/subjids/ids.txt`;do
mkdir -p ${c... |
a4ed0be7b03316fbd32f504d1c7c8a6917ad7f2f0dd53cd10633f2723971b66b | Shell | 510 | 10 | #!/bin/sh
## Download JARVIS data (version 1.1) from Vitsios et al., Nature Communications (2021)
## Preprocessing
gzcat *hg38.tsv.gz | awk 'BEGIN{OFS="\t"} {print "chr"$1, $2-1, $2, $3}' | sort -k1,1V -k2,2n -k3,3n -t$'\t' | bgzip -c > sorted.jarvis.all_chr.bed.gz
tabix -p bed sorted.jarvis.all_chr.bed.gz
gzcat sor... |
e4196fa77ce9d924ce863e2aa3379c139026475cceb31b942545af32f6af72b5 | Shell | 510 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=200G,h_vmem=200G,h_fsize=50G
#$ -N prepare_mashr
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modu... |
542a371ced9e53031a6dd774d8185d92be32b3c4b78863fe30a1c530d527ddd9 | Shell | 512 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5G,h_vmem=5G,h_fsize=50G
#$ -N dRFE_curve
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reprodu... |
1e359f36070073b46dd363aee20079cd883a202e5c44987df9f2a99704a75886 | Shell | 513 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N sz_coloc_comp
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modul... |
60a4cdb6d26fc98d858a210a3f1b560578c1a8dd4fe23904dd9efe86fda6876c | Shell | 513 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'correlation'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### List module... |
be6e43618183996f29ed5283118164e9f4b3c66960da7e344d9c708778a6b8ad | Shell | 514 | 17 | #!/bin/bash
# Builds docker container and tags it. Takes 1 arg:
# arg1: docker image tag (Optional)
# Example usage: scripts/build.sh v1.0.0
set -e
# cd to project root directory
cd "$(dirname "$(dirname "$0")")"
# Set docker tag to first arg or latest if arg not given.
[[ ! -z "$1" ]] && DOCKER_TAG="$1" || DOCKER_TA... |
da9252a503c027bef98ef2416854a6ba5105eb4bc9bf0e48e50cca89e9dda27c | Shell | 514 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N gsea_plotting
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
mo... |
9fe1d49b100e541ef6ad676896991161efed1b36fbe6ca5db3e90a9e7c5b6498 | Shell | 515 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5G,h_vmem=5G,h_fsize=50G
#$ -N dRFE_summary
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for repro... |
d560fff5881e8cb1d4f3a211be40abd077c5a4d7896c0666fc18d259542b3ed4 | Shell | 516 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N upset_plot
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
modul... |
d7f52238f6b90252f5ff61aa7eb2c16cbb9b0a46c13b782de41caba33c1e5448 | Shell | 516 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -pe local 15
#$ -l mem_free=8G,h_vmem=8G,h_fsize=100G
#$ -N 'network_dlpfc'
#$ -o ./network.out
#$ -e ./network.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
m... |
214511941e1cbff183a587ebb9a6736b1f7f12844831d950328a54ebf4719b80 | Shell | 517 | 21 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
# Generate New Scanlist File
>SCANLIST.txt
# Loop over directories in Bruker raw folder
for Scan in ${BRUKER_RAW_DIR}/*/; do
if test -f "${Scan}/acqp"; then
echo "Scanning File $Scan";
python3 ${SCRIPTS}/print_scan_name.py "${Scan}/acqp... |
c7fba78ea7e19a7f40549d460d83ae1f2fcafb882968f687fd453ffb3ca00b93 | Shell | 517 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'correlation'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### List module... |
256b9b0e28118a360a8f0c38563384ade3372eb5d20c10e1f528f47e87e97dc2 | Shell | 518 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -pe local 15
#$ -l mem_free=8G,h_vmem=8G,h_fsize=100G
#$ -N 'network_caudate'
#$ -o ./network.out
#$ -e ./network.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
... |
29a3a55ec7c3564342c5578ecf479193a4a8b755b8f12a157ae0a95cc2d8ee5e | Shell | 519 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5G,h_vmem=5G,h_fsize=50G
#$ -N dRFE_summary
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for repro... |
9ae76d0d812923dba669b0431a9ea1f1775e2f22fecf8c1356f694e09b629e71 | Shell | 520 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N 'softpower_dlpfc'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### Load mo... |
a7722ba8bbd6d2c1b4ca53d605735258bbdf96cd42f9b0fc8278db4e59a055e4 | Shell | 521 | 36 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${PARALLEL:-}" ]; then
PARALLEL=1
fi
i=0
trap "kill 0" EXIT
for RAW in $RAWDIR/t1_sa/*.hdr ; do
RAW... |
0a62ad2bdb53fbb71b62d4a959c8fe27412445e0364f7da9295fbf2b41a4e01f | Shell | 522 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N 'softpower_caudate'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### Load ... |
4233f97be588229c3e5a47d0e9d332fd327293e305b30dcde61f087a46ba6f2b | Shell | 522 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -pe local 15
#$ -l mem_free=8G,h_vmem=8G,h_fsize=100G
#$ -N 'network_hippocampus'
#$ -o ./network.out
#$ -e ./network.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAM... |
a058d0b99a338130d321db9732f707cb3a7e7dc4d004f57abfc18a03343a773d | Shell | 523 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N eigen_corr
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
modul... |
a5c9426a15993bc3c60259fcc92bd6c612b646964ea1a82ba84bcecf669f69a4 | Shell | 523 | 14 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=03_t1_svd
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=history --train-... |
b3d081295aae3caf92aef2aa6bb4d43609faa46bf63734052cb318879d0132ef | Shell | 523 | 14 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=03_t1_svd
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=history --train-... |
f95cfe5867f40acdad38407e97456ff92fae1a116e87c1d4e3080c7ca78911f9 | Shell | 523 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5.0G,h_vmem=5G,h_fsize=50G
#$ -N enrichment_heatmap
#$ -o ./plotting.log
#$ -e ./plotting.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules... |
38ca0734834e969cf8e0e861db85a54da30d1b401721827afcef873d03c92284 | Shell | 524 | 18 | # Remove default output dir and smk internal dir
cleanup () {
rc=$?
rm -rf .snakemake/
rm -rf ../output/
cd "$user_dir"
echo "Exit status: $rc"
}
trap cleanup EXIT
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
set -u # ensures that script exits whe... |
e4c2871040fa55490eaec83c65af5b0a6e7707da0c0aee705e4f7dbdc94495ee | Shell | 525 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N rrho_plot
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
module... |
334440466fd43a7ea97da4aa7d85b09517f6769c45ea5cc9474450c6cd846813 | Shell | 526 | 23 | #!/bin/bash -l
#SBATCH --time=5:00:00
#SBATCH --partition=prod
#SBATCH --account=proj100
#SBATCH --nodes=1
#SBATCH --job-name=metrics
#SBATCH --exclusive
#SBATCH --mem=0
echo 'load venv'
module purge
module load archive/2023-06 python
source /gpfs/bbp.cscs.ch/project/proj100/analysis/vbca/bin/activate
cd /gpfs/bbp.... |
44bb74270577f13193a2ef2965dfa4ac2a360954d1fe0cac94689a13291faa34 | Shell | 526 | 29 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=15.0G,h_vmem=15G,h_fsize=50G
#$ -N 'softpower_hippocampus'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### L... |
5ced5db92c4a5fcece5d7891867f5c1be676e07b98b8e89166c2a5a50054b2dc | Shell | 526 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N mash_allpairs_clean
#$ -o ./clean_mash.log
#$ -e ./clean_mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cur... |
66888fbf14dff9ba465f9bb45b0b7f2692d7286e63f7739bcbc47f5d0ede8977 | Shell | 526 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=20.0G,h_vmem=20G,h_fsize=50G
#$ -N gsea_analysis
#$ -o ./summary.out
#$ -e ./summary.out
#$ -m e -M jade.benjamin@libd.org
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ... |
6ad461924d4947e62cdb4cfe0dbe2c483a16f3dc36672f98bc106d2566172ec3 | Shell | 526 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=80G,h_vmem=80G,h_fsize=100G
#$ -N run_mashr
#$ -o ./mash.log
#$ -e ./mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for rep... |
844945675fcc26cf9984b77e9b0f46d6f76faa08369253f1e569aa75c0f83fcf | Shell | 526 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N boxplots
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
module ... |
bf02c101777fdd4880cf3e18cf1b76c82f1321bdaa9c733ab7528f2077eeab0b | Shell | 526 | 10 | FILE=$1
echo "Note: available models are apple2orange, facades_photo2label, map2sat, orange2apple, style_cezanne, style_ukiyoe, summer2winter_yosemite, zebra2horse, facades_label2photo, horse2zebra,monet2photo, sat2map, style_monet,style_vangogh, winter2summer_yosemite, iphone2dslr_flower"
echo "Specified [$FILE]"
... |
276508a76c6a95eba886e6001ba4ff08ce85861d51f7b8002dc19a6587432407 | Shell | 528 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=150G,h_vmem=150G,h_fsize=100G
#$ -N run_mashr
#$ -o ./mash.log
#$ -e ./mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for r... |
83112a30115c5712cb14d602b69682537872677e79050172df2043602dc9b305 | Shell | 528 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=150G,h_vmem=150G,h_fsize=100G
#$ -N jxn_mashr
#$ -o ./mash.log
#$ -e ./mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for r... |
b631f4796fcee568c984f335ad7bdc6f7e9b69cdc576184dcc80e2f045741172 | Shell | 528 | 17 | #!/bin/sh
##
##
#SBATCH -p gpu-super.q
#SBATCH --exclude=nova002,nova003,nova00[5-7],nova01[1-4]
#SBATCH --cpus-per-task=6
#SBATCH -n 1
#SBATCH -N 1
#SBATCH --job-name=ep_100
#SBATCH --output=output.log
#SBATCH --gres=gpu:1
export NCCL_P2P_DISABLE=1
python scripts/inference_end_to_end_w_igfold.py --batch_size 1 --wei... |
4a638535f717e1c3ff25b56963e5d07eadca6ad653b611f3bbbe81bee0a26051 | Shell | 529 | 35 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${PARALLEL:-}" ]; then
PARALLEL=1
fi
i=0
trap "kill 0" EXIT
for RAW in $RAWDIR/rt_sa_st/*.hdr ; do
R... |
d903ef799181523fafeddaafe972688cd1e131e1d90e673723bf833236952ad0 | Shell | 529 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N pca_plot
#$ -o ./plotting.log
#$ -e ./plotting.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for rep... |
50183be7c83d213d112ee33b0c9c151b7722d36be64550feb11c6fd3fe8784ae | Shell | 530 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N extract_model
#$ -o ./mash.log
#$ -e ./mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for... |
7bc0528747110747e98acefc78df10d9269170c0fd297487a148cc9662af875a | Shell | 530 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=25G,h_vmem=25G,h_fsize=100G
#$ -N extract_model
#$ -o ./mash.log
#$ -e ./mash.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for... |
88bbe965b373430c669ec1f3315c95eb5e4decbb3e71e65abd6796edfdcd606e | Shell | 531 | 18 | #!/bin/bash
set -eu
# Initialize a variable to keep track of errors
errors=0
# make sure not importing from langchain or langchain_experimental
# allow langchain.agents and langchain.tools (v1 middleware)
git --no-pager grep "^from langchain\." . | grep -v ":from langchain\.agents" | grep -v ":from langchain\.tools"... |
76fb56557c4bc0f13dee00d167d2d3d9396aaeb74f8c71adbab75d769a7122ff | Shell | 532 | 16 | #!/bin/bash
# Note that in the example below the indices in the
# input_pdbs/7zkr_GABARAP.pdb file have been shifted
# by +2 in chain A relative to pdbID 7zkr.
../scripts/run_inference.py \
--config-name base \
inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
inference.num_designs=10 \
'contigmap.con... |
f7d9e0825317b20f4553c7b73899630bd8d30f52b912c6c10a3179b1df42e32d | Shell | 532 | 12 |
# cellranger mkfastq
conda activate scrnaseq
module load cellranger/6.0
bsub -Is -R 'rusage[mem=10000]' -n 4 /bin/bash
cd /data/bioinformatics/projects/hassan2022/output/FC_07379
nohup cellranger mkfastq --id=01_cellranger_mkfastq \
--run=/data/bioinformatics/projects/hassan2022/data/FC_07379/220... |
37135651eba68207d2101f12a1026353cd3d724e2d2ad5d8a5c087a80d2bad85 | Shell | 533 | 19 | #!/bin/bash
FEATURE="gene" ## change based on feature to process
FAM="/location/of/FAM/genotypes.fam"
PHENO="/location/of/phenotype/file.csv"
TPM="/location/of/TPM/file.csv"
## Match counts with feature short hand
if [[ $FEATURE == 'transcript' ]]; then
VAR="tx"
elif [[ $FEATURE == "junction" ]]; then
VAR="jx... |
8d9e7068c18d6cc38e508a3d2f7211dea5de73e6a355dfaa2aa5097872932524 | Shell | 533 | 26 | #!/bin/bash
filelist=`ls ./*/task.feat/artef_clean.feat/filtered_func_data_clean.nii.gz`
for ID in $filelist ; do fslswapdim $ID -x y z ${ID:0:end-7}_flipx.nii.gz; done
filelist=`ls ./*/T1_BC.nii.gz`
for ID in $filelist ; do fslswapdim $ID -x y z ${ID:0:end-7}_flipx.nii.gz; done
filelist=`ls ./*/T1_BC_brain.ni... |
c9431dae631f0cb55cf636603baa1b8bb443162314d9ae8da9585a87be4208e7 | Shell | 533 | 25 | #!/bin/bash
# 64GB = 68719476736 bytes
MX_DOCKERIMAGE=${MX_DOCKERIMAGE:="ghcr.io/imsb-uke/maxomod_pipeline-r-python"}
MX_TAG=${MX_TAG:="latest"}
which docker
if [ "$?" = "0" ]; then
docker pull "${MX_DOCKERIMAGE}:${MX_TAG}"
docker run \
--rm \
--name "$USER-maxomod-pipeline-$$" \
--volume "$PWD:/wor... |
0a27e47e3260970d21ebdc99bdaed3a6f95cde52711669ece550f10584e3912f | Shell | 534 | 7 | #!/bin/bash
# Here, we're making some unconditional designs, and also using the 'monomer_contacts' auxillary potential function
# We specify the path for the outputs
# We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
# We generate 10 such designs
../scripts/run_infer... |
9cbd15377d75dfe810270f05d032dab7d3aaee7235da9663e5ad43eb48b9e9ca | Shell | 534 | 14 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=03_t1_svd
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 --mask=msk -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=histo... |
b33fdc687a262c8391fc3727cdf6957340a17f5a6c0ba3955b429534f29b66c9 | Shell | 534 | 14 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=03_t1_svd
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 --mask=msk -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=histo... |
7160b15bc643297d6780f5dfc99450f991831827e9bd35bfa08a242044c78308 | Shell | 537 | 15 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=04_t1_rovir
ROVIR=" -V"
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=hi... |
aa0551856d0c2e9cfffec8f8ffc339f49b1619d0a50a3a695e761710a43fbd8d | Shell | 537 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -pe local 5
#$ -l mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N coloc_supp
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List cur... |
e7139d0f6e2bcf38c2c9234406487e2bb8bb87aceb9f386c370f67905c8ced52 | Shell | 537 | 15 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=04_t1_rovir
ROVIR=" -V"
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 -b16 -Te=250,dump-mod=50,r=0.001 -Texport-history=hi... |
34017e8789533fa1cff8d4f5cc16488b5e83bce572777067912855d37d04ed2a | Shell | 539 | 21 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -u
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/../
if [ -z "${RECODIR:-}" ]; then
RECODIR="$SCRIPT_DIR/../"
fi
rm -r $RECODIR/21_recos_rt/vol0082_vis1_slc16
rm -r... |
64fb1301a4ad1b8d4db359ee2fc51f7a627fa0d40e59e743104cc4d96dda5951 | Shell | 540 | 20 | #!/bin/bash
mkdir -p pca
mkdir -p plots
mkdir -p results
python ../scripts/calculate_combined_principal_components.py \
--ref_file_a 'traj/condition-a_receptor.gro' \
--trj_file_a 'traj/condition-a_receptor.xtc' \
--ref_file_b 'traj/condition-b_receptor.gro' \
--trj_file_b 'traj/condition-b_receptor.xtc' \
--out... |
8f565ccab3751a4dd19f83899ab89eb70fa90c18f6ca5d717813026ecae0eb00 | Shell | 541 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N estrogen_dependent
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibili... |
46be928dda6971fb364def42309cd4c7274feb1c90178e03b1f93df99ef209a9 | Shell | 542 | 32 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10G,h_vmem=10G,h_fsize=10G
#$ -N process_gene
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for rep... |
0add4dfffba8cf1a5cacf20367817b2832c2d287412dc87bff672743a56ded12 | Shell | 543 | 30 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N gsea_similarity
#$ -o ./similarity.log
#$ -e ./similarity.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducib... |
56dc8fb056edbc5d737d11c94f0d4a9442e75e7ec210d09c062c723b254aebc0 | Shell | 543 | 18 | # create_tabix_gtex_allpairs.sh
# by Brian Chen
# This script takes GTEx v8 eQTL all pair files and outputs index file for tabix
# $1 is path to tissue file
module load htslib #or module load tabix
module load vcftools
tissueName=$(echo "${1##*/}" | cut -f 1,2 -d '.')
echo $tissueName
zcat $1 | sed '1D' | tr '_' '\t... |
0dd66db2404d96826d34ea4a7cc4497789c35f402105db9a775987300a9ba491 | Shell | 544 | 27 | #!/bin/bash
save_dir=<path to the generated sequences>
python evaluate.py \
--save_dir ${save_dir} \
--ca_only \
--largest_frag \
--use_openbabel \
--train_data_foler "two_digit_smiles_reorder_cutoff_15_ligand_only_frag" \
### calculate vina score
python analysis/docking.py \
--pdbqt_dir ./sample_output/test_pdb... |
76c9ca3bd2ba6362ca25d664344d84f4075cbd901ffb7ce1b4757187489359f7 | Shell | 544 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N estrogen_dependent
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibili... |
829ce7de35062bcff1efd542eeeca5741a3cfe932f9ed88138fe6b4564a3beae | Shell | 546 | 9 | #!/bin/sh
GPU=0
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.0 --dataname='36_node_square_lattice'\
--num_spin=36 --data_dir='../dataset/' --savefolder='36_square_J00' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --model=... |
9ec15b4b3a575aea08a467b908080f86ca4bfac3fa72874e44d2c62cc05293fd | Shell | 546 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N estrogen_dependent
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibili... |
cbe83863bfb66eab74e1c6a9166e2fd83dd0b739fe428a0e84666165c921afc8 | Shell | 546 | 19 | #!/bin/bash
# Global variables
ALL_IDS=$1 #all_ids.txt
SIGNIFICANT_IDS=$2 #significant_ids.txt
ENRICHMENT=$3 #"$FISHER_FOLDER"/go_enrichment.csv
GO_DATABASE=02_go_database/go-basic.obo
ANNOTATIONS=06_fisher_tests/all_go_annotations.csv
FISHER_FOLDER=06_fisher_tests
# Running goa tools
echo "Running en... |
d7ef5fcb66a533970fbf8ae99ad1ddf22fdf246e0c9bfcdb796f4982c3cd22b4 | Shell | 546 | 9 | #!/bin/sh
GPU=1
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.5 --dataname='36_node_square_lattice'\
--num_spin=36 --data_dir='../dataset/' --savefolder='36_square_J05' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --model=... |
4dd374b9cc854c656f6ee8a68e125342b9cdb656ba476974897794fa73e11413 | Shell | 547 | 12 | #!/bin/bash
script='/home/dlopezma/RFdiffusion/scripts/run_inference.py'
python $script \
inference.output_prefix=outputs-test/binder_ \
inference.input_pdb=channel-toxin.pdb 'contigmap.contigs=[A1-110/0 B111-220/0 C221-330/0 D331-440/0 30-50/H462-463/20-50]' \
'ppi.hotspot_res=[A68,A70,B178,B180,C288,C290,D398,D400... |
53877722ad18e2db9d6861acec7b8178323abbe34c8d554f0c5406ff3aa85de7 | Shell | 548 | 9 | #!/bin/sh
GPU=2
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.0 --dataname='100_node_square_lattice'\
--num_spin=100 --data_dir='../dataset/' --savefolder='100_square_J00' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --mod... |
b1e21ac1cf496bb3f5724cfc76280013c732ab71bd4b0a49c80ab4cc69b2db0d | Shell | 548 | 9 | #!/bin/sh
GPU=0
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.5 --dataname='100_node_square_lattice'\
--num_spin=100 --data_dir='../dataset/' --savefolder='100_square_J05' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --mod... |
e745f38707f5dc04f892bb2ec655b52d346a4eac1fd6d61a87a27ff309f01cdf | Shell | 548 | 15 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=04_t1_rovir
ROVIR=" -V"
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 --mask=msk -b16 -Te=250,dump-mod=50,r=0.001 -Texport... |
fe3bfc61b05b6c15cb3e35aa9f295e44747ed9c9ff0c8e5db71a690eeab618ba | Shell | 548 | 15 | SBATCH_OPTIONS=" -p gpu-a100 -t 0-15:00:00 --ntasks=4 --gres=gpu:4"
SPLIT="0.75"
SPLIT_FLAG="2"
OS=1.5
COS=1.25
DATASET=04_t1_rovir
ROVIR=" -V"
NETWORK=" -i15 --resnet-block=no-batch-normalization,F=64 --iter-net=3 --alpha-min=0.001"
TRAINING="--lambda-sens=-0.001 --mask=msk -b16 -Te=250,dump-mod=50,r=0.001 -Texport... |
3f1a7b2da4a2f778259f700ce519393ed97761d78fa506bf8f8b9976ac7fe20b | Shell | 552 | 18 | # Remove default output dir, default index dir and smk internal dir
cleanup () {
rc=$?
rm -rf .snakemake/
rm -rf ../output/ ../index
cd "$user_dir"
echo "Exit status: $rc"
}
trap cleanup EXIT
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
set -u # e... |
a1382f904e951115ae729952bebc45061b5261a27ead09e0ff86298211561bb2 | Shell | 552 | 32 | INPUT=$1
OUTPUT=$2
PATH_SET_VARIABLES=$3
INPUT_DIR=$(dirname "${INPUT}")
source ${PATH_SET_VARIABLES}
mkdir -p ${INPUT_DIR}/tmp_degibbs_in/
mkdir -p ${INPUT_DIR}/tmp_degibbs_out/
${FSL_LOCAL}/fslsplit \
${INPUT} \
${INPUT_DIR}/tmp_degibbs_in/
for i in ${INPUT_DIR}/tmp_degibbs_in/*;
do
i_File=$(basename "${i}"... |
142b8864c19bab5593788e62d5c344e209fb399603f6f618cf6597349f29dd0c | Shell | 555 | 11 | #!/bin/bash
annotation=$1
conda activate scrnaseq
module load cellranger/6.0
cd /data/bioinformatics/projects/hassan2022/output/FC_07379/02_cellranger_count_expectedCells
cellranger count --id=$annotation \
--transcriptome=/data/bioinformatics/referenceGenome/Drosophila_Melanogaster/Ensembl/dm6/Droso... |
c62cfb7639257a98a52510fdc5003c45146df8e83830c0ff27e328a635e32d19 | Shell | 558 | 23 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --mem=20G
#SBATCH --partition=rondror
#SBATCH --constraint=GPU_MEM:12GB
#SBATCH --qos=high_p
mkdir -p plots
mkdir -p vispdb
mkdir -p results
python ../scripts/compare_feature_distributions.py \
--ref_file_a traj/condition-a_receptor.gro \
--trj_file_a traj/condition-a_re... |
96c23d859afc37a1cd66462f2853953aefce99a7e9c80a0abf378ca6f53150a4 | Shell | 559 | 19 | #!/bin/bash
# This script will perform Level 3 stats across social
# and nonsocial conditions in the ISTART Social Doors task
# for models containing covariates
# Ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
basedi... |
2272344564653e941bead59dadbe477b04ae2b005f950b6c9920518a90eac3ca | Shell | 560 | 9 | #!/bin/sh
GPU=0
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.0 --dataname='32_node_honeycomb_lattice'\
--num_spin=32 --data_dir='../dataset/' --savefolder='32_honeycomb_J00' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --... |
3b2e6a884618ecc5d5a5568974790ad95e42b1df51e83d17d42c93a4385d22a3 | Shell | 561 | 19 | #!/usr/bin/env bash
# definitions
scriptDir=/vols/Scratch/comparative_scripts/m2_homologies
workDir=$scriptDir/seeds
mkdir -p $scriptDir/seeds
refImg=/vols/Scratch/Valerio_data/Template/QBI_atlas100_AP_swap.nii.gz
ROIlist="S1Left S2Left M1Left M2posterior M2anterior A1 V1 IL PL CG12 Retrosplenial Orbitofrontal BLA V... |
bdbe7c35b825fec07968e7a64110b09121ab971201c9725c33f7f797e4899a0b | Shell | 561 | 9 | #!/bin/sh
GPU=4
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.2 --dataname='32_node_honeycomb_lattice'\
--num_spin=32 --data_dir='../dataset/' --savefolder='32_honeycomb_J02' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --... |
4f278c6d688ebb346c41851d14d37fa9c686903334e8d5f36108cc2fcdf87298 | Shell | 562 | 10 | #!/bin/sh
GPU=0
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.2 --dataname='98_node_honeycomb_lattice'\
--num_spin=98 --data_dir='../dataset/' --savefolder='98_honeycomb_J02' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' --... |
e7199dd3f0d55e6c3000822031eac3b8a2fdb1b7f378c84e7d3547999b990fe5 | Shell | 562 | 10 | #!/bin/sh
GPU=5
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=0.0 --dataname='98_node_honeycomb_lattice'\
--num_spin=98 --data_dir='../dataset/' --savefolder='98_honeycomb_J00' --save_dir='../result/Heisenberg/'\
--checkpoint_dir='../checkpoints/Heisenberg/' --log_dir='../log/Heisenberg/' -... |
1533c60995ab2fecc9b7f5659e159faa16a9157e71a126a7d8492d6019d4ccd4 | Shell | 564 | 23 | #!/bin/bash
set -e
cd "$(dirname "$0")"
# Resolve the Python interpreter: prefer `uv run` against Python/pyproject.toml
# (which carries pyyaml in the dev group), fall back to system python if uv
# isn't installed.
if command -v uv >/dev/null 2>&1; then
PY=(uv run --project ../Python python)
else
PY=(python)
fi
"... |
f160f2c1ddb47593ee51d2348210443400c237e47d9f380041828b67bbd4ced6 | Shell | 566 | 8 | # This runs the 10-fold CV on Pan's human PPI dataset. This is not a part of the results in our ISMB paper, but here are what we've got:
# Acc=98.11 Prec=98.99 F1=98.03
cd ../lasagna
mkdir results
CUDA_VISIBLE_DEVICES=2 python rcnn.py ../../../sun/preprocessed/Supp-AB.tsv -1 results/sun_wvctc_rcnn_25_5.txt 3 25 1... |
6ed6d2d83d25627148905903ab36737e399cbb94347e464384471c1727d6efce | Shell | 568 | 15 | export nnUNet_results="nnUNet_training/nnUNet_results"
export nnUNet_raw="nnUNet_training/nnUNet_raw"
export nnUNet_preprocessed="nnUNet_training/nnUNet_preprocessed"
export nnUNet_predictions="nnUNet_training/nnUNet_predictions"
GPU_ID=0 # Put the GPU IDs here
DATASET=557
TRAINER=nnUNetTrainer
nnUNetv2_plan_and_prep... |
9ae0ece158a482788c7c1d5cebfd46a8820de370a89a766ab2037d56397b6dfc | Shell | 569 | 18 | # Check arguments and usage guide
if [ "$#" -lt 1 ]; then
echo "Usage: $0 <path_swconfig_json> <debug_mode> <print_swconfig> <sweep_progress>"
echo " path_swconfig_json: [*/swconfig*.json]"
echo " debug_mode: [true|false]"
echo " print_swconfig: [true|false]"
echo " sweep_pro... |
d6e9c740e1ccf26d7881a7d685f1ddecd237c5c3a74d518925f93a88dddf3bd7 | Shell | 572 | 9 | #!/bin/sh
GPU=1
CUDA_VISIBLE_DEVICES=${GPU} python ../src/main_fast_new.py --GPU --J2=-0 --lr=0.001 --dataname='108_kagome_lattice'\
--savefolder='108_kagome_lattice_pbc_J2_0_f_64_non_local_preact_regularconv_clip_grad_1_lrdecay_4000' --data_dir='../dataset/' --save_dir='../result/Heisenberg/' \
--checkpoint_dir='.... |
2006dcc42a4d41ffc7cc8da914ee25d4c2ef7abbb844950a2ca3e74c92d0f401 | Shell | 574 | 31 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N gene_covariates
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
... |
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