sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
91322c9f5d2cda41673f13aa9d667aab708e635ef46e39d00957343252f6140c | Shell | 857 | 40 | #activate your conda environment beforehand
##################
#
# Medical patch net with 8x8 patches
# -patchSize 64
# -imgSize 512
#
# EfficientNet-B0 => image is one patch so the backbone gets the whole image and mean is computed over one vector => same as EfficentNet-B0
# -patchSize 512
# -imgSize 512
#
########... |
eb679f6edfe956acdee5e5f2378c422dd1efb26f876eeccba0675ad977f84994 | Shell | 860 | 16 | eval "$(/pollard/home/sdrusinsky/miniforge3/bin/conda shell.bash hook)"
source /pollard/home/sdrusinsky/miniforge3/bin/activate test_pt231
cd "$(dirname "${BASH_SOURCE[0]}")" #cd into the directory containing this script
cd .. #cd into `code` directory
path_to_metadata=/pollard/data/projects/sdrusinsky/enformer_fine_... |
4df30562a8f4baef117401b17d07b4d2a75a4176cb0bdef3f0f76e9b34ab2697 | Shell | 862 | 31 | #!/bin/bash
# set variables
datasets=("HBN")
tract_list="/cbica/projects/luo_wm_dev/input/tract_list/tract_list.txt"
inputarray=()
while IFS= read -r line; do
inputarray+=("$line")
done < "${tract_list}"
tract_count=${#inputarray[@]}
# submit job array for each dataset
for dataset in "${datasets[@]}"; do
lo... |
6aa1b77daf0431f9e00d6170e72eb4f69a2b36c4e2445fcb0c5717976cc2c6a6 | Shell | 862 | 34 | #!/bin/bash
# Script to run all steps of dannce in a single job using multi-gpu prediction.
#
# Inputs: com_config - path to com config.
# dannce_config - path to com config.
# Example: sbatch com_and_dannce_multi_gpu.sh /path/to/com_config.yaml /path/to/dannce_config.yaml
#SBATCH --job-name=com_and_dannce
#SB... |
f1c05526c878d30bd14845f89bb1103f9298fcce403f4e08a1e092e83c565c3a | Shell | 864 | 30 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
dcbb23c4a74a923c37a3b059f6a6d89a ${pref}_0
7b7419dea9e3917c2e27b7a7a35f64ca ${pref}.histo
7b7419dea9e3917c2e27b7a7a35f64ca ${pref}_S.histo
8ac9533ccb34203fdac1f80b58774898 ${pref}.stats
8c9400cd7064ea24374fe68817da9926 ${pref}_LU.histo
EOF
echo "Cou... |
151715828db7bc5ae3878d65b4f4ba700118eb208e31ff77591b793ed021ba5a | Shell | 865 | 28 | COMPILE_MODEL_LIB () {
local LIB_NAME=$1
local MODEL_FILE_CPU=$2
local MODEL_FILE_GPU=$3
local COMMON_HEADERS="../model_common.h ../default_solvers.c $4"
local EXTRA_C_FLAGS=$5
local EXTRA_STATIC_LIBS=$6
local MODEL_SOURCES="$MODEL_FILE_CPU"
local MODELS_STATIC_DEPS="config_helpers ut... |
892f9352f3f2145e3960f544015b913f8909ee48a8c1f1977c1f08de96d70e4f | Shell | 867 | 25 | #!/bin/bash
#Make Filepaths
BFILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim"
LD_FILE="/path/to/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld"
OUT_DIR="/path/to/output_dir"
TRAIT1_FILE="/path/to/trait1.txt"
TRAIT2_FILE="/path/to/trait2.txt"
EXTRACT_DIR="/path/to/snp_output"
REP="${SLURM_ARRAY_TASK_ID}"
#Run ... |
58f0559fa38f32805010339f63da7c8c42585f13163fdbb1262b8e1f626886bd | Shell | 868 | 26 | # 1. cohort + cancer_group level plots
# only tumors: GMKF + PBTA + TARGET
Rscript 01-tumor-gtex-plots.R \
--expr_mat '../../data/gene-expression-rsem-tpm-collapsed.rds' \
--hist_file '../../data/histologies.tsv' \
--map_file '../../data/ensg-hugo-rmtl-mapping.tsv' \
--cohort_list 'GMKF, PBTA, TARGET' \
--tumor_vs_norm... |
9698675313924915a617a5a10abfc5d7711aa92c1b07f265eaef31cca71e12ff | Shell | 869 | 25 | #!/bin/bash
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
# Module author: Sangeeta Shukla, Alvin... |
b4e410df3026651eb77d37e63c11acf20bf915736c029606d2edc122c88c8c60 | Shell | 873 | 28 | # Generate the dihedral index file
#bash VMD_GenPhiPsiIndices.sh
# Write the dpca.ndx file for PCA use
# 16 dihedrals, each dihedral has (sin, cos) elements, totally we
# have 16x2 = 32 coordinates, we need at least 32/3 = 11 atoms to store
# these coordinates
#CHANGE prot, NT, and TIME depending on your system
NT=1... |
49c9ab677e1baca8541b8de252c9697eb472e59e4a1a06ebb5928a8ae7c0a7e5 | Shell | 878 | 55 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
5d9dce204e01d4ca69a9f1bba6465c598a60e3893764d88645bb0601ce098fac | Shell | 878 | 34 | #!/bin/bash
#$ -M mzarodn2@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -pe mpi-24 24 # Specify parallel environment and legal core size
#$ -q debug # Specify queue
#$ -N STAR # Specify job name
# this remains the same for all j... |
5ee783e07812714ccf37b939a68a4808d8caee4ef31c51fee301b2783f997d41 | Shell | 883 | 25 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
2e0b715bb66acfd324d5879141b1f8a626c0e56bde5b2a03955e0d916e3392f5 | Shell | 886 | 23 | ##### Install the next-flow pipeline #####
# curl -s https://get.nextflow.io | bash
# chmod +x nextflow
# mv nextflow $HOME/.local/bin/
# nextflow run nf-core/chipseq -profile test,docker --outdir outest
'''nextflow info
Version: 25.04.2 build 5947
Created: 13-05-2025 21:58 UTC (23:58 CEST)
System: Linux 5.15.0-1... |
3c4db5ad8ddd5cd40e7dd1d7363740aec201af4130b698b57087edb01c9df2c8 | Shell | 887 | 37 | #!/bin/bash
# Upload website to gh-pages
USAGE="$0 <html_dir> <project-name> [<organization-name>]"
HTML_DIR=$1
if [ -z "$HTML_DIR" ]; then
echo $USAGE
exit 1
fi
if [ ! -e "$HTML_DIR/index.html" ]; then
echo "$HTML_DIR does not contain an index.html"
exit 1
fi
if [ -d "$HTML_DIR/.git" ]; then
echo "... |
a66bc5f558270bcc2cb41c9b6a7fa31727c37792eb4ba1f0c2a253d5e981d29d | Shell | 890 | 21 | #!/bin/bash
#SBATCH --mem=140G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=30:0:0
#SBATCH --gres=gpu:v100l:1
#SBATCH --array=1987-2007
cd $project/moralization_temporal
module purge
module load python/3.10 scipy-stack
source ~/venv2/bin/activate
year=$($SLURM_ARRAY_TASK_ID)
model='bert-base-unca... |
0eb531f28dc9bb3f017158d31646e8e02e9d001c7849de5c788f4692d080d733 | Shell | 891 | 27 | input_dir="/data/wuqinhua/phase/covid19/datasets/pre_data/4_Combes_2021"
filter_dir="$input_dir/filter_data"
output_dir="$input_dir/data"
# Create output directory if it doesn't exist
mkdir -p "$output_dir"
# Move and organize files
for file in "$filter_dir"/*.gz; do
if [ -f "$file" ]; then
base_name=$(ba... |
330770197537c3b119b598830b10309ea6a3c4f8a8fe5e58a60c9083cdf8d958 | Shell | 892 | 14 | snakemake --version | sed -e "s/^/Snakemake: /"
python --version 2>&1 | sed -e "s/^Python/Python:/"
bwa 2>&1 | grep "^Version" | sed -e "s/Version/bwa/"
samtools --version 2>&1 | head -1 | sed -e "s/samtools/samtools:/"
fastqc --version 2>&1 | sed -e "s/FastQC/FastQC:/"
cutadapt --version | sed -e "s/^/cutadapt: /"
mul... |
b7121fad28e5b5a2d4b85cf0df7346a4ff4376ec5b2e6d31efaf648baf86aebe | Shell | 894 | 26 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
ed0b763c09d20a9bd0382debc3802a279a54d1491f0cb6d828a0f8a3ecc770de | Shell | 894 | 21 | #!/bin/bash
# set variables
datasets=("HCPD" "HBN")
r_script="/cbica/projects/luo_wm_dev/two_axes/code/covbat_harmonization/covbat_multisite_tract_profiles.R"
# loop through each multishell dataset
for dataset in "${datasets[@]}"; do
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/tw... |
2c6ee2b6ef1c623ed1e7e125f952fad1daf3822a3c456b9499a6e873d64853ec | Shell | 897 | 32 | #!/bin/bash
echo Starting deployment...
mkdir -p ~/.ssh
chmod 700 ~/.ssh
echo -e "Host tucana.uberspace.de\n\tStrictHostKeyChecking no\n\n" >> ~/.ssh/config
eval $(ssh-agent -s)
echo "${DEPLOY_KEY}" | ssh-add -
echo Key length: "${#DEPLOY_KEY}"
ssh-add -l
mkdir -p deploy
branch=$(echo $CI_COMMIT_REF_SLUG | cut -d... |
ed2abb6679b49a5419a36364f45c0da2f98f25c566558b0d46a507b1e566ba27 | Shell | 897 | 25 | # 1. cohort + cancer_group level plots
# tumor vs normal: GMKF + PBTA + TARGET + GTEx
Rscript 01-tumor-gtex-plots.R \
--expr_mat '../../data/gene-expression-rsem-tpm-collapsed.rds' \
--hist_file '../../data/histologies.tsv' \
--map_file '../../data/ensg-hugo-rmtl-mapping.tsv' \
--cohort_list 'GMKF, PBTA, TARGET, GTEx' ... |
33b0722ed2e9742524e487ed875384b3af98e6de078ebe0fad7f1faf3c4b763a | Shell | 898 | 29 | K=20
H=512
pooling_method=attention1d
# your fine-tuning dataset
dataset_dir=data/finetune_example/PDBSol
pdb_dir_name=esmfold_pdb
# where to save your fine-tuned model
output_model_dir=result/PDBSol/protssn_k"$K"_h"$H"
output_model_name=protssn_"$pooling_method".pt
CUDA_VISIBLE_DEVICES=0 python run_ft.py \
--gnn_h... |
7cbfa0793da3f3adde8a6ab5335be50950926b99be5db59e4803c77e5a8fc6a7 | Shell | 904 | 34 | #!/bin/tcsh -xef
#Set the input folder
set inpath = path/to/thresholded/tICA/components
#Set the output folder
set outpath = path/to/output/folder
# Define non-noise components to be processed
set components = ( 1 2 3 4 5 6 7 8 9 10 14 18 )
# Set total number of components to sum
set ncomp = 12
# Set current dire... |
9f044a885cd31cf1eb45a5987bbecd8c13d92cfb7f5803ca93064599117cf8ad | Shell | 904 | 23 | #!/bin/bash
if [[ "$#" -ne 2 ]]; then
echo "-------------------------------------------------------------------"
echo "Usage:> $0 <AP_DIR> <AP_PREFIX>"
echo "-------------------------------------------------------------------"
echo "<AP_DIR> = Directory where the results of the simulation are stored"
... |
be21208716c74725f1b0e130e32c5c0b109b0e3fc6b653662063cf50f919d013 | Shell | 905 | 52 | #! /bin/bash
set -e
anterior_persistence() {
local m=$1
shift 1
sleep 10
python -m rscvp.behavioral.$m \
-D 211210,220322,211207,220325,220901,221216 \
-A YW022,YW033,YW032,YW036,YW045,YW048 \
-P ,,,,0, \
"$@"
}
posterior_persistence() {
local m=$1
shift 1
sleep 10
python -m rscvp.statistic... |
17366047ddbd4d55a91a9e452d67fe6e3aade69e5bbf7116ce2ae6e237e44ea8 | Shell | 906 | 26 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
64a60b28d39534e99a3c4e6d497d29f155a315434f8207726e0c1d10c792c8cb | Shell | 906 | 33 | #!/bin/tcsh -xef
#Set the input folder
set inpath = path/to/thresholded/tICA/components
#Set the output folder
set outpath = path/to/output/folder
# Define the non-noise components to be processed
set components = ( 1 2 4 5 6 7 8 9 10 12 13 15 16 18 )
# Set total number of components to sum
set ncomp = 14
# Set cu... |
8509711989c1ea2780d2d77f65ab1050570586896b33aa0788b4188d71ad305a | Shell | 906 | 25 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
ba53eb79cca60b1376109755014965d13500d2263b73dbce5ad50a9f9bc3f5c1 | Shell | 906 | 22 | # evaluates the ensemble performance of distilled DeepSTARR models trained to predict stdev + mean
# generates plot of true vs. predicted values
MODEL_DIR=../results/DeepSTARR_lr-decay/distilled_with_std
N_MODS=1
DATA=../data/DeepSTARR/all_data_with_ensemble_metrics_hierarchical.h5
export LD_LIBRARY_PATH=$LD_LIBRARY... |
4c6e29c8dfb2eb9dca746e4d698b565766374c233b745800b9e6008d9f2a0988 | Shell | 907 | 21 | #!/bin/bash
# set variables
datasets=("HBN")
r_script="/cbica/projects/luo_wm_dev/two_axes/code/covbat_harmonization/covbat_multisite_tract_profiles_HBN_withACT.R"
# loop through each multishell dataset
for dataset in "${datasets[@]}"; do
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_d... |
405970a1a70d4041709d7266d8da5c9662b4d9e8c6aa52a99df579d30c387ce9 | Shell | 908 | 27 | #!/bin/bash
set -e
set -o pipefail
set -u
BASE=/scratch/users/surag/retina/
RUNNAME=20220202_bpnet
JOBSCRIPT=/home/users/surag/kundajelab/retina-models/jobscripts/jobscript.sh
# make a copy of code run
mkdir -p $BASE/models/$RUNNAME/fold0/interpret
cd /home/users/surag/kundajelab/retina-models/src
for x in `ls $B... |
84968d86d8cf75f7e323b8d51ab11d89cda35f922c048191e1dd2f521e7859e2 | Shell | 909 | 44 | #!/bin/bash
#
# [description]
# Post a comment to a pull request.
#
# [usage]
# append-comment.sh <PULL_REQUEST_ID> <BODY>
#
# PULL_REQUEST_ID: ID of PR to post the comment on.
#
# BODY: Text of the comment to be posted.
set -e -E -u -o pipefail
if [ -z "$GITHUB_ACTIONS" ]; then
echo "Must be run inside Git... |
40daba60205f81b57d4dd91abac176c81bd07f6f446c8f8090f93cc728aa9ae7 | Shell | 910 | 26 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=8
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=1000G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train... |
14faccb608eb10e30243f28e47d910b9d0aa06a23eb9bc4e5a4f1348432b0255 | Shell | 912 | 21 | #!/bin/bash
# set variables
datasets=("HCPD" "HBN")
r_script="/cbica/projects/luo_wm_dev/two_axes/code/covbat_harmonization/noddi/covbat_multisite_tract_profiles_noddi.R"
# loop through each multishell dataset
for dataset in "${datasets[@]}"; do
# where to save output and error logs
logs_dir="/cbica/projects/l... |
079d668a6dcdd9c10129fe1d48169b4012375080f77adc8dd449507d6f2211a0 | Shell | 913 | 25 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
4b61d184da73705d5981ec6ae67797359e8166449e1d582fef682bd7d7eef8e5 | Shell | 915 | 33 | #!/bin/bash
# ReCEP Environment Installation Script
set -e
echo "Starting RoBep environment installation..."
# Check if conda is installed
if ! command -v conda &> /dev/null; then
echo "Error: conda is not installed. Please install Anaconda or Miniconda first."
exit 1
fi
# Create conda environment
echo "Cre... |
641f43cd1fd1f54eaffd1b95bdb5a9aa38c77256c90fa1f231d6d99d7587ef38 | Shell | 915 | 21 | #!/bin/bash
# set variables
datasets=("HCPD" "HBN")
r_script="/cbica/projects/luo_wm_dev/two_axes/code/covbat_harmonization/mapmri/covbat_multisite_tract_profiles_mapmri.R"
# loop through each multishell dataset
for dataset in "${datasets[@]}"; do
# where to save output and error logs
logs_dir="/cbica/projects... |
64ec4b2d3f4d0679a91eff4a0fa7527a7adad10f32d2dc5f76218d6d5abb1037 | Shell | 915 | 35 | #!/bin/bash -l
#SBATCH -J batch_export_optimized_EIANN_mnist
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist.%j.e
#SBATCH -p normal
#SBATCH -N 1
#SBATCH -n 6
#SBATCH -t 6:00:00
#SBATCH --mail-user=mi... |
a41e406668407c9033d6d6f74f20765df7ae0f7b1c92182d917a8194ac364082 | Shell | 917 | 35 | #!/bin/bash
BASE=/path/to/univ_TWAS_allchr/
NAME=$(sed -n "${SLURM_ARRAY_TASK_ID}p" /path/to/regions.txt)
REGION="${BASE}${NAME}"
export REGION
export NAME
Rscript - << 'EOF'
require(GenomicSEM)
library(data.table)
library(devtools)
region <- Sys.getenv("REGION")
name <- Sys.getenv("NAME")
files <- list(
paste0(... |
dc2038b9d15c05aee6b7884512f176bb8b83aea47389da8541179b5c7fc6899d | Shell | 918 | 15 | #!/usr/bin/env bash
git clone -b releases/2.10 https://gitlab.dune-project.org/core/dune-common.git
git clone -b releases/2.10 https://gitlab.dune-project.org/core/dune-geometry.git
git clone -b releases/2.10 https://gitlab.dune-project.org/core/dune-grid.git
git clone -b releases/2.10 https://gitlab.dune-project.org/... |
12359f53fdbdff5b2e2df78019c5c019baa77825f6e7d5bae3e2a1c87d922352 | Shell | 919 | 28 | #!/bin/bash -l
#SBATCH --job-name=conn_rewire
#SBATCH --partition=prod
#SBATCH --nodes=2
#SBATCH --tasks-per-node=18
#SBATCH --cpus-per-task=4
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --out=logs/%j.txt
#SBATCH --err=logs/%j.txt
. /etc/profile.d/modules.sh
unset MODULE... |
b7d3be9914d9a43a3724b33c2ff04bf0640a053df059e491ecf93447ad612192 | Shell | 919 | 14 | #!/bin/bash
python $prefix/src/main.py --desc "[WeightedCDRInterface Ignore] 8515 egnn norm mdn 1e-3 & node & prob 2e-3 r73 NT 500:500" \
--datapath $data_prefix \
--embed_path $data_prefix/all_embeds \
--filepath $prefix/data/metadata/ab_nondock_metadata_cluster_v6_3_native_cdr_v2.csv \
--ckptpath $ou... |
0a5128aa72ec6b3dfaaa53be15d4e842db0486b795bde713b3dd1eff447e4025 | Shell | 921 | 34 | #!/bin/bash
#
# avgtrials.sh <filename> <avgname> <trial_duration> <TR> <trial_onsets ...>
#
# - event related trial averaging
# - uses 3ddeconvolve to estimate a finite impules model (TENT)
filename=$1
avgname=$2
trial_duration=$3
TR=$4
trial_onsets="${@:5}"
N=$(echo "scale=0;${trial_duration}/${TR}" | bc -l)
a=0
b=... |
7c9b484ec8750b57f5502311b143e64bb24ff4f5bab4f69eb1a22750d06cc01d | Shell | 922 | 25 | #!/bin/bash
iskids="$1"
START=$(pwd)
OUT="$(mktemp -d /tmp/stich.XXXXX)"
cp ../bids_dataset/derivatives/bootstrap_clusters/figures_ventral/${iskids}_task-category_ctr-*_maths.png $OUT
cp background_3.png $OUT
cd "$OUT"
to_stich=""
for c in "c_number" "all_shapes"; do
convert "${iskids}_task-category_ctr-${c}_math... |
7d1c5736f241198f542dc37b4d112020a49a66a46977b9b3fe70dbc12da7fbc6 | Shell | 923 | 28 | # train an ensemble of DeepSTARR models on downsampled training data
# loops through an array of different downsampling proportions
ENSEMBLE_SIZE=10
DOWNSAMPLE_ARR=( 0.1 0.25 0.5 0.75 )
DATA=../data/DeepSTARR/Sequences_activity_all.h5
OUTDIR=../results/DeepSTARR_lr-decay
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_... |
6b406a09d95f3c7af7485acf06c5ac45397d98a131d0cb8fc8e76bbcd0e8cc25 | Shell | 927 | 25 | #!/bin/bash
iskids="$1"
START=$(pwd)
OUT="$(mktemp -d /tmp/stich.XXXXX)"
cp ../bids_dataset/derivatives/bootstrap_clusters/figures_ventral/${iskids}_task-category_ctr-*_ventral.png $OUT
cp background.png $OUT
cd "$OUT"
to_stich=""
for c in "vwfa" "ffa" "house" "tool"; do
convert "${iskids}_task-category_ctr-${c}_... |
b024d8f8c775577812ddae77feff29c9e9508d7d2a358266b7eb66bff5bd7db4 | Shell | 928 | 38 | #! /bin/bash
#
# This is a shell script to register GRE image to T1w image
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit:
############################################################
script_dir=`readlink -f "$0"`
SEPIA_HOME=`dirna... |
269615e6d696f374c2b5e09f20f90172c8f6b7a3412fa62b6fe65859fc99d594 | Shell | 932 | 22 | source /share/scripts/gromacs-2018.4-plumed-2.5.0.env
numomp=6
gmx_mpi grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_charmm2gmx.pdb -r step3_charmm2gmx.pdb -p system.top -n index.ndx
gmx_mpi mdrun -deffnm step4.0_minimization -ntomp $numomp
# step4.1 minimization
gmx_mpi grompp -f step4.1_m... |
6b1dff2bc7be8b4cfa13e0b6d8f9d3f3e06d564b132dce6fb45f52ffb622c09a | Shell | 933 | 36 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_ddd_data_start
#SBATCH --output=logs/gnn_ddd_data_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Ensure the script is called with the necessary argument for 'name'
if [ "$#" -ne 1 ]; then
echo "Usage: $0... |
820ab514a77594242078d081e7972097712ce4424d374427c88fa854772a9d12 | Shell | 935 | 29 | #!/bin/bash
# Wrapper for running HIPS THOMAS in docker container for T1 MPRAGE or SPGR files.
#
DK_IMG=anagrammarian/sthomas:latest
if [ $# -lt 1 ]; then
echo "Usage: $0 T1-input-image"
echo "where: T1-input-image = an T1 MPRAGE or SPGR NIfTI file in the current directory"
echo " (for WMn MPRAGE/FGATIR fi... |
9d548fb6c2ee6288cf80f915687fa8861861b492bf6485be54fa69661b5c6062 | Shell | 936 | 47 | #! /bin/bash
set -e
anterior_persistence() {
local m=$1
shift 1
sleep 10
python -m rscvp.statistic.persistence_agg.$m\
-D 210601,210505,210423,211126,211112,220930,220908,211208,210507 \
-A YW006,YW010,YW017,YW032,YW033,YW048,YW049,YW036,YW018 \
-P 0,0,0,,,,,,0 \
"$@"
}
posterior_persistence() {
... |
a123e1b7c62915294065d0f6d4c4f6bd25c93fe2ebb8789b78da4a991e6eff8d | Shell | 936 | 29 | #! /bin/env bash
set -e
REPO_ROOT="$(dirname "$0")/.."
PYTHON="${PYTHON:-python3}"
BLACK="${PYTHON} -m black"
ISORT="${PYTHON} -m isort"
if ! ${BLACK} --version >/dev/null 2>&1; then
echo "black is not found, please check it is installed"
exit 1
fi
if ! ${ISORT} --version >/dev/null 2>&1; then
echo "isor... |
d0f229ffc92d469911fe45afbb17b752cd61c229a58418b912369670c77c7234 | Shell | 944 | 35 |
#!/bin/bash
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate babs
########################
# HCPD - noddi
########################
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/babs_noddi
# after test job finishes successfully:
babs-submit --project-root $PWD --all
#######... |
ffb13f0f63572d459fad982969323ee905ef49d228b8838ac6c239cffd21aba6 | Shell | 944 | 18 | #!/bin/bash
CUDA_VISIBLE_DEVICES=0 python3.5 run.py --do_train --cuda --do_valid --do_test --evaluate_train \
--model TransE -n 128 -b 512 -d 2000 -g 20 -a 1.0 -adv \
-lr 0.0001 --max_steps 300000 --cpu_num 2 --test_batch_size 32
CUDA_VISIBLE_DEVICES=1 python3.5 run.py --do_train --cuda --do_valid --do_test --ev... |
722330112911a397f1412de1511205c27601b28fdec24316f6459379d248dfe7 | Shell | 946 | 32 | #!/bin/bash
set -e
set -o pipefail
set -u
BASE=/scratch/users/surag/retina/
RUNNAME=20220202_bpnet
JOBSCRIPT=/home/users/surag/kundajelab/retina-models/jobscripts/jobscript.sh
# make a copy of code run
mkdir -p $BASE/models/$RUNNAME/fold0/modisco
cd /home/users/surag/kundajelab/retina-models/src
for x in `ls $BAS... |
6933d8926c2bdd11e973340f8bd8a1ded7802fb158b41d184617e9a0916c4e50 | Shell | 947 | 55 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
ff21298e9b65e6ff6e213b0c4637d480d90e9b7198a180db285e35e0ac11130f | Shell | 947 | 31 | #!/usr/bin/env bash
set -euo pipefail # Will fail on error
# ==============
# How to run this script
# 1) Load the input data
# https://scilpy.readthedocs.io/en/latest/documentation/getting_started.html
# 2) Call this script with
# ---> bash btensor_scripts.sh path/to/your/data path/to/save/outputs... |
723b13e7ed71dfa7acc7c7c35704fddd92edad4cfb5caef39bb9e55606083f08 | Shell | 951 | 32 | #!/bin/bash
# author : sjn
# date : July.2023
set -euox pipefail
if [[ $# != 3 ]]; then
printf "Expect $0 <clustering-vs-null.bed.gz> <fire.peaks.and.coverages.bed.gz> <outfile>\n"
exit 1
fi
oe=$(zcat $1 |
awk '{ \
coverage[$4][$5]+=$3-$2; \
} END { \
real_bp = 0; \
... |
44322f25b440d5360f3b7819b99e66892f6ad86d21ca44b4e4b4a8301d20beb1 | Shell | 952 | 30 | #!/bin/bash
set -e -u
echo "checking that all OpenMP pragmas specify num_threads()"
get_omp_pragmas_without_num_threads() {
git grep \
-n \
'pragma omp parallel' \
-- '*.c' '*.cc' '*.cpp' '*.cu' '*.cuh' '*.h' '*.hpp' '*.tpp' \
| grep -v ' num_threads'
}
# 'grep' returns a non-0 exit c... |
04b6d92fe1fb19b9d0b65481c67af814c3ef4b6fbbe9403155988b4a9ecd8157 | Shell | 954 | 25 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
2ea26eac78a3a7de610b4a2baba4b93cd2189ee78b508a95300892f1cf3fe76f | Shell | 955 | 28 | #!/bin/bash
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print... |
6e89a4f1645a3751b8bbd4d60a80d143586f969533e24e456f95435cfb2d4ba7 | Shell | 955 | 30 | #!/bin/bash
# JN Taroni for ALSF CCDL 2022
# Use git shortlog and git log to extract git contributions to the current
# branch
set -euo pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Create directory to hold intermediate files
comp_dir="../../scratch/count-co... |
bfd7c896c7c5c14fe9d4e8b54f202be33123bd991decedb9c910f089a12a564b | Shell | 956 | 38 | #!/usr/bin/env bash
set -e
fsl_anat_dir=$1
bianca_mask_out=$2
if [[ $# -ne 2 ]]; then
echo "Usage: $0 <fsl_anat_dir> <bianca_mask_out>"
exit 1
fi
if [[ ! -d "$fsl_anat_dir" ]]; then
echo "Error: fsl_anat_dir '$fsl_anat_dir' does not exist or is not a directory."
exit 1
fi
# output dir: dirname of bianca_ma... |
b265b5637c04f5d028ef7485038090939ef5ddc45bd974c38afe1ba7be5c7c13 | Shell | 960 | 39 | #!/bin/bash
# Set input directory and FreeSurfer home directory
module load freesurfer
source "$FREESURFER_HOME/FreeSurferEnv.sh"
echo "Freesurfer home: $FREESURFER_HOME"
conda activate mne1.4.2
subject="sub-$1"
# set subjects_dir
SUBJECTS_DIR="/imaging/hauk/rl05/fake_diamond/data/mri"
echo "SUBJECTS_DIR: $SUBJECTS... |
dad20c5f5527535c45a4f062bc3e7722712f36f86edee58aae1efb275815141c | Shell | 961 | 29 | #!/bin/bash
set -ex
# convert to gff3 alignment format
../../util/gtf_to_alignment_gff3.pl supertranscripts.gtf > supertranscripts.gff3
# extract the transcript sequences
../../util/gtf_genome_to_cdna_fasta.pl supertranscripts.gtf supertranscripts.fasta > transcripts.fasta
# run TransDecoder
cmd="../../TransDecoder... |
c138f27b02326af0647763ffeccdd118f060b09b27316e42e8fde02bc8a78ea9 | Shell | 962 | 28 | #!/bin/bash
#SBATCH -J kneaddata_${P1}
#SBATCH -A b1057
#SBATCH --mail-type=ALL
#SBATCH --mail-user=elizabeth.mallott@northwestern.edu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --mem=24G
#SBATCH -t 24:00:00
#SBATCH --output=/home/ekm9460/kneaddata_array_%A_%a.out
#SBATCH --error=/home/ekm9460/kneaddata_array_%A_%a.err
#SBATCH... |
e9f77363d11df241314d63529eaaa6fd5885e7eed1ddb4bbf7580cbe61ce43d4 | Shell | 962 | 38 | #!/bin/bash
set -e # Exit on any error
ENV_NAME="unimol_env"
PYTHON_VERSION="3.12"
echo "Creating conda environment: $ENV_NAME with Python $PYTHON_VERSION"
conda create -n $ENV_NAME python=$PYTHON_VERSION -y
source $(conda info --base)/etc/profile.d/conda.sh
conda activate $ENV_NAME
echo "Installing PyTorch 2.6 wi... |
ef84016dbc7901755c735b12042b590e6711164186e38b13ca0e2543e5d8e323 | Shell | 962 | 27 | #!/bin/bash
# COCO 2017 dataset http://cocodataset.org
# Download command: bash data/scripts/get_coco.sh
# Train command: python train.py --data coco.yaml
# Default dataset location is next to YOLOv5:
# /parent_folder
# /coco
# /yolov5
# Download/unzip labels
d='../' # unzip directory
url=https://github.com/... |
fa805f14edb948e153395ecd209254f36314c04fbf578a98eb9cbe273618dd9b | Shell | 965 | 26 | #!/bin/sh
mkdir -p test
mkdir -p test/faidx
cat > test/emptyfile <<EOF
EOF
cat > test/xx#pair.sam <<EOF
@SQ SN:xx LN:20
a1 99 xx 1 1 10M = 11 20 AAAAAAAAAA **********
b1 99 xx 1 1 10M = 11 20 AAAAAAAAAA ****... |
a7bc96eae400342bafcb707faf69bce4ec27662e57c00f9da9bf110577b10289 | Shell | 966 | 27 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=8
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=1000G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train... |
5ce9733b3831584c866d5bc4bb7e501e9addf53470d9b0ba30292652d4e40675 | Shell | 976 | 40 | #!/bin/bash
file_in=$1
coeff_path=${2:-/data/hu_dchaimow/owncloud/pfc-layers/sequences/coeff_SC72CD.grad}
export FSLOUTPUTTYPE=NIFTI
curDir=$(pwd)
tmpdir=$(mktemp -d)
imcp ${file_in} ${tmpdir}/infile
cp ${coeff_path} ${tmpdir}/coeff.grad
cd ${tmpdir}
gradient_unwarp.py $(imglob -extension infile) corrected_tri.nii ... |
74974a96ec5068914fe8ec01d7c6c1b217d992172d0631b5f4faffbe764122c3 | Shell | 976 | 53 | #! /bin/bash
function usage() {
cat <<USAGE
Usage: $0 [-c config_path] [-d dataset_path]
Options:
-c, --config_path: Path to config file (e.g. traditional_machine_learning/params/xgb_50hz/config.yml)
-d, --dataset_path: Path of the HARTH dataset
USAGE
exit 1
}
if [ $# -eq 0 ]; then
u... |
1a3ca495ef64fe8aca35b24e780c47f3ef0f6d8a60a09efb80956b4b6316f2a6 | Shell | 979 | 35 | #!/bin/bash -l
#SBATCH -J batch_export_optimized_EIANN_mnist_extended
#SBATCH -o /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist_extended.%j.o
#SBATCH -e /scratch1/06441/aaronmil/logs/EIANN/batch_export_optimized_EIANN_mnist_extended.%j.e
#SBATCH -p normal
#SBATCH -N 1
#SBATCH -n 6
#SBATCH -t 6:0... |
7350a68e7ee6f4e2e41e4d9a1f36c058ec05f5e0ee8502e0ef1050242a8d705c | Shell | 981 | 52 | #! /bin/bash
WHAT=$1
DIR=$2
MINIC=$3
MAXIC=$4
MINOC=$5
MAXOC=$6
prefix=$8
meanstatsfilename=$2/mean.html
WORK_DIR=tmp
mkdir $WORK_DIR
DATA_FILE=`find $DIR -name "*.dat" | grep _${WHAT}`
if [ -n "$DATA_FILE" ]; then
echo ""
echo "$1..."
for FILE in $DATA_FILE
do
##echo hello ... |
98f5f08529343dacf639cc481b96a559f1386941bc355bb9965490ac6d0e7128 | Shell | 981 | 29 | # Bethell and Taroni for CCDL 2019
# Generates lists of scatter plots for dimension reduction techniques.
#
# Usage: bash 02-get-dimension-reduction-plot-lists.sh
COLORVAR=${COLOR:-broad_histology}
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e... |
94404d644c9942eddd5c9927dcbad6e1ffdf53457afd3a993eef395a18eeb93f | Shell | 983 | 33 | #!/bin/bash
# Module author: Komal S. Rathi, updated Kelsey Keith
# 2022-07
# This script runs the steps for immune deconvolution using xCell and quanTIseq.
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Base... |
924d196cf276d3d6eda7261babd8a1bd8df011190c6908fc04216d9d66af2ec8 | Shell | 985 | 27 | #!/bin/bash
#SBATCH -J humann2
#SBATCH -A b1057
#SBATCH --mail-type=ALL
#SBATCH --mail-user=elizabeth.mallott@northwestern.edu
#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 240:00:00
#SBATCH --output=/home/ekm9460/humann2_array_%A_%a.out
#SBATCH --error=/home/ekm9460/humann2_array_%A_%a.err
#SBATCH -p b1057
#SBATCH --array=1-5... |
670947eedf824304e0c7bf12543248b1c0f732393c08be40c89990e8dcf80bdc | Shell | 987 | 31 | #!/usr/bin/env bash
set -euo pipefail
ENV_FILE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/environment.yml"
ENV_NAME="methylkey"
if command -v mamba >/dev/null 2>&1; then
CONDA="mamba"
elif command -v conda >/dev/null 2>&1; then
CONDA="conda"
else
printf '%s\n' "Error: install Miniforge, Mambaforge, or... |
7a2f248644d981a6122a0216fe9ec323d178c758ee2a137c268aeb27e37bae48 | Shell | 988 | 23 | #!/bin/tcsh -xef
#Set the paths for input list, output and mask
set inpath = /path/to/input/list
set outpath = /path/to/output/folder
set maskpath = /path/to/mask
#Set current directory to inpath
cd $inpath
#Run tICA for the marmoset sample
#Set TR to 1.5s, use a mask of the same resolution of the functional data (0... |
23126a6f2805ec66e0c5c0fea8995300b18acadd3d931f0911654a4d336d53c4 | Shell | 989 | 29 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
b2df0e86cae44e81f10c5e5871ff399c39e690b151b7cd11b14661154687a114 | Shell | 989 | 40 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_eve_data_start
#SBATCH --output=logs/gnn_eve_data_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Ensure the script is called with the necessary argument for 'name'
if [ "$#" -ne 1 ]; then
echo "Usage: $0... |
ab6141d1f1a42af9c687ec95c544d46f4ccbbf8e2a0203e749b49eada3f49039 | Shell | 994 | 33 | #!/bin/bash
DEVICE="0"
# Define the range of energy indices
ENERGY_START=0
ENERGY_END=66
# Paths and directories
TXT_DIR="./Data/XANES_00089/AC3_C4p6_3DXANES/AC3_C4p6_3DXANES_TOMO-XANES.txt"
HIGHEST_PROJ="./Data/XANES_00089/highest_energy/alignment_8346.mat"
RESULT_DIR="./Data/XANES_00089/alignment_result/"
# Itera... |
99ee5a38fdd51767a5991fe14ec2a563f546d656051495aff3a7785c82980cb2 | Shell | 995 | 39 | #!/bin/sh
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
# However in order to give Docker access to all the code we have to... |
90c4ae219eb0278068f7bb2e8cdde2ed0b7a3a9dbfbc87b26e11488b5be1e283 | Shell | 999 | 38 | #!/bin/bash
# Output CSV file
#OUTPUT="scores_with_mutation.csv"
#Folder="test"
Folder="$1"
OUTPUT="$2"
# Define the column names you want
COLS="total_score,dslf_fa13,fa_atr,fa_dun,fa_elec,fa_intra_rep,fa_rep,fa_sol,hbond_bb_sc,hbond_lr_bb,hbond_sc,hbond_sr_bb,omega,p_aa_pp,pro_close,rama,ref,yhh_planarity,mutation"... |
3f927d04b9c35318dec532f8bc44975c3b6f12248d312a80fdbcec6a1254e97f | Shell | 1,001 | 22 | # runs plot_ensemble_saliency_logos.py for DeepSTARR ensembles
# SALIENCY_DIR=$HOME/ensemble_distillation/results/DeepSTARR_lr-decay
SALIENCY_DIR=$HOME/ensemble_distillation/results/DeepSTARR_lr-decay/ensemble_distilled
METHOD=shap
AVG_FILE=$HOME/ensemble_distillation/results/DeepSTARR_lr-decay/average_top500_${METHOD... |
14675add3a62fa401172182cc575ab19d7b9e1df8ac4570198ee656357f549cf | Shell | 1,002 | 28 | #!/usr/bin/env bash
# Golden-count checks for the single-sample regression test.
# Run with the working directory set to fire-test-data after `pixi run test`.
set -euo pipefail
V="v$(echo "$PIXI_PROJECT_VERSION" | cut -d. -f1-2)"
PEAKS="results/test/test-fire-$V-peaks.bed.gz"
ELEMENTS="results/test/additional-outputs-... |
fdca7df5d62bb55a44a0abcbd6ad49fa15cc006d40891c81640cab378373a2f3 | Shell | 1,003 | 40 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_eve_data_start
#SBATCH --output=logs/gnn_eve_data_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=regular
# Ensure the script is called with the necessary argument for 'name'
if [ "$#" -ne 1 ]; then
echo "Usage: $0... |
dd86efb6b324045eb48feefe22c908305ca25fb134d4b731d7feb7afd246480e | Shell | 1,004 | 29 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
00671d91266beeca9dc27109d55dde39f64d98117c988bcf25844543cda76ba3 | Shell | 1,005 | 36 | #! /bin/bash
#SBATCH --job-name=epoch_decodetype
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=20G
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=4
#SBATCH --output=slurm-%j.out
#SBATCH --account=torch_pr_467_general
# load matlab
module load matlab/2025b
#where output will be pla ed
savedir=/scratch/dh148/dyn... |
f4cdb55275f481169e8afce18f1886f190eece88df13205f0a4e5f12a966b48c | Shell | 1,007 | 40 | #! /bin/bash
#
# This is a shell script to register GRE image to T1w image
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit:
############################################################
script_dir=`readlink -f "$0"`
SEPIA_HOME=`dirna... |
04469ced5091d71688ba55f5c311c1cecc0f37e2d32702b9f1838ffdb92286c2 | Shell | 1,008 | 20 | [ -z "${MASTER_PORT}" ] && MASTER_PORT=10086
[ -z "${n_gpu}" ] && n_gpu=$(nvidia-smi -L | wc -l)
export NCCL_ASYNC_ERROR_HANDLING=1
export OMP_NUM_THREADS=1
run_name=bert_example
save_dir="./save/${run_name}"
mkdir -p ${save_dir}
torchrun --standalone --nnodes=1 --nproc_per_node=$n_gpu $(which unicore-train) ./example... |
f5e10e541eec9156318b5a04388e782ea31e72c922b14fd446e2361d240f80c4 | Shell | 1,008 | 29 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
e63e4b1f96f7c9145c06fa1e02f201b3ed1329ea4b87c9f5054a177adee8f7a9 | Shell | 1,014 | 25 | #!/usr/bin/env bash
set -ex
# This is the master script for the capsule. When you click "Reproducible Run", the code in this file will execute.
echo "Plotting prediction accuracy for each participant (Figure 2A)."
python plot_prediction_accuracy.py
echo "Creating bar plots and performing permutation test for en vs z... |
631bfbb88597ee5a47c680e06a2de931261bd8597df6ea1baa0291ad1856ddfd | Shell | 1,018 | 44 | #!/bin/bash
INITIAL_PARAMS=""
VALID_TESTS="libs mesh solvers simulations"
function PRINT_USAGE() {
echo "Usage $0 [test]" >&2;
echo "Valid tests: all ${VALID_TESTS} (default is all)" >&2;
}
function RUN_TEST() {
lower_case_name=$1
test_bin_name="$(tr '[:lower:]' '[:upper:]' <<< "${lower_case_name:0:1... |
03e432c950de302eb0f00f1a91904bbf26197222cc848549da1c81ab940481a7 | Shell | 1,019 | 27 | #run with default settings and make sure all works
sbatch slurm_default.sh
# learning rate sweep, including an experiment with normal hyperparameters
#5e-6 is the original
#running 5e-5, 5e-4
for lr in 0.00005 0.0005 0.0000005; do
sbatch slurm_lr_sweep.sh $lr
done
for alpha in 0 1; do
sbatch slurm_alpha_sweep... |
32571f63b43afc787eee8409141d48e6bf8bb1e491f2eabf0aa56e80cddd8076 | Shell | 1,020 | 53 | #! /bin/bash
function usage() {
cat <<USAGE
Usage: $0 [-c config_path] [-d dataset_path]
Options:
-c, --config_path: Path to config file (e.g. traditional_machine_learning/params/xgb_50hz/config.yml)
-d, --dataset_path: Path of the HARTH dataset
USAGE
exit 1
}
if [ $# -eq 0 ]; then
u... |
23315b7e38774990b3ab81c776436900871f6c82514856166e8e30f648ced482 | Shell | 1,021 | 30 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
a3f2037d7c09f52330ab17f4a3f17b97c582173df90627e87b645f4cfb23a192 | Shell | 1,022 | 34 | #!/bin/bash
# Sample commands to deploy nuclio functions on CPU
set -eu
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
FUNCTIONS_DIR=${1:-$SCRIPT_DIR}
export DOCKER_BUILDKIT=1
docker build -t cvat.openvino.base "$SCRIPT_DIR/openvino/base"
nuctl create project cvat --platform local
... |
b26e19e2200eaca9a7a38eb18402b9e21d188fd8272c34c888b14ecabf2f5c58 | Shell | 1,022 | 21 | #!/bin/bash
if [ ! -e Trinity.fasta ]; then
gunzip -c Trinity.fasta.gz > Trinity.fasta
gunzip -c genome_alignments.gmap.gff3.gz > genome_alignments.gmap.gff3
fi
docker run --rm -v `pwd`:/data trinityrnaseq/transdecoder:latest util/TransDecoder.LongOrfs -t /data/Trinity.fasta -O /data
docker run --rm -v `pw... |
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