sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
e67794f58f67e0f3cf11a4d2c1da066ea9b5565158be206f5004d7ad7da97463 | Shell | 852 | 32 | #!/bin/bash
#SBATCH --job-name=jupyter-notebook
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=8000
#SBATCH --cpus-per-task=1
#SBATCH --qos=standard
#SBATCH --partition=main
#SBATCH --time=02:30:00
# Get tunneling information
XDG_RUNTIME_DIR=""
node=$(hostname -s)
port=$(python -c 'import socket; s=socket.socket()... |
c9e5132643c0140f8f957fe2fd69f7302d80d8aefffa97e8456a756a4f532d4b | Shell | 858 | 29 | #!/bin/bash
cell="$1"
CHR="$2"
module load samtools
module load bcftools
module load python/3.8.2
orgvcf="path/to/genotype.vcf.gz"
bcftools view -S ID/${cell}.exp_bed.vcfID.order -Oz -o vcf/${cell}.chr${CHR}.hg19.updated.eQTL.vcf.gz ${orgvcf}
tabix -f -p vcf vcf/${cell}.chr${CHR}.hg19.updated.eQTL.vcf.gz
/path/to/... |
d81ac2344018a1390f397a3d2bdf10dc9358c4f7777f2775281badfe484047a5 | Shell | 858 | 36 | # raw Makefile configuration
LINE () {
echo "$@" >> Makefile.config
}
cp Makefile.config.example Makefile.config
LINE "BLAS := open"
LINE "WITH_PYTHON_LAYER := 1"
if $WITH_PYTHON3 ; then
# TODO(lukeyeager) this path is currently disabled because of test errors like:
# ImportError: dynamic module does not de... |
337d431a3238e8b683706c9c54ddf9675ce020ae10cdbf7f4a142d1364ab70dc | Shell | 880 | 17 | s=$1
module purge
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
censor_doc=${fmriprepDir}/sub-${s}/func/frames_to_remove.csv
filtered_fd=${fmriprepDir}/sub-${s}/func/filtered_fd.csv
fd_overall_metrics=${fmriprepDir}/sub-${s}/func/fd_overall_metrics.csv
remove_p=${... |
2b5b1c6c30abe1a0d8c6b643f6906e5ea4c9e77c15f77669b8bba61e7f0fee46 | Shell | 885 | 30 | #!/bin/sh
#
echo "Installing Gurobi"
if [ -f /solvers/gurobi8.0.0_linux64.tar.gz ]; then \
cp /solvers/gurobi8.0.0_linux64.tar.gz /opt && \
cd /opt && \
tar xvfz gurobi8.0.0_linux64.tar.gz && \
cd /opt/gurobi800/linux64 && \
python3 setup.py install && \
rm /opt/gurobi8.0.0_linux64.tar.gz; fi
#if [... |
eb31fb3c01f372bf33523c9c049ead8d3a59f588751ad4e7329c07bd50db86bf | Shell | 889 | 35 | #!/bin/bash
# Provide a unified interface for the different logging
# utilities CI providers offer. If unavailable, provide
# a compatible fallback (e.g. bare `echo xxxxxx`).
function startgroup {
# Start a foldable group of log lines
# Pass a single argument, quoted
case ${CI:-} in
azure )
... |
9cbb26b246cfa02a2207275ceba7ce256665e7ab333ff7211b07272bf7de6d8f | Shell | 892 | 17 | s=$1
module purge
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
censor_doc=${fmriprepDir}/sub-${s}/func/frames_to_remove.csv
filtered_fd=${fmriprepDir}/sub-${s}/func/filtered_fd.csv
fd_overall_metrics=${fmriprepDir}/sub-${s}/func/fd_overall_metrics.csv
remove_p=${... |
7028545e2ff10d1ac1caf5e27118275a8bab15aadc121e0ed0109a47faae94ae | Shell | 900 | 29 | #!/bin/bash
#SBATCH --ntasks=4
#SBATCH -o slurm_logs/slurm-%j.out
#SBATCH --time=48:00:00
#SBATCH --partition rhu
DATA_PATH=${1};
INIT_PATH=${2};
RES_DIR=${3};
STAN_FNAME=${4};
SAMPLING_ITERS=${5};
WARMUP_ITERS=${6};
NCHAINS=${7}; # $SLURM_NTASKS
DELTA=${8};
MAX_DEPTH=${9};
JITTER=${10};
FNAME_SUFFIX=${11};
LOG_DIR=${... |
27c8d600bd929c22c29c6811ee4538f791f95c5b2e2ab9c1df683ce6a86dac73 | Shell | 904 | 38 | #!/bin/bash
# Sundails 5.1.0
#wget https://github.com/LLNL/sundials/releases/download/v3.1.1/sundials-3.1.1.tar.gz
#tar -xzf sundials-3.1.1.tar.gz -C $HOME
#cd $HOME/sundials-3.1.1
#
#mkdir $HOME/sundials-3.1.1/builddir
#cd $HOME/sundials-3.1.1/builddir
#cmake -DLAPACK_ENABLE=ON \
# -DSUNDIALS_INDEX_SIZE=64 \
# ... |
f92cef248d0d7f8f07da05486503a68c69d10cfdbb6ca9edb406a390d2891b0c | Shell | 905 | 23 | #!/bin/sh
# Thanks to cdiener: https://hub.docker.com/r/cdiener/cobra-docker/~/dockerfile/
# For the solution of simply getting the bins and python hooks
#
echo "Installing and Moving CPLEX files"
# Default Py3.5 install
#if [ -d /solvers/ibm ]; then cd /solvers/ibm/ILOG/CPLEX_Studio1271/cplex/python/3.5/x86-64_linu... |
9b7a28b4f1b19be310a77d68644236cf9929c5d8b0e836aa68c19acfd0bcbb84 | Shell | 908 | 26 | #!/bin/bash
module load tabix/0.2.6-GCCcore-11.2.0
# hap_file = $1
vcf_file="$1"
echo "$vcf_file"
sample=$(echo "$vcf_file" | sed "s/strandphaser.*//g" | rev | cut -d'/' -f 2 | rev)
# touch "$vcf_file"
echo '##fileformat=VCFv4.2
##fileDate=2023-01-31
##source=StrandPhase_algorithm
##reference=BSgenome.Hsapiens.UCS... |
dff928b656fbee257dac0943611a0c96661a3db0a3557d3514c964fab1707099 | Shell | 909 | 22 | #!/bin/bash
# Setup script for Snakemake caching on EMBL HPC
#
# USAGE:
# source setup_cache.sh # Enable for current session
#
# OR add to ~/.bashrc for permanent setup:
# echo 'export SNAKEMAKE_OUTPUT_CACHE=/scratch_cached/korbel/shared/snakemake_cache' >> ~/.bashrc
# SHARED cache for computed outputs (BWA ind... |
95211ab0376115a38592ee78d4dc314cdb91dbc47a80bd5591e61acfc8dddb20 | Shell | 915 | 44 | #!/bin/env bash
#SBATCH --job-name=kimmdy_run
#SBATCH --output=kimmdy_%j.o.log
#SBATCH --error=kimmdy_%j.e.log
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --mincpus=40
#SBATCH --exclusive
#SBATCH --cpus-per-task=1
#SBATCH --gpus=2
#SBATCH --partition=cascade.p
current_dir=$(basename "$(pwd)")
# Setup up your en... |
2ca80f93f35a103502e2d92901c451ed277928ce3e65fe3c098d9c613a26da53 | Shell | 917 | 35 | #!/bin/bash
#The purpose of this script is to generate activations and run
#the regression for the contextual embeddings of untrained models.
#LLM.py: generates static and contextual embeddings.
#lua.py: performs linear (w/ a layer norm) uniform attention over the static embeddings
#call_banded_reg.py: runs the regre... |
42127b9f01e386f2baa16378a8e0ef2e1444826d675d8f8e6edeecc129e6ef3b | Shell | 919 | 30 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=decoding_images
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8000 # specifies ... |
20409d799d1adb8ab2ca1389bf4afb4cc01ba4f807bdf583450a8d88512aff6f | Shell | 929 | 28 | #!/bin/bash
#SBATCH --mail-user=alexandel91@zedat.fu-berlin.de
#SBATCH --job-name=decoding_videos
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8000 # specifies ... |
3332eb6f91de3b1b12dbd35c752b3cbffcc81cd33e8bff05a58c5abf6d4c1fb8 | Shell | 937 | 21 | #!/usr/bin/env bash
set -euo pipefail
# This script submits jobs to run all analysis (from fMRI preprocessing to
# group-level aggregation of results) in sequence.
extract_jobid() {
awk '/Submitted batch job/ {print $NF}'
}
taskfmri='/oak/stanford/groups/menon/projects/branigan/2023_abcd_glm/scripts/taskfmri'
s... |
8d8f9e9e01eecf1992083dd6e514d8e663cf33c8658993c5b88e005d18f92f65 | Shell | 951 | 32 | #!/bin/bash
#SBATCH --job-name="Pore_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G # Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
# Auto-detect PDB and XTC files
PDB_FILE=$(ls ../*.pdb)
XTC_FILE=$(ls ../*.xtc)
e... |
b6c3d2ed30a13f220ead4c8b156cddf8a694855f5c7a42a02c1bb5f65e353b1a | Shell | 951 | 32 | #!/bin/bash
#SBATCH --job-name="Pore_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=37G # Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
# Auto-detect PDB and XTC files
PDB_FILE=$(ls ../*.pdb)
XTC_FILE=$(ls ../*.xtc)
e... |
ed856cd9387065dc53da7ded348bccea84a57ad074364113fcf821d3c3a29b23 | Shell | 958 | 37 | #!/bin/bash
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_6_2 \
--input_type "miniclips"
python ../../EEG/Encoding/encoding.py \
--c... |
9a1f7446aa9e7b0a8fbbcae3bfe271ad4522281c10f4d32a121d930144ba85ef | Shell | 959 | 32 | #!/bin/bash
#SBATCH --job-name="Pore_Z"
#SBATCH --output=out
#SBATCH --error=err
#SBATCH --partition=accardi-gpu4
#SBATCH --nodes=1
#SBATCH --mem=50G # Large Request
#SBATCH --ntasks-per-node=16
#SBATCH --gres=gpu:1
#SBATCH -t 48:00:00
# Auto-detect PDB and XTC files
PDB_FILE=$(ls ../*.pdb)
XTC_FILE=$(ls ../*.xtc)
e... |
d11baeda8263327c3257a1f5ddabf4d3d6be854f54ada16c143fd3874a0cc9e2 | Shell | 959 | 38 | #!/bin/bash
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_6_2 \
--input_type "images"
python ../../EEG/Encoding/encoding.py \
--conf... |
9fdbcaea47b80095291792919ce35fa807c0d70a85926e5cbf3ba6bef5e371d7 | Shell | 960 | 23 | # Script will rsync fastq folders from the mosaicatcher-pipeline to the scratch space for dedicated analysis
while IFS=$'\t' read -r date_folder subfolder; do
date_folder=$(echo "$date_folder" | xargs)
subfolder=$(echo "$subfolder" | xargs)
src_path="/g/korbel/STOCKS_WF/mosaicatcher-pipeline/${date_folder}/${subfold... |
618110e50725330b9eefb2fe1c0ba4df3f4bdc5f6c2fcf3ef01ac8022df2f1ea | Shell | 976 | 31 | #!/usr/bin/env bash
# setup_shared_caches.sh
#
# Creates shared MosaiCatcher cache directories on the EMBL HPC with correct
# group permissions. Run once by the group admin before first use.
#
# Usage: bash workflow/scripts/toolbox/setup_shared_caches.sh
set -euo pipefail
GROUP="korbel"
DIRS=(
"/scratch/korbel/s... |
7d52a518ab306bf4ba2716c9199aca6f04c8355ad2148f631bbbe473abdf04e0 | Shell | 979 | 33 | #!/bin/bash
#SBATCH --job-name=run_sammy_seq_analysis
#SBATCH --output=logs/run_sammy_seq_analysis.out
#SBATCH --error=logs/run_sammy_seq_analysis.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=3:00:00
#SBATCH --partition=workq
# SAMMY-seq analysis pipeline for ide... |
0db11805d669b610b02b8ac2bdea133120992dae254069d88857a6dc49ae4391 | Shell | 1,010 | 39 | #!/bin/bash
#SBATCH --job-name=build_mm10_index
#SBATCH --output=logs/build_mm10_index.out
#SBATCH --error=logs/build_mm10_index.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=24:00:00
#SBATCH --partition=workq
# Set WORKDIR to your working directory
WORKDIR="" # ... |
2700a923915796fded78cbc717e590a4b2759203aa60e86977feb603706bd55c | Shell | 1,024 | 38 | #!/bin/bash
# Run control analysis 9 for miniclips (excluding guitar trials)
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_9 \
--input... |
fee8556e360a7fd24ef22e08faaf391d4926c6217840a62b7736f2edaf401c55 | Shell | 1,026 | 36 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
ee21eb58cfdce43ba778e190ceb74468c9c503d410dab030621541904ff8194f | Shell | 1,033 | 35 | #!/bin/bash
#SBATCH --job-name=0_run_sammy_seq_analysis_blacklisted
#SBATCH --output=logs/0_run_sammy_seq_analysis_blacklisted.out
#SBATCH --error=logs/0_run_sammy_seq_analysis_blacklisted.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=3:00:00
#SBATCH --partition=wo... |
8af0875500370b9a99c4a0ba012cc4391150d6c24031c63ebbd6e40762014c67 | Shell | 1,039 | 38 | #!/bin/bash
# Run control analysis 9 for miniclips (excluding guitar trials)
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_9 \
--input... |
ffcaff9d9e8f8566655a72497b6304d2425341e663be7109205ffed3d42c85e8 | Shell | 1,047 | 34 | #!/bin/bash
# Check if a Dockerfile path is provided
if [ "$#" -ne 1 ]; then
echo "Usage: $0 <path-to-Dockerfile>"
exit 1
fi
DOCKERFILE=$1
# Check if the Dockerfile exists
if [ ! -f "$DOCKERFILE" ]; then
echo "Dockerfile not found: $DOCKERFILE"
exit 1
fi
# Extract the R environment variable
Renv=$(g... |
e4b96e59f6eaac884c0eecb20f6788c7725fc50445e82d95fd42fd877c568caf | Shell | 1,058 | 37 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l walltime=10:00:00
#PBS -l nodes=1
#PBS -m a
set -uvex
source "$TOOL_WORKFLOW_LIB"
printInfo
# Check for single lane pr... |
a3c65698d7633e7f2f207d8d2cb9ac7fde740103a69434c2ccef361fd417a113 | Shell | 1,060 | 53 | #!/bin/bash
#
# Jeff Eilbott, 2017, jeilbott@surveybott.com
# inputs
PROJECT="/ysm-gpfs/project/ejh22/bioinfo/startle"
UPLOAD="$PROJECT/upload"
DATA="$PROJECT/data"
LOG="$PROJECT/log"
CORES=12
QUEUE="general"
EMAIL="jeilbott@surveybott.com ellen.hoffman@yale.edu"
BASE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )... |
aa1df3098e66958be497c04c56a595a7e0b501e844f78c0c2a0bd2f50c46424a | Shell | 1,061 | 38 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in BIDS standardised T2w MRI datasets
# Author: William Pham
# Date: 2025-03-04
# Description: This script runs a nnUNet to label perivascular spaces in T2w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR arguments, then... |
505a252ffd886058bd9a667fee002ca4a073a380cb5269d92901244cfc2a6924 | Shell | 1,074 | 38 | #!/bin/bash
# nnUNetv2 for the segmentation of perivascular spaces in BIDS standardised T1w MRI datasets
# Author: William Pham
# Date: 2025-03-04
# Description: This script runs a nnUNet to label perivascular spaces in T1w MRI scans.
# Usage:
# Modify the script to include the INPUT_DIR and OUTPUT_DIR arguments, the... |
3bdfb682745c7bd6e832622a2d918793b73c42af4427809be7dcbaa825720b5e | Shell | 1,090 | 36 | #!/bin/bash
# Setup model directory structure for Git
# This creates the directory structure while keeping models folder tracked in Git
echo "Creating model directory structure..."
# Create main models directory
mkdir -p models
# Create subdirectories for each model architecture
mkdir -p models/unet/models
mkdir -p ... |
fcbec642a75fe64f5fddc07846a6140693fcc28c5e372c369f9643595fdf54a5 | Shell | 1,092 | 35 | echo "Activating conda environment mri_brain"
conda activate mri_brain
# activate Pytorch
#module load PyTorch/1.0.1-intel-2018a
# setup freesurfer development version of dd 10/03/2021
echo "Activating Freesurfer7 development versions centos7 of 10/03/2021"
export FREESURFER_HOME=$VSC_DATA/apps/freesurfer
export SUBJ... |
0ab4e85d173cf7947e431ca6ba80258820ce3eba1ff4b30018fce281e9025471 | Shell | 1,096 | 39 | module load fsl
output_file="subjects_unsuccessfully_run.txt"
# Start with a clean output file
> "$output_file"
for subject_number in sub-*; do
if [ -d "./${subject_number}" ]; then
# Remove "sub-" prefix for consistency
subject_number_clean=${subject_number#sub-}
# Check for cras... |
dc340debd28e73b5b5cff260a92b6034fb894d5c670ef33952a60135287486db | Shell | 1,096 | 35 | #echo "Activating conda environment mri_brain"
#conda activate mri_brain
# activate Pytorch
#module load PyTorch/1.0.1-intel-2018a
# setup freesurfer development version of dd 10/03/2021
echo "Activating Freesurfer7 development versions centos7 of 10/03/2021"
export FREESURFER_HOME=$VSC_DATA/apps/freesurfer
export SU... |
ddd4731667594fd9df2d5ce744877152e1742239ba9e452501182a15e17bf9a1 | Shell | 1,104 | 40 | #!/bin/bash
# Generate bin BED file for a reference genome
# Usage: generate_bin_bed.sh <reference_fasta> <output_bed> <window_size>
set -e
REFERENCE_FASTA=$1
OUTPUT_BED=$2
WINDOW_SIZE=${3:-200000}
if [ -z "$REFERENCE_FASTA" ] || [ -z "$OUTPUT_BED" ]; then
echo "Usage: $0 <reference_fasta> <output_bed> [window_s... |
255c12f04f54a6a31a3de7fcead2abacf5b9a10846fbf234d67c4ec97b2949bb | Shell | 1,140 | 42 | #!/bin/bash
# Standard encoding analysis with all features for images
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Performing hyperparameter tuning..."
# python ../../CNN/Encoding/hyperparameter_optimization_cnn.py \
# --config_dir ../config.... |
6c98387bb57119c74ac99d83644976d059fa1efc72261a14ef56f066c8b41661 | Shell | 1,141 | 29 | #!/bin/bash
# Assemble documentation for the project into one directory via symbolic links.
# Find the docs dir, no matter where the script is called
ROOT_DIR="$( cd "$(dirname "$0")"/.. ; pwd -P )"
cd $ROOT_DIR
# Gather docs from examples/**/readme.md
GATHERED_DIR=docs/gathered
rm -r $GATHERED_DIR
mkdir $GATHERED_DI... |
364e333b2dad67185dea9b092cc0f214d2981cb6487ce96bd8eb5124b2b29e7b | Shell | 1,149 | 29 | DIRECTORY="experiments/FigC1_dPC_linear"
for net in 2-1 4-2-1 8-4-2-1 16-8-4-2-1 32-16-8-4-2-1
do
for model in dPC
do
python runner.py --params $DIRECTORY/$net/$model/params.json --task fw_only --compare BP &
python runner.py --params $DIRECTORY/$net/untrained_$model/pa... |
288fc31bbd1ffd0498242214377a7e02271c9044313702d4f51f014f5d247231 | Shell | 1,158 | 42 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Performing hyperparameter tuning..."
# python ../../CNN/Encoding/hyperparameter_optimization_cnn.py \
# --config_dir ../conf... |
7b4bce3aa47ebe6bd89a0d4712ccc6522fe093f76524af46e61c0c4ef3fdf22b | Shell | 1,161 | 32 | #!/bin/bash
#
# Set the job name and wall time limit
#BSUB -J train-gnn
#BSUB -W 168:00
#
# Set the output and error output paths.
#BSUB -o train-gnn-%J.o
#BSUB -e train-gnn-%J.e
#
# Set any gpu options.
#BSUB -q gpuqueue
#BSUB -gpu num=1:j_exclusive=yes:mode=shared:mps=no:
#
#BSUB -M 32
# ===================== cond... |
105cd409d2f456e3830502763cb771d567eba11f207d367c486d1cccce0adf13 | Shell | 1,176 | 46 | #!/bin/bash
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
echo "Hyperparam tuning"
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_6_1 \
--input_type "miniclips"
echo "Encoding"
python... |
6c41c82e36fbe43988b3394d078f7f72605baead9b7dad244de91ed670ca5f47 | Shell | 1,178 | 34 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Load a Conda environment.
source activate "${condaEnvironmentName:?No Conda environment name defined. Please set 'conda... |
348670943ce1143e4334de411a05dbefd18a2fc3d0241899461314ff611896a2 | Shell | 1,182 | 38 | #!/bin/bash
# Check for valid directory
DIRNAME=$1
if [ ! -f $DIRNAME/readme.md ]; then
echo "usage: upload_model_to_gist.sh <dirname>"
echo " <dirname>/readme.md must exist"
fi
cd $DIRNAME
FILES=`find . -maxdepth 1 -type f ! -name "*.caffemodel*" | xargs echo`
# Check for gist tool.
gist -v >/dev/null 2>&1 ... |
6ad1e06f4e95164bf739da1b093e221823381b4fb5764c14bda468d1e6323fd6 | Shell | 1,183 | 58 | #!/bin/bash
while [ $# -gt 0 ]
do
case $1 in
-c | --cache) shift; cache=$1 ;;
*) break ;;
esac
shift
done
. /etc/profile
. $HOME/.bashrc
export PATH=/opt/python/2.7.2/bin:$PATH
export LD_LIBRARY_PATH=/opt/python/2.7.2/lib:$LD_LIBRARY_PATH
module load psi/tip.opt
# echo "#================... |
e92d15087b002521423031d24ddd5065f7d12caccd97d48571d751cb10bc3d31 | Shell | 1,184 | 38 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
f5bb063d19e69b1b681096e22c9555ac1d5005ab77d1d1aa4df829054da5a5fd | Shell | 1,186 | 43 | #!/bin/bash
# Must be invoked with $PACKAGENAME
echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH
PUSH_DOCS_TO_S3=false
if [ "$TRAVIS_PULL_REQUEST" = true ]; then
echo "This is a pull request. No deployment will be done."; exit 0
fi
if [ "$TRAVIS_BRANCH" != "master" ]; then
echo "No deployment on BRANCH='$TRAVIS_BRA... |
8941d7101c4207a8f65ea393f3ab2c97942b9a082ac2da11a7234003249cc994 | Shell | 1,187 | 35 | #!/usr/bin/env bash
previous_tag=0
FILTER="${1:-.*}"
NHEAD="${2:-999}"
for current_tag in $(git tag --sort=-creatordate | head -n ${NHEAD})
do
if [ "$previous_tag" != 0 ];then
tag_date=$(git log -1 --pretty=format:'%ad' --date=short ${previous_tag})
printf "### ${previous_tag} (${tag_date})\n\n"
... |
bb66be595f17cc927f3ecb8d14b09903780a95774ddd1fd71fa77fc686544d11 | Shell | 1,188 | 45 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
# First step: MVNN
python ../EEG/Encoding/mvnn_encoding.py \
--config_dir ./config.ini \
--config default \
--input_type "miniclips"
python ../EEG/Encoding/annotation_prep_vid... |
fc9cd280ef294b870233e9466d9bb26fc98a170a28cb6154757942997e4961f1 | Shell | 1,193 | 43 | #!/usr/bin/env bash
input_gz_file="$1"
# Check if the file exists
if [ ! -f "$input_gz_file" ]; then
echo "Error: File '$input_gz_file' not found!"
exit 1
fi
output_dir="$2"
mkdir -p "$output_dir"
# Process the gzipped file and split it into separate tracks
zcat "$input_gz_file" | awk -v outdir="$output_dir... |
c9f97868270bab4a54e87247a6868d4052fec197ebbc455227acf40f4556eecd | Shell | 1,209 | 37 | #!/bin/env bash
#SBATCH --job-name=IQMs
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --mem-per-cpu=14G
#SBATCH --time=24:30:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#SBATCH --array=1-X
# Assign input args
SUBJECT_LI... |
8d75ad28e937edad0fb425ed0d876337545899f5249beaf735949945e52071da | Shell | 1,213 | 53 | #!/bin/bash
# Control analysis 8
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# python ./time_generalization.py \
# --config_dir ../config.ini \
# --config default \
# --input_type "miniclips"
# echo "Time gen done for miniclips"
# python .... |
cc2763503f3765e6ddb46792cf742c5a648d2020d107502cbeba20144fbf1929 | Shell | 1,214 | 28 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l nodes=1:ppn=1
#PBS -l mem=750m
#PBS -l walltime=00:10:00
#PBS -m a
## the outfile name structure is necessary for the R ... |
0995caaf6f8a1e69905cc640f9c952f443dd6ef6187cce8854e12ec717145c2d | Shell | 1,229 | 49 | #!/bin/bash
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
echo "Hyperparam tuning"
python ../../EEG/Encoding/hyperparameter_optimization.py \
--config_dir ../config.ini \
--config control_6_1 \
--input_type "images"
echo "Encoding"
python ..... |
d871957d70c6312f8d2b7baa3cc4af9f984a9cf6f387c4ff483d27098a1512cc | Shell | 1,231 | 33 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
fb6252d3c271924da99438eed9dcd633a28e429769c41d7d70773ba6a74cc9da | Shell | 1,258 | 41 | #!/bin/bash
# Analyze coverage for all mouse samples
BASE_DIR="/g/korbel/STOCKS_WF/mosaicatcher-pipeline"
OUTPUT_DIR="coverage_analysis"
mkdir -p "$OUTPUT_DIR"
# Mouse samples to analyze
declare -A SAMPLES=(
["PDAC10265"]="2024-12-18-HKFJFAFX7/PDAC10265wholeCellsp1"
["PDAC70301"]="2024-12-18-HKFJFAFX7/PDAC70... |
87e6164d6cf76fb02143b0b26be011cad87af56f546cddf7d95495b4effab9ad | Shell | 1,263 | 39 | #!/bin/bash
#SBATCH --job-name=1_run_gene_chromatin_state_analysis
#SBATCH --output=logs/1_run_gene_chromatin_state_analysis.out
#SBATCH --error=logs/1_run_gene_chromatin_state_analysis.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=3:00:00
#SBATCH --partition=workq... |
8b51a5ad4454010a847dc656a7b0a8203fc18ee463d240b3d85742c7dd249dc2 | Shell | 1,276 | 44 | #!/bin/bash
#SBATCH --job-name=model1_singleMod
#SBATCH --output=logs/ml_model_%A_%a.out
#SBATCH --error=logs/ml_model_%A_%a.err
#SBATCH --ntasks=1
##SBATCH --array=0-9##2303
#SBATCH --cpus-per-task=2 # Request only 1 CPU core
#SBATCH --mem=4G # Minimal memory for basic testing
#SBATCH --time=1... |
91253baf1d605c46d2c526a9dc6eb11c83b620f595fd9dc5087ede39e70f843d | Shell | 1,282 | 35 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
9eeaef01903e5d0ec2d23985672fa1f4834118a03762374bbc3f0136a861d693 | Shell | 1,287 | 39 | #!/bin/bash
#SBATCH --job-name=2_run_gene_chromatin_state_comparison_nsc
#SBATCH --output=logs/2_run_gene_chromatin_state_comparison_nsc.out
#SBATCH --error=logs/2_run_gene_chromatin_state_comparison_nsc.err
#SBATCH --time=01:00:00
#SBATCH --mem=32G
#SBATCH --cpus-per-task=32
#SBATCH --partition=workq
# Chromatin stat... |
f9a7764c8017772e8d944e1679cbd31b3bb89b8096f734f1b6adc3bcc268a1bf | Shell | 1,287 | 39 | #!/bin/bash
#SBATCH --job-name=2_run_gene_chromatin_state_comparison_neu
#SBATCH --output=logs/2_run_gene_chromatin_state_comparison_neu.out
#SBATCH --error=logs/2_run_gene_chromatin_state_comparison_neu.err
#SBATCH --time=01:00:00
#SBATCH --mem=32G
#SBATCH --cpus-per-task=32
#SBATCH --partition=workq
# Chromatin stat... |
7577922b161f6585d4ab3753929447fc2c3d0e514aa2e6cddd41b9981b7f8b0d | Shell | 1,292 | 36 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
1eaeb308a491ea6747960daee66d085f6be1045c0c5535c896737f694c025321 | Shell | 1,301 | 45 | #!/bin/bash
# Control analysis 12
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# python ../../EEG/Encoding/hyperparameter_optimization.py \
# --config_dir ../config.ini \
# --config control_12 \
# --input_type "images"
# echo "Starting enco... |
c45fe800193f72fc7395e61be5e502b931d0852e73be81473855180d038b8199 | Shell | 1,308 | 39 | #!/bin/bash
#
# Set the job name and wall time limit
#BSUB -J search-hyperparameters
#BSUB -W 168:00
#
# Set the output and error output paths.
#BSUB -o search-hyperparameters-%J.o
#BSUB -e search-hyperparameters-%J.e
#
# Set any gpu options.
#BSUB -q gpuqueue
#BSUB -gpu num=1:j_exclusive=yes:mode=shared:mps=no:
#
#B... |
feaf90ea5614f092cf3f972548328a1c88965bade3858f8315fae9dc2c0509e5 | Shell | 1,319 | 27 | #!/bin/bash
#SAMPLE="FN_S1256"
SAMPLE="FN_S3478"
WD="/data/analysis/data_mbouamboua"
DEMUXAFY="/data/analysis/data_mbouamboua/Demuxafy"
OUTDIR=${WD}/data_analysis/hudeca/WS_demuxafy/${SAMPLE}
OUTDIR_MAJORITY=${WD}/data_analysis/hudeca/WS_demuxafy/${SAMPLE}/combine_majoritySinglet
OUTDIR_ANYDOUBLET=${WD}/data_analysis/... |
4c77cae53e7bd443db5718584e008977f44914faa658ef1cb15b24c783fe1977 | Shell | 1,323 | 46 | #!/bin/bash
# After running decoding scripts for images and miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
echo "Decoding bootstrapping images..."
python ../EEG/Stats/decoding_bootstrapping.py \
--config_dir ./config.ini \
--config defaul... |
8c464fc72e648e04ba8c780376c9ee716e1f9af9dfcd81eccb365af27878dc1c | Shell | 1,323 | 69 | #!/bin/bash
chr=$chr_test
## GWAS Zscore files
Zscore=$path_to_gwas_file
## LD covariance file
LD_file=$path_to_LD_file
# TIGAR DIRECTORY
TIGAR_dir=$path_to_tigar
# LOAD virtual environment for TIGAR
conda activate tigarenv
############# RUN TWAS
# TIGAR DPR weights
weight=$path_to_DPR_weight
gene_anno=$path_to_... |
6d80f0368df68a4523702138feed0a18f41c8357cef44b57eba6647e372f4391 | Shell | 1,324 | 56 | #!/bin/bash
user=$(whoami)
timestamp=$(date +%Y%m%d_%H%M%S)
repo_dir=/workspace-vast/$user/truesight # Adjust to your actual repo location
SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
# Create job-specific directory
job_dir=$repo_dir/logs/jobs/${timestamp}
mkdir -p $job_dir
# GPU and memory configuration... |
4f29a791c48b4ec5a4c7dc924a7e3939cf62602bcf0d9716e03c20a2fc50e872 | Shell | 1,329 | 45 | #!/bin/bash
# Control analysis 12
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# python ../../EEG/Encoding/hyperparameter_optimization.py \
# --config_dir ../config.ini \
# --config control_12 \
# --input_type "miniclips"
# echo "Starting e... |
1758a205d59cdea5eac0c66be9a6829118c8b66e20933701339e777b28ea4863 | Shell | 1,332 | 39 | #!/bin/bash
OUTPUT_DIR=$1
SUBJECT_ID=$2
SUBJECTS_DIR=$3
# Define and create the QC directory
SUBJECT_QC="${OUTPUT_DIR}/${SUBJECT_ID}/QC"
mkdir -p "${SUBJECT_QC}"
# Path definitions
IMG="${OUTPUT_DIR}/${SUBJECT_ID}/${SUBJECT_ID}_space-fsnative_desc-micro.nii.gz"
SURF_DIR="${SUBJECTS_DIR}/${SUBJECT_ID}/surf"
# 1. Cre... |
45131053b516c4645a0101b8cec8d463d9e2316e796ae24cce783006b4f6a651 | Shell | 1,332 | 21 | #!/usr/bin/env bash
#####################################################################################
### CIRCLEseq_prepare_test_genome.sh: assemble reference test
#####################################################################################
### Get chromosomes
wget ftp://ftp.ensembl.org/pub/grch37/current/... |
c3a15999d813c9909c42c6b097bc3fd1a412e07d8f4ca2fda5c34133e65f82f9 | Shell | 1,334 | 50 | #!/bin/bash
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# First step: MVNN
python ../EEG/Encoding/mvnn_encoding.py \
--config_dir ./config.ini \
--config default \
--input_type "images"
# Second step: Preprocess the features of the first fra... |
8a7bc131750346c6bebec21ca8bf45ee47cd271fd3641c3d6052292020aae432 | Shell | 1,344 | 41 | # Temporarily change directory to $HOME to install software
pushd .
cd $HOME
# Make sure some level of pip is installed
python -m ensurepip
# Install Miniconda
if [ "$TRAVIS_OS_NAME" == "osx" ]; then
# Make OSX md5 mimic md5sum from linux, alias does not work
md5sum () {
command md5 -r "$@"
}
M... |
2af772e4b7a740b37c1fa89acc08023873aeecd0d0cf6e5322abc09450c8bdd4 | Shell | 1,362 | 70 | #!/bin/bash
chromnum=$chr_train
TIGARDIR=$path_to_tigar
DATADIR=$output_path
# TIGAR PARAMETERS
Gene_Exp_train_file=$path_to_expression_file
train_sample_path=$path_to_sampleID_file
geno_file_path=$path_to_genotype_file
genoformat=GT
mafval=0.01
hweval=0.00001
crossval=1
# OUT DIRECTORY
OUTDIR_DPR=${DATADIR}/DPR_... |
cf1c8265b19321b3db30f328cf41b05a0033c9b38a38d493da9c386d6bd91b1d | Shell | 1,362 | 44 | #!/bin/bash
# Control analysis 3: Encoding analysis with image annotations for miniclips EEG data
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
echo "Starting hyperparameter optimization for miniclips..."
# First step: Hyperparameter optimization
python .... |
7b07edfd5b83bf1457e0aa69e9974afbfd6eb645fc723ce1bb993f4d116ddac0 | Shell | 1,388 | 35 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public_bme/data/lishr/Cross_modal/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2022/freesurfer/mni... |
d808ae55429e1cc5f5fb41653c9715c3955bfcfd5bcef0a574e966fe5766e24c | Shell | 1,399 | 27 | #
# 1 Bond 2 Morse 3 Angle 4 Proper-Dih.
# 5 Per.-Imp.-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
# 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential
# 13 Kinetic-En. 14 Total-Energy 15 Conserved-En. 16 Temperatu... |
0639ee513ff34cccc31da15d0806a815fc3be4587d0c95cb27850b32b299f85e | Shell | 1,401 | 21 | #!/bin/bash
#SBATCH --job-name photo_sim # Set a name for your job. This is especially useful if you
#SBATCH --partition quick # Slurm partition to use: quick, norm,
#SBATCH -c 1 # Number of tasks to run 3
#SBATCH --ntasks-per-core=1 # Do not use hyperthreading (this flag typically used for parallel jo... |
c3a002b4f9f837b2d4e4add38dba0662c6ba29d69830a1d868f455669fff955d | Shell | 1,406 | 57 | #!/bin/bash
#SBATCH --job-name=01_fastqc
#SBATCH --mem=64GB
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=32
#SBATCH --error="./logs/01_fastqc.err"
#SBATCH --output="./logs/01_fastqc.out"
# RNA-seq Pipeline Step 1: Quality Control with FastQC
# This script runs FastQC on all raw FASTQ files
# Set up cond... |
c6ec44128c3949a3dae589f3526e70dc97a3d818b833f47b3546a85fc53536c1 | Shell | 1,444 | 46 | # Temporarily change directory to $HOME to install software
pushd .
cd $HOME
# Make sure some level of pip is installed
python -m ensurepip
# Install Miniconda
if [ "$TRAVIS_OS_NAME" == "osx" ]; then
# Make OSX md5 mimic md5sum from linux, alias does not work
md5sum () {
command md5 -r "$@"
}
M... |
6e637b929fbd168a85b5b939b5049007499279fde6bbf4d034608b7b4ca4ed0a | Shell | 1,459 | 24 | #!/bin/bash
#### https://github.com/Yangqing/mincepie/wiki/Launch-Your-Mapreducer
# If you encounter error that the address already in use, kill the process.
# 11235 is the port of server process
# https://github.com/Yangqing/mincepie/blob/master/mincepie/mince.py
# sudo netstat -ap | grep 11235
# The last column ... |
ff877a2ee412bf3a963f88ff0e29c6639e59b1a0f248b2650b04c394ff99843f | Shell | 1,464 | 37 | #!/bin/env bash
#SBATCH --job-name=ME_AROMA
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=12G
#SBATCH --time=24:30:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#SBATCH --array=1-8
# Assign input args
SUBJECT... |
2a977e5f284839c9de3f9bdbe02c8b91100546b34718b81c2cd9d1f3c3aebc28 | Shell | 1,471 | 42 | #!/bin/bash
# Pre-commit hook to build assets with Vite when source files are modified
# Check if any source files were passed as arguments (prek filters by the files pattern)
if [ $# -gt 0 ]; then
echo "Source files modified: $*"
echo "Building assets with Vite..."
# Change to the default template direct... |
b3e3bb65b4cdc30ab306f9149e150ff2b8f3d8430b6fee822a1d9981f96003a4 | Shell | 1,478 | 50 | #!/bin/bash
# Example: Multi-Species Run with NanoporeToBED Pipeline v1.5.0
# Scenario: 11 Minipigs (barcodes 1-11) + 5 Penguins (barcodes 12-16)
# SLURM headers (adjust for your cluster)
#SBATCH --job-name=MultiSpecies_NanoporeToBED
#SBATCH --output=multispecies_run.out
#SBATCH --error=multispecies_run.err
#SBATCH -... |
1974d2152b5182b677e9c6ea476f5118d062621ee1d4201a4347ff23cbfd3934 | Shell | 1,492 | 53 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Applying PCA to the activations..."
# python ../CNN/Activation_extraction_and_prep/pca_activations.py \
# --config_dir ./con... |
1e8426ec8f938e44c61e028f037c555fcfe70a3a394e422ff65bb08af1040cf2 | Shell | 1,500 | 65 | #!/bin/bash
# This wrapper script is for running TINKER jobs on clusters.
# Command line switch indicates whether to do backups
do_bak=0
while [ $# -gt 0 ]
do
case $1 in
-b) do_bak=1 ;;
*) break ;;
esac
shift
done
# This is the command that we want to run.
COMMAND=$@
# Load my environmen... |
7119d2079a1be25827b1d4575e387c766a4cf52c1708e8a0484c4ab7b15466a0 | Shell | 1,514 | 54 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Applying PCA to the activations..."
# python ../CNN/Activation_extraction_and_prep/pca_activations.py \
# --config_dir ./con... |
ecd246685dba12e803135cd46c1cfa07786c7fc2dc0cb8def4ef78f55b255d60 | Shell | 1,534 | 55 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
DIR_SCRATCH="${RODDY_SCRATCH}"
#otherError="0"
# if the sequencing protocol is mate_pair the fastq data must be reverse complem... |
4a35e9c938aea37b27fbabbe421abf2b6ad7ee7515c110d16eb0aa0bc62f6844 | Shell | 1,536 | 43 | #!/bin/bash
# Sarah Cappelle & Stefan Sunaert
# 15/12/2020
# This script is the first part of Sarah's Study1
# We have data from IDE, but this is cluttered
# We sort the data into named DICOM folders
# We delete unwanted derived data (MPRs mostly)
# We convert these dicoms to BIDS format
# STEP 1 - sort the dicoms
# w... |
78a5f3e68228e153e7afcc614026c331ea72af5915a748115010f540d692723f | Shell | 1,540 | 53 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Applying PCA to the activations..."
# python ../../CNN/Activation_extraction_and_prep/pca_activations.py \
# --config_dir ..... |
99a98d793d0efeb3e0f78d60b39d350e25f4dc8a4ea7ed9aa7e30fab0cf76239 | Shell | 1,545 | 53 | #!/bin/bash
# Standard encoding analysis with all features for miniclips
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# echo "Applying PCA to the activations..."
# python ../../CNN/Activation_extraction_and_prep/pca_activations.py \
# --config_dir ..... |
063471e1e39f8bbedccd1efa447e78edc6ef1e885c390afb6288dc7b88dff057 | Shell | 1,547 | 40 | echo "This (experimental) update script will create a new repo according to your config file. It will:"
echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)."
echo "(2) and add missing files, if any."
set -e
OID=cl
ROOTDIR=../..
SRCDIR=.... |
2878fd10ea3456c032abae216cbf13b22053a3a9dce676712bba26af1d39c933 | Shell | 1,551 | 22 | #!/usr/bin/env bash
#####################################################################################
### CIRCLEseq_prepare_test_data.sh: assemble the fastq files for the test
#####################################################################################
### Regions
on_target="2:73160981-73161004"
off_target... |
e95baa56d219d0e331ad0ed29bef0f750f90cb729c0fd5eb878a95d9533fe665 | Shell | 1,552 | 68 | #!/bin/bash
# This wrapper script is for running AMBER jobs on clusters.
# Command line switch indicates whether to do backups
do_bak=0
while [ $# -gt 0 ]
do
case $1 in
-b) do_bak=1 ;;
*) break ;;
esac
shift
done
# This is the command that we want to run.
COMMAND=$@
# Load my environment... |
cfd6ced4a0af636042562dfd7626912e7781fbc50519479d641d5f98f3f84094 | Shell | 1,566 | 49 | #!/bin/bash
#SBATCH --job-name=3_run_mecp2_metaprofile_heatmap
#SBATCH --output=logs/3_run_mecp2_metaprofile_heatmap.out
#SBATCH --error=logs/3_run_mecp2_metaprofile_heatmap.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=3:00:00
#SBATCH --partition=workq
# Generate... |
bd12a0bcce070ef9f3b0c0bd6a895fe8ad5e87a87842f55444fab32ad3faf0a2 | Shell | 1,569 | 50 | ##!/bin/bash
toolbox_home=/cerebro/cerebro1/dataset/bmpd/derivatives/thibault_test/code/toolbox
anaconda_dir=/export02/data/landelle/anaconda/
# matlab
LD_PREFIX="/export01/local/matlab23b/sys/os/glnxa64:/cerebro/cerebro1/dataset/bmpd/derivatives/thibault_test/code/toolbox/libraries"
export LD_LIBRARY_PATH=/export0... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.