sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
10993773d716ad776a3d042eb93a325a6e733f31656ad034b72b41659db87199 | Shell | 1,731 | 82 | #!/bin/bash
POSITIONAL=()
while [[ $# -gt 0 ]]
do
key="$1"
case $key in
--PLINK_prefix)
target_plink="$2"
shift # past argument
shift # past value
;;
--phenotype_file)
phenotype_file="$2"
shift # past argument
shift # past value
;;
--coordinate_file)
coordinate_file="$2... |
debc1a99727fad9d21046521b812a0e0f5f17c9e2cbbb89b7819f332bd4e7c5a | Shell | 1,736 | 95 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
SLICE=-1
CC=10
EPOCH=""
RAW=0
RSSNORM=" --rss-norm"
while getopts "hC:s:E:Rn" opt; do
case $opt... |
6259a5fa600ad9b29efae82f96b7123f8ec69c755f450ef7f40a675d5b79af03 | Shell | 1,738 | 24 | #!/bin/bash
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=40G
#SBATCH --time=24:0:0
# mantis-ml
python updated_benchmark_module.py -c ../../conf/ALS_config.yaml -o ../../../out/ALS-production-Full/ -e ../../../misc/overlap-collapsing-analyses/ALS_Science_2015/ALS/Dom_LoF_collapsing_ranking.ALS.sorted.csv -x 41 -y 60... |
23a2a612863e7efa6293cbff7cfa1a08690c439b68e8df9efe0158284adce302 | Shell | 1,762 | 48 | #!/bin/sh
cd /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper//Pathformer_code
echo 'plasma'
python3 Pathformer_predict.py \
--modal_all_path ../Result/plasma/modal_type_all.txt \
--modal_select_path ../Result/plasma/modal_type_all.txt \
--gene_all ../reference/gene_mRNA_cfRNA.txt \
--gene_select ../referen... |
3e4968a45c62164779a2d15870079b19d45345818f6c7680d4fdd3d73cc436f8 | Shell | 1,764 | 10 | # & means run these methods at the same time, and && means run these methods one by one
python -u train_fully_supervised_3D.py --labeled_num 25 --root_path ../data/BraTS2019 --max_iterations 30000 --exp BraTS2019/Fully_supervised --base_lr 0.1 &&
python -u train_fully_supervised_3D.py --labeled_num 250 --root_path ../d... |
079766599cc45a492f11f29ae74972a47b7ea68aba3c632eec66f1c1df49ce11 | Shell | 1,774 | 53 | DATA_ROOT=${1}
Cell_Type=${2:-GM12878}
if [ -z "$DATA_ROOT" ]; then
echo "Error: DATA_ROOT is not provided."
exit 1
fi
# Seq2Exp-soft
python -m train \
experiment=hg38/gene_express \
wandb.mode=online \
wandb.group="CAGE_${Cell_Type}_bimambaRNP_MI" \
wandb.name=sigall_sigscale10_kl001_r01_eva... |
103efca8b9a954c9eb4670fb3caf1a44936bdddae1a72e11d8055c76ebf8996a | Shell | 1,778 | 40 | #!/bin/sh
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
echo "BRCA_stage"
python3 ${root_path}/comparison_methods/PathCNN/1.omics_image_PCA.py \
--dataset 1 \
--label_path ${root_path}/data_TCGA/2.sample_id/sample_cross_stage_new_final.txt \
--data_path ${root_path}/data_TCGA/4.data_feature... |
00e411b53a95f356599eae125a01f051151890c3d86cff794c37c89ff3d713c8 | Shell | 1,787 | 67 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
DATASET=(
wikipedia
)
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
mkdir -p "${MODELDIR}"
mkdir -p "${... |
862aec7e1eb3ad279be8f3ff0c0acf73547d3b803547f1d8910eabe442261eed | Shell | 1,788 | 48 | #!/bin/sh
cd /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/Pathformer_code
echo 'BRCA_stage'
python3 Pathformer_predict.py \
--modal_all_path ../Result/BRCA_stage/modal_type_all.txt \
--modal_select_path ../Result/BRCA_stage/modal_type_all.txt \
--gene_all ../reference/gene_all.txt \
--gene_select ../ref... |
2797ce2ad1436bab0f1acd8312c4fde7e064e7be1e180b13587084cacf5f32ef | Shell | 1,796 | 88 | #!/bin/bash
TAG="[BioemuS]"
# Define environment variable for BIOEMUS_PATH if not already set
if [ -z "$BIOEMUS_PATH" ]; then
echo "$TAG Error: BIOEMUS_PATH is not set"
exit 1
fi
# Define directories
DRIVERS_DIR="$BIOEMUS_PATH/drivers"
FIRMWARE_DIR="$BIOEMUS_PATH/firmware"
SOFTWARE_DIR="$BIOEMUS_PATH/app"
# ... |
e1ed055554180846aedad5ccf9407abe6c38f233e0c391c5e3c1fed214bc2915 | Shell | 1,806 | 60 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to i... |
63df75280cba33b6414b84efd85c1315b866c7c3fb8d6179ea1a7a91ffc66e97 | Shell | 1,807 | 73 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
myshuf() {
perl -MList::Util=shuffle -e 'print shuffle(<>);' "$@";
}
normalize_text() {
tr '[:upper:]' '[:lower:]'... |
4b074ce95635c20d111326106ae02d648168ea729ad44bbf4cc0a3d10fbc0225 | Shell | 1,813 | 44 | #!/bin/bash
animal_folder=/media/hanlin/Liuyang_10T_backup/jiaaoZ/data_converted/mda_files/MustangContinuous/Mustang_220126_125248
output_folder=/media/hanlin/Liuyang_10T_backup/jiaaoZ/msort_results/MustangContinuous/Mustang_220126_125248/dt375Segged
geom_file=map.csv
# geom_file=map_corolla24ch.csv
#animal_folder=/med... |
e104c88e406591f3669dcd96cc1e829e104915fa2575dbb744ca0d17c87a97cd | Shell | 1,813 | 57 | #!/usr/bin/env bash
#Create a VM to run the pipeline and submit jobs
gcloud beta compute --project=my-project instances create ubuntu1904-nopreempt-rnaseq-n1-standard-8 \
--zone=us-west1-b \
--machine-type=n1-standard-8 \
--subnet=default \
--network-tier=PREMIUM \
--maintenance-policy=MIGRATE \
--service-a... |
d114cf044f4dd65ebfc7ddaa631cba11154cf90f9996dda2ba36da70515f160b | Shell | 1,816 | 61 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
DATASET=(
wikipedia
)
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
mkdir -p "${MODELDIR}"
mkdir -p "${... |
5220394680f999164a44c444ece1201bed007ceb726e6c2de25bddbf36cb1491 | Shell | 1,826 | 44 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_5.out
source activate mlfold
folder_with_pdbs="../inputs/PDB_complexes/pdbs/"
output_dir="../outputs/example_5_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_chains=$ou... |
b369a366dbc455fc322fd1076e716f8624b9e242a4716f7859caa0dc7479ba74 | Shell | 1,830 | 74 | #!/usr/bin/bash
geno_dir=$1
pheno=$2
filehead=$3
LDdir=$4
Score_dir=$5
LDwindow=$6
module load tabix
bfGWAS_SS_dir="/home/jluningham/Projects/bfGWAS_SS"
# geno_dir=/home/jyang/Collaborations/IrwinSAGE/BU_GWASs_CDSymptomDimensions/lddetect_Dosage_Files
echo ${SGE_TASK_ID}
echo ${filehead}
line=$(head -n $SGE_TASK_I... |
24deb05d5f7b9232906ea9c2f6da10f25fec5e8085406d22b0a6dea72541c496 | Shell | 1,845 | 53 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
da0afa36580dfb40bb2fc76851626d284d99f5781b35f67f8a2003d047f46cb8 | Shell | 1,845 | 60 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to i... |
e4ddd0d449266d429b256f642d2cb6b456b27d668881b1071547b16a2fba534c | Shell | 1,845 | 29 |
# ------------------------------- inference arguments -------------------------------
# --bs: batch size, a tuple of length n for n input images. e.g. 3 7 for 2 input images
# --num_seg_window_x: number of segmented patch along x axis for each input image, a tuple of length n for n input images. e.g. 3 7 for 2 input ... |
5e23243ea5d0ab9b4827645659b12c0172db92ea0cc5ce23bc583ccc412d5805 | Shell | 1,863 | 93 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
SLICE=-1
CC=10
EPOCH=""
RAW=""
FRAMES=""
while getopts "hE:RVF:" opt; do
case $opt in
E)
EP... |
30c286872e039172497726698e1cd7352443ece435089070a4735623567ec91a | Shell | 1,886 | 41 | #Purpose: Calculate SA per network using fsaverage6 resolution surfaces
#Inputs: Kong2019 parc parc2annot and annot2gii output. Midthickness Conte69 in fsaverage6 space.
#Output: Surface area for LH and RH for 17 networks
#Software: wb_command (HCP), freesurfer
#Written by M. Peterson, Nielsen Brain and Behavior Lab u... |
878b87d67a2d6c22fb754567699ec4d974c77adebc2e2952d6cb7a3c9925da82 | Shell | 1,897 | 43 | wget https://data.nemoarchive.org/biccn/grant/rf1_tilgner/tilgner/transcriptome/scell/pacbio/mouse/raw/P14_M5_
wget https://data.nemoarchive.org/biccn/grant/rf1_tilgner/tilgner/transcriptome/scell/pacbio/mouse/raw/P28_M1_
wget https://data.nemoarchive.org/biccn/grant/rf1_tilgner/tilgner/transcriptome/scell/pacbio/mouse... |
676e1b90586dd16c48491ecdfcef1051f013dd47004254dbbeaf087302dc02e5 | Shell | 1,904 | 54 | #!/bin/bash
# This run_* script is a wrapper for L3stats.sh, so it will loop over several
# copes and models. Note that Contrast N for PPI is always PHYS in these models.
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd... |
1b03aa966667dc8b275b8eb77384dc873dcf665fe180844d8d2700b67291c44a | Shell | 1,915 | 24 | set -e
for model in coxph rsf deepsurv deephit naive_ldacox scholar_ldacox scholar_ldadraft scholar_sagecox scholar_sagedraft
do
for dataset in SUPPORT_Coma SUPPORT_Cancer SUPPORT_COPD_CHF_Cirrhosis SUPPORT_ARF_MOSF
do
n_outer_iter=1 # Number of random train/test splits, this is not the same as number of f... |
b009846d8cb448b6b047ed828e7fc9d3000944f30d50867af900b9c768cc5a5f | Shell | 1,921 | 51 | #!/bin/bash
# Usage
# from base dir run: bash bash/wes/03_collect_hsmetrics.sh metadata/Twist_Comprehensive_Exome_Covered_Targets_hg38.bed sarek_run/results/Preprocessing/*/DuplicatesMarked/*.bam
interval_file="$1"
bam_files=("${@:2}")
ref_base=igenomes_ref
ref_path=${ref_base}/Homo_sapiens/GATK/GRCh38/Sequence/Whol... |
0cb06c8c2a1b142e76732af645e6cc4fb52e01b680c1b1fef6a8ff26aacbc1e8 | Shell | 1,922 | 68 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
DATASET=(
wikipedia
)
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
mkdir -p "${MODELDIR}"
mkdir -p "$... |
98445cd765d40d4a1be04c6879d63428e2ac9a94285c904783cdf83a99e601c1 | Shell | 1,934 | 59 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request 4 CPUs
#$ -pe omp 3
#$ -m ea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=1:00:00
module load python3/3.8.10
module load pytorch/1.9.0
# conda info -e
conda activate py3.8
export LD_LIBRARY_PATH=/share/pkg.7/miniconda/4.9.2/install/lib/
cond... |
f1560ba079028896bb77355b84ac3e58145149154684d81047d04edbe49c2dcd | Shell | 1,935 | 51 | #!/bin/bash
#Purpose: Take raw nifti files and conform naming conventions to BIDS
#Inputs: Utah dataset nifti files (time 5 multiecho)
#Outputs: Utah dataset in BIDS format
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2023
#PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/Utah_ana... |
0b94e3f7ff0d9bb0591e97f5b87b5073800a7c1735f41a3f671df61835c54c92 | Shell | 1,938 | 60 | STEP_DIR="$ROOT_DIR/4-start-training"
# Reset folder
rm -rf "$STEP_DIR"
mkdir -p "$STEP_DIR"
# activate environment
source "$ROOT_DIR/.venv/bin/activate"
# Start training
tacotron-cli train \
"$ROOT_DIR/3-create-train-val-set/export/train" \
"$ROOT_DIR/3-create-train-val-set/export/val" \
"transcription" \
"... |
5ad55d0327facee849371f456789d0f979539618340c2aaf5d2b49fbf6ede14a | Shell | 1,942 | 64 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N coloc_plots_dlpfc
#$ -o ./summary_dlpfc.log
#$ -e ./summary_dlpfc.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## Li... |
4d2196e1de4bf0663a8bd2cf731dc5de1c6677751b4792a6abec6c2447c99735 | Shell | 1,955 | 76 | # Creates subsample of input data for RRBS
# ex: bash createTestDataSample.sh Muscle2
# NOTE THE CONDA ENVIRONMENT ONLY NEEDS SEQTK, GZIP, and GUNZIP
# PLEASE REPLACE bioinfo OR REMOVE CONDA ENVIRONMENT LINE IF IT DOESN'T WORK
set -ueo pipefail
if [[ $# -eq 0 ]] ; then
echo 'ERROR: REQUIRED ARGUMENT MISSING'
... |
64f1e0045a1b0e4f71c8cf928163ce22a0adcf68facd2ec8a2035a1826a02d39 | Shell | 1,959 | 61 | #!/bin/bash
# Create overlay montage of a probabilistic atlas on tissue boundaries from the associate structural template
#
# AUTHOR : Mike Tyszka
# PLACE : Caltech
# DATES : 2017-05-23 JMT From scratch
if [ $# -lt 3 ]
then
echo "USAGE : atlas_montage.sh <4D prob atlas> <3D structural template> <p threshold>"
ex... |
6cebec76b307e7a6932458ba1b593f7b4f292ddc5f6867611d2415ba1c381089 | Shell | 1,963 | 45 | #!/bin/bash
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
echo "BRCA_stage"
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/late_integration_method
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/late_integration_method/LR
mkdir ${root_path}/comparison_methods/Result/BRCA_s... |
ba06fdb3217c5dcd8d8e83343ff5a33efbfe246f22cba2816020240ca079bc85 | Shell | 1,966 | 64 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N coloc_plots_hippocampus
#$ -o ./summary_hippocampus.log
#$ -e ./summary_hippocampus.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: $... |
aa0667db8db148b9ee252f547f7b5c80196fac57b323a1765d38fe809b938dcc | Shell | 1,970 | 113 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
SLICE=-1
CC=10
ITER=6
COS=1.25
OS=1.5
BR=160
SPOKES=13
RAW=0
ROVIR=""
RSSNORM=""
while getopt... |
b2fc2f219695db068605812a05c16654254832c5dd5a0c70bc4b6fb4c7e7c6e2 | Shell | 1,970 | 101 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
SLICE=-1
LAM=""
ROVIR=""
CC=10
OS=1.5
FRAMES=""
RAW=0
while getopts "hC:O:l:VF:R" opt; do
case... |
b18893d210ed74cbeb1f574ea9d09416a34dc91ab5990ecb9c3f8b4adbe64208 | Shell | 1,976 | 45 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exist
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CH... |
4150355edb24ea2b5364a56c6e4242c238d5aa6cc4692c46345b55004a21c746 | Shell | 1,979 | 75 | #!/bin/bash -euo pipefail
# The command loops through sarek results/VariantCalling directory and writes to
# results/Annotation/${sample}/VEP and results/reports/${sample}/VEP directories.
# Run with sarek-2.7.2/singularity-images/nfcore-sarekvep-2.7.2.GRCh38.img
input_path=$1
threads=$2
ref_dir=igenomes_ref
if [[... |
ec4873685caa3228c483e466d51f550e109b6545659781525ecfd8786a73dc2b | Shell | 1,979 | 67 | #!/usr/bin/env bash
set -euo pipefail
python_bin=${PYTHON_BIN:-python}
sleep_seconds=${SLEEP_SECONDS:-60}
dry_run=${DRY_RUN:-0}
max_jobs=${MAX_JOBS:-1}
current_jobs=0
log_mlflow=${LOG_MLFLOW:-1}
log_tb=${LOG_TB:-0}
log_dvclive=${LOG_DVCLIVE:-0}
n_trials=30 # The number of hyperparameter configurations to try
n_repe... |
0e2ba6c14194323f1f89cf3ea70a4d3334cb2c8efbebd437f6f94907ac0257bd | Shell | 1,987 | 20 | #!/bin/bash
# Here, we're generating a C4-symmetric oligomer scaffolding a symmetric nickel-binding site
# This is described in the manuscript
# First, we specify we want a C4 symmetric oligomer, and 15 designs, to a specific output path
# We then apply potentials to promote compact structures
# This external potential... |
18130847013714e52075f0a45b68609a7fe4cf6928430984cc631a14fbd0e24d | Shell | 1,991 | 69 | #!/bin/sh
gpu=(5 0 2)
PDE='diff-react'
field_dim=2
scale_factor=8
sw=4
HR_resolution=128
LR_resolution=$((HR_resolution / scale_factor))
reference_model='SRCNN'
content_loss_weights=0.5
freeze_modes=8
freq_center_size=36
emb_dim=64
suffix_list=(
"${PDE}_LRinput_supervised_${reference_model}_bicubic_init_s_${LR... |
813bad430bf8a5645530eb27c12cc5f56837cd77cc8d8d35d322cf5b73cdd5d3 | Shell | 1,992 | 96 | #!/bin/bash
# Deface all identifiable structural images in a Freesurfer 6/7 subject directory
#
# AUTHOR : Mike Tyszka, Ph.D.
# PLACE : Caltech
# DATES : 2020-04-01 JMT From scratch
# 2023-09-29 JMT Switch to voxface for defacing
#
# Full list of mgz images generated by FS 6/7 recon-all in <subj_dir>/mri
#
#... |
a120a98dd0aa9005a51194d953d238cf9ec40504bf8747219c081dc8aeead16f | Shell | 2,003 | 45 | #!/bin/bash
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
echo "BRCA_stage"
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/early_integration_method/
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/early_integration_method/LR
mkdir ${root_path}/comparison_methods/Result/BRC... |
8b987c0e9c80742c60506611fd9ba327858b5b33e1cd6b8ea44a4093bfa2e66a | Shell | 2,009 | 36 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
c55e85fa60b2df6b2571dab9e495fc64dfc58fc36e4aa3abd2fd57bb103c228a | Shell | 2,010 | 38 | #!/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 $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0056_vis1_s... |
65b1054751eccb3bf147dc6fb1adbe596933d21fd40c827277250f50ac13794c | Shell | 2,014 | 83 | #!/usr/bin/env bash
# Takes as input two conda env files:
# * the first one is expected as output generated by cgat_conda_deps.sh
# * the second one is expected as output generated by "conda env export"
# The expected output is a new conda env file matching conda packages
# listed in the first file with the version n... |
2a8696ac775bd02bba3b35e4ccac258809c63e2ee0c51696b08c0a35771d1be3 | Shell | 2,017 | 65 | #!/bin/sh
cd /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper//Pathformer_code
python3 Pathformer_main.py \
--modal_all_path ../Result/plasma/modal_type_all.txt \
--modal_select_path ../Result/plasma/modal_type_all.txt \
--gene_all ../reference/gene_mRNA_cfRNA.txt \
--gene_select ../reference/Pathformer_sel... |
f96e7e47d3b02dcd46918238976a2f27abf8e87ae26d5b0492a62824be8cce09 | Shell | 2,018 | 93 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
TRNDIR=${TRNDIR:-$SCRIPT_DIR/../00_data/11_train_data}/01_rt_svd/
mkdir -p $TRNDIR... |
648db55cdd02f323ce59710339ce1ec0300e5602a48a72d3a7d1f852b06706d4 | Shell | 2,023 | 93 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
TRNDIR=${TRNDIR:-$SCRIPT_DIR/../00_data/11_train_data}/02_rt_rovir/
mkdir -p $TRND... |
65a557624bb189303a3dbbd4fe091dfa7e9c3b4e9f5604706bb5b9639746194e | Shell | 2,025 | 66 | #!/usr/bin/env bash
###############################################################################
#
# Clean up large files and directories after MAPP run.
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREA... |
2ec9232a08024ebec5372808309f53c9513c4c0c331146904cc661097991503c | Shell | 2,038 | 46 | #!/usr/bin/env bash
# definitions
origDir=/vols/Scratch/preclinicalMPM_scripts
workDir=/vols/Scratch/comparative_scripts/mouse_MPM_results
subjList="20210517_175914_AL2_MPM_1_1
20210604_181641_AL3_AL3_MPM_3_1_3
20210609_200948_AL5_MPM_1_3
20210607_192507_AL6_MPM_4_1_6
20210611_205425_AL7_MPM_2_1_3
20210402_231711_AL8... |
f884844681cd2b8b8e1832745e07a8d233f151a4dfc24024cd9ad51d4604abdb | Shell | 2,044 | 65 | #!/bin/sh
cd /apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/Pathformer_code
python3 Pathformer_main.py \
--modal_all_path ../Result/BRCA_stage/modal_type_all.txt \
--modal_select_path ../Result/BRCA_stage/modal_type_all.txt \
--gene_all ../reference/gene_all.txt \
--gene_select ../reference/Pathformer_sel... |
bb64501d701eb2c940e45574fe70eb03d0f8df7e9428dd8a2bc199e37f7a0682 | Shell | 2,056 | 73 | #!/usr/bin/env bash
###############################################################################
#
# Create snakemake report for the whole MAPP run.
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREATED: ... |
a0e7aa964bae7ba5c9d1b171c8fb818382968147444d71ad2675790823771cf9 | Shell | 2,058 | 52 | #!/bin/bash
#
# Pathways:
# BIDSderiv = folder where the processed fieldmaps need to be sent to
#number of subjects = folder names in BIDS
subjList="sub-01 sub-02 sub-03 sub-04 sub-05 sub-06 sub-07"
#conditions = sub-folders in BIDS
timeList="Pre_stim Post_stim_5min Post_stim_2h"
targetList="ontarget off... |
ef3564423ee54307a3cafb3f62d062a9bc267554406904a85be987a427e1c3ac | Shell | 2,071 | 54 | #!/usr/bin/env bash
# Wrapper script for running the ENCODE ATAC-seq pipeline
###
# working directory needs to be base directory (not src/)
# USAGE: src/atac-seq-human-wrapper.sh
###
set -eu
### VARIABLES TO SET ###
NUM_CORES=12
BATCH_PREFIX=batch1_20220710
GCS_BUCKET=my_bucket
ATAC_OUTPUT_DIR="gs://my_bucket/atac-s... |
42210f6fd098e106e653917d8a481797eaa3d09dd423ec92fb10fab68bf3b8fb | Shell | 2,082 | 45 | #!/bin/bash
# test.sh — End-to-end example pipeline for running FLEX, FLEX-cond-test, and FLEX-summ-h2
geno=gene # PLINK BED/BIM/FAM prefix for genotype data
cont_pheno=cont.pheno # Continuous phenotype file
bin_pheno=bin.pheno # Binary phenotype file
null_pheno=null.pheno ... |
ebf5432daea29f1ff6b5dd1ddef3e0bcdb5db366891a6cc458366ceeeece7077 | Shell | 2,112 | 26 | #!/bin/bash
#conda activate scrnaseq
module load cellranger/6.0
cellranger count --id=P251L1merged \
--transcriptome=/data/bioinformatics/referenceGenome/Drosophila_Melanogaster/Ensembl/dm6/Drosophila_melanogaster.genome \
--fastqs=/data/bioinformatics/projects/hassan2022/output/FC_... |
0bbbca0f84bcd042d5a55c9eb129699ae445628e0a2bbf5d3abee7a46bca9a1b | Shell | 2,127 | 51 | #! /bin/sh
# Last successfully run on Jan 12nd, 2018
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exist
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CH... |
a3038e610550cb1d092ab0ae4fae415a6bdc9199f7b586edb428c859bf4837ad | Shell | 2,135 | 57 | #!/bin/bash
# Deploys to kubernetes. Takes 2 args.
# arg1: environment, ie staging. This should match up with filename prefixes for lib/${arg1}.env.sh and k8s/${arg1}.yml.
# arg2: docker image tag to deploy. This argument is optional. If omitted, you will be prompted with a list of tags in GCR to select from.
# Example... |
f37c15a636155f7bd98eed0f1389ebef8a85825c1dc8f2b0e8013d0b0add634e | Shell | 2,158 | 29 | #!/bin/bash
# This script will perform Level 3 stats across social
# and nonsocial conditions in the ISTART Social Doors task
# for models containing covariates
# Ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindi... |
8bd1f8c2987d292196ab756c31a878110bc63a40e5d00fa6c4722108828d7955 | Shell | 2,165 | 53 | #
# Save TVFC estimates
#
# d2
python benchmarks/fmri/sim/train_models/save_TVFC_estimates.py d2 all N0400_T0200 correlation SVWP
python benchmarks/fmri/sim/train_models/save_TVFC_estimates.py d2 all N0400_T0200 correlation sFC
python benchmarks/fmri/sim/train_models/save_TVFC_estimates.py d2 LEOO N0400_T0200 correl... |
8a5e5e4a81459b985c9f38c08f7c16680fb93e7049e582645bbfddb28f637b5a | Shell | 2,167 | 55 | #!/usr/bin/env bash
# Build an optimal univariate (T1w only) brain midspace using ANTS.
# This will take from several hours to several days depending on the number of
# individual images, image dimensions and computing resources.
#
# SETUP:
#
# 1. Place all T1w .nii.gz images in a single directory.
# 2. Copy this scrip... |
5beaff52815f77999dd7a4ff7bd6f9318c44eef9d661d84fc897e3d799988733 | Shell | 2,169 | 43 | #
# Save TVFC estimates
#
python benchmarks/fmri/rs/HCP/train_models/save_TVFC_estimates.py d15 all correlation SVWP_joint
python benchmarks/fmri/rs/HCP/train_models/save_TVFC_estimates.py d15 all correlation sFC
python benchmarks/fmri/rs/HCP/train_models/save_TVFC_estimates.py d15 LEOO correlation SVWP_joint
python ... |
50593851b7ac6080073e4b56f7a584d32550b8d9bb615517caf784284f1a681d | Shell | 2,172 | 62 | #!/bin/bash
set -e
module load unstable git python python-dev py-notebook
echo "*******************************************************************************"
echo "SPACK_INSTALLED_HASH (steps) : " ${SPACK_INSTALLED_HASH}
echo "*******************************************************************************"
which ... |
3f3ed3afc8b3c3509cb695d606d1baa0b77984923ed41eabad86d69c66fbb636 | Shell | 2,175 | 55 | #!/bin/bash
# This script trains and tests ANNA16 (Python)
python
import pandas as pd
import numpy as np
from sklearn.metrics import mean_squared_error
from math import sqrt
from anna16 import CopyNumberPredictor
import warnings
warnings.filterwarnings("ignore")
performance = {}
path = "data/cv/datasets/kmer_splits"
... |
28d6141a230bc25064f8648974b8af566d7964625567153521ee4a296579cc0a | Shell | 2,182 | 45 | #ID for user's trait of interest. (Can be any string)
trait="BMI"
#path to the input GWAS summary stats files
traitFilePath="/project/ritchie21/personal/wbone/ColocQuiaL_test/test_runs_dir/BMI_ColocQuiaL_test/BMI_Pulit_data_rsID_ready.txt"
#column IDs from trait file
trait_A1col="Tested_Allele"
trait_A2col="Other_Allel... |
4499f68ed099f7a60b69f7dbbae60fa015e01ff4aa6183b005e8579dd59c6029 | Shell | 2,197 | 55 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/22_recos_t1/vol0084_vis1_m... |
1144662e407689e4f889373aff8495eb30bb69f9adb09c46578209c773290af9 | Shell | 2,205 | 69 | #!/bin/bash
# Create bilateral probabilistic labels from unilateral labels using precalculated mirror warp
#
# AUTHOR : Mike Tyszka
# PLACE : Caltech
# DATES : 2015-07-30 JMT From scratch
# 2016-03-25 JMT Separate calc and apply components of mirror warp
# 2016-03-31 JMT Update for new directory str... |
20d12e6c1c31c2f5a86da3d62f972b47b9753b9ac40c75e1b4dfcc8308361ef4 | Shell | 2,209 | 69 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N coloc_plots_caudate
#$ -o ./summary_caudate.log
#$ -e ./summary_caudate.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
... |
9b601a8366f5b6710db529da85a02d1e48faaf4eeb938fc08dd8d5105842da41 | Shell | 2,217 | 41 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in... |
992bda9e9317b791b72c84a4032dc2bb36bca9acf77916cfc2c2eeec692fa4c8 | Shell | 2,220 | 77 | #!/usr/bin/env bash
###############################################################################
#
# Download ATtRACT database and extract a clean set of hsa PWMs
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com... |
a60b12b8ece107d75fa94dd1db39875d9e4c07dc3aed57bdc74b7603bada53a1 | Shell | 2,223 | 75 | #!/usr/bin/env bash
CONTAINER_NAME=mysql_cromwell
FASTQ_RAW_DIR="gs://my_bucket/atac-seq/batch1_20220710/fastq_raw"
BASE_JSON="batch1_20220710_base.json"
# you need to have a service account with access to the life sciences API on the VM
REMOTE_KEY_FILE=~/.keys/service_account_key.json
# constants
JSON_DIR=json/
OUT_... |
b9b597d6d989a3b38f788a8a86e0ed099b21c9ac6b0b3fb531f2e988ea6e51e9 | Shell | 2,223 | 63 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is licensed under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with the
# License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... |
8687a83b40f61c0ad2e0a998444afd2c2be294df0ceaca25f6af6ce47338d784 | Shell | 2,236 | 30 | cd rcnn
mkdir results
#0.25
CUDA_VISIBLE_DEVICES=4 python rcnn.py ../../../multi_species/preprocessed/CeleganDrosophilaEcoli.actions.filtered.25.tsv -1 results/0.25_yeast_wvctc_rcnn_50_5.txt 3 50 150
CUDA_VISIBLE_DEVICES=4 python rcnn.py ../../../multi_species/preprocessed/CeleganDrosophilaEcoli.actions.filtered.25.ts... |
0879bae66200d7ed9dab24762df3c74c162ed8cf1100ef82adc147eca9bdc8e4 | Shell | 2,237 | 73 | #!/bin/bash
# Create a CIFTI dlabel file from a 4D probabilistic atlas in MNI152 space
#
# DEPENDENCIES:
# - HCP workbench installation
# - HCP Pipeline installation with HCPPIPEDIR set
# - FSL installation with FSLDIR set
#
# AUTHORS : Julien Dubois and Mike Tyszka
# PLACE : Caltech
# DATES : 2017-02-01 From Julie... |
af462143e30037ccb849d8e9de21b6a9fbffe95353712f72b94b328c7063c9de | Shell | 2,246 | 64 | #!/bin/bash
# Slurm Parameters
#SBATCH -p medium
#SBATCH --time 8:00:00
#SBATCH --job-name=neoloop
#SBATCH -o neoloop_%A.log
#SBATCH -e neoloop_%A.err
#SBATCH -n 1
#SBATCH -c 1
#SBATCH --mem 20G
#SBATCH -C scratch
#SBATCH --array=0-14
#THIS SCRIPT CAN PRODUCE ALL CNV/CNV-bw/SV/filtedSV/NEO-LOOP/NEOTADS/deleted or d... |
f418e84d5ce29a49bacfeb21e66ca57a25dface32a43a81cb82b4d2f5116bf3a | Shell | 2,255 | 88 | #!/usr/bin/env bash
# ============================
# Setup script for VANTAGE
# ============================
# ===== Configuration =====
VENV_NAME="venv_vantage"
REQUIRED_MAJOR="3"
REQUIRED_MINOR="12"
echo "Checking Python installation..."
# ===== Python candidates =====
PY_CANDIDATES=("python3.12" "python3" "pytho... |
70b2abccf4bae5c893da1a2652c0b16e75fa7e9057bd69cec52e75983d1cc51b | Shell | 2,271 | 55 | #!/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 $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/22_recos_t1/vol0084_vis1_m... |
d6cbb8b8b127cd127659fa2c28af8841e12eff0cf0b52519cada588708e4906a | Shell | 2,282 | 53 | #!/usr/bin/env bash
# Script: Rice_C.sh
# Reformat ice'd normalized Hi-C matrices.
# ./Rice_C.sh <ICED matrix file> <RAW Reference bed> <CellType>
[[ -f $1 ]] || { printf ' [ICED] file %s not found\n' $1 ; exit 0 ; }
[[ -f $2 ]] || { printf '[REFERENCE] file %s not found\n' $2 ; exit 0 ; }
# Make the outdir self-... |
783cdca5d1541f9ce048490dd286f9c48237e3e01f98e09bac368d3e5e298810 | Shell | 2,288 | 90 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# This scripts provides an example of user/artists recommendation on the
# Last.FM (http://www.lastfm.com) dataset
MO... |
da3111ec335142e27a641053d75a3874cff55311e001f196888cd5d4bb01132d | Shell | 2,293 | 65 | #!/bin/bash
set -eux
#Usage : src/croo.sh <list_of_atac-seq_workflow_ids> <GCP_PATH_to_atac_seq_pipeline_workflows_without_trailing_slash> <gcp-path-to-output-without-trailing-slash> >>croo_copy_jobs.txt
#Contributors : Archana Raja, Nicole Gay
if [ $# -lt 3 ]; then
echo "Usage: ./croo.sh [WORKFLOW_SUBMISSION_MAP] ... |
7f92a3e77727bea91a16adeb43f0abd24a9681dbf62ca7bfaf7f548df63e6735 | Shell | 2,296 | 65 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is licensed under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with the
# License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... |
180f3e8e65bfc88f5f4a3f5640baba3740c4af5b67a49083a5507ece8fd1b095 | Shell | 2,305 | 47 | #!/bin/bash
# Script to recursively search a root folder for files with a given extension and log their MD5 sum and relative path in a CSV file
# Usage: md5_checksum_listing.sh root_folder output_file file_extension
# Example: bash md5_checksum_listing.sh /labs/samenilab/data/physionet.org/files/challenge-2017/1.0.0/t... |
05067145043ae7db5c6efe9e2092d522012e299d60013fb9081c0311885bcb7c | Shell | 2,322 | 45 | #!/bin/bash
# #This script does the preprocessing on the structural scan (T1w.nii.gz), the T2-weighted single-band reference for the task fMRI scan (sbref_task.nii.gz)
#it also processed the fieldmaps from the magnitude image (fmap_mag.nii.gz) and phase difference image (fmap_phdif.nii.gz)
#Folder structure is
#${bi... |
4eae7628f2871b2613ec156afe7e0320fc3e714da97e3fa851186e429440592b | Shell | 2,333 | 61 | # To Start a GPU-interactive job:
# srun --nodes=1 --ntasks=1 --cpus-per-task=8 --gpus=1 --mem=100g --time=04:00:00 --pty bash -i
name=activ72h_B
rep=rep1
peak_name=${name}_${rep}
g2a_input=/mnt/BioAdHoc/Groups/RaoLab/Edahi/Projects/09.TimeCourse5hmC/ForFerhatGit/ghmc_to_abc/ABC_input
g2a_output_orig=/mnt/BioAdHoc/Gro... |
131b07a140b32988ab3b29e055724662aadf1890947499924cc4b100a85325ad | Shell | 2,338 | 65 | #!/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 $SCRIPT_DIR
RAWDIR=${RAWDIR:-../00_data/10_raw_data}
RAW=$(readlink -f $RAWDIR/rt_sa/vol0056_vis1)
WDIR=$(mktemp -d 2>/dev/null || ... |
ab8efde6819f04cade82dc42168bb5fea25f357c3f337124a0322600f733b265 | Shell | 2,344 | 94 | #!/bin/bash
# Write JSON files for ENCODE ATAC pipeline input
# Assumes that reads are paired-end
set -eu
if [ $# -lt 3 ]; then
echo "Usage: ./make_json.sh [JSON_BASE] [FASTQ_DIR] [JSON_DIR]"
echo
echo "Example: make_json.sh base.json /home/user/fastq jsons"
echo
echo "[JSON_BASE]: The base JSON file to us... |
54194ef268c60fb897bd428e7cbf2a9574b366fc758621596f7f59f039de5c98 | Shell | 2,367 | 70 | #!/bin/bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
# setting inputs and common variables
sub=$1
type=$2
task1=socialdoors # edit if necessary
task2=doors
sm=6 # edit if nece... |
1de0273577d14fbc7061e84fc71299d369e2091eef851fc0ff737945c2e6a694 | Shell | 2,379 | 64 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/../
download()
(
URL=$1
DST=$2
if [ ! -f "$DST" ] && [ ! -z "${DATA_ARCHIVE+x}" ] ; then
REPO_NAME=$(<meta/name... |
fe000f6fd29f23b9c263387327d928086226d85f39ce67cb2a23605d35fd3eb8 | Shell | 2,389 | 61 | #!/bin/bash
# Pathways:
#BIDSderiv = folder where the melodic single subjects are
#fix_dir = folder where fix is installed
#fix_training_data = folder where training data is located
#fix_dir=./fix
#fix_training_data=/fix/training_files/UKBiobank.RData
#number of subjects = folder names in BIDS
subjList="sub-01 sub-... |
10316f486dc278a2760693853863397b71d98582cae1227aaf5f17834327a4ea | Shell | 2,392 | 69 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request 4 CPUs
#$ -pe omp 3
#$ -m ea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=1:00:00
module load python3/3.8.10
module load pytorch/1.13.1
# # conda info -e
conda activate py3.8
export LD_LIBRARY_PATH=/share/pkg.7/miniconda/4.9.2/install/lib/
c... |
467d16d26b798d39bd3a9837bd8a5619f879f512172d94610ab629d83e358c3e | Shell | 2,400 | 48 | #ID for user's trait of interest. (Can be any string)
trait="BMI"
#path to the input GWAS summary stats files
traitFilePath="/project/voight_GWAS/wbone/PAD_and_CAD_Bivariate_scan/BMI_Pulit_data_rsID_ready.txt"
#column IDs from trait file
trait_A1col="Tested_Allele"
trait_A2col="Other_Allele"
trait_SNPcol="SNP"
trait_CH... |
0459185b231332ecea52231d367fb9f1f00c680f32345d86a0e514c333c911bd | Shell | 2,409 | 23 | #!/bin/bash
## New from Known
singularity exec ../../../singularity_containers/bernardo_article_analysis.sif bedtools getfasta -fi ../../references/Homo_sapiens.GRCh38_ERCC.fa -bed ../../data/processed/MEME/five_prime_splice_sites_nfk_12s.bed -s -name -fo ../../data/processed/MEME/five_prime_splice_sites_nfk_12s.fa
s... |
cacf48bc91a181f3a268d3327b2e2c0f2547b46c86ec7331a12a549be64467ef | Shell | 2,415 | 49 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in... |
db99512c4fbe8c8736906a110ad20b9c1693600baccb7f9026b20d151d0564c9 | Shell | 2,422 | 48 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in... |
880555dbc95708c28d2d72e12c8584cae526e439f520dceded98ed83512c9fbe | Shell | 2,428 | 80 | #!/bin/bash -euo pipefail
# The command loops through sarek results/VariantCalling directory and writes to
# the respective subdirectories.
# Run with sarek-2.7.2/singularity-images/nfcore-sarek-2.7.2.img
input_path=$1
threads=$2
ref_dir=igenomes_ref
if [[ $1 != *results/ ]]; then
echo "Error: You must provide a... |
1e60d0c47bb85aa184168a2d4da0e26aadde2378a678e7792c960dce51801eb3 | Shell | 2,438 | 92 | # Benchmark script to test rayx Execution Time.
# To run use chmod or bash or sh
# HELP
if [ "$1" == "-h" ]; then
echo "Benchmark script to test rayx Execution time."
echo "Usage: `basename $0` filename.rml number_of_trials"
echo " -h Print this message"
echo "args:"
echo "filename.rml: RML File name, make s... |
0d6f4213aceb3fdcdcc0abeffb69b287c03dbbe0129408c4532ef68a6fd07d6a | Shell | 2,458 | 82 | #!/bin/bash
input_mdapath=$1
ouput_dir=$2
samplerate=$3
geom_file=$4
# Run bandpass filter stage of Mountainsort
ml-run-process ephys.bandpass_filter \
--inputs timeseries:$input_mdapath \
--outputs timeseries_out:$ouput_dir/filt.mda \
--parameters samplerate:$samplerate freq_min:250 freq_max:5000
ml-run-process e... |
a884d856c9c26d34c36d8481d4f1f5bee8dac133c424da56881aae226440608e | Shell | 2,475 | 79 | #!/bin/bash
# Calculate the diffeomorphic warp required to map one hemisphere onto the other.
# Requires an initial reflection of images about the midsagittal plane followed by the
# diffeomorphic warping of the reflected to the unreflected image.
#
# This implementation requires both T1 and T2 contrasts for a multivar... |
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