sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
98c26a8fd9389c6679dcb7a850c3f94abb777956348af466b268927b4924c434 | Shell | 1,711 | 43 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
804d66ff10d52cde5040a6d7f88bb64422fd8b0cb5cb7ad997956fe991135792 | Shell | 1,716 | 36 | #!/usr/bin/bash
annotator=$1
thres=$2
# --taxonomy_predictions /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/vaevaeout/results_taxonomy_predictor.csv \
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/longread_taxonomy_2023.tsv \
# --cuda \
vamb \
--model vaevae \
--o... |
b859f328fcbd8419185b1bcb47d1dbc04f41e2379c1cee02c0e3a4e3fcba8289 | Shell | 1,716 | 35 | #!/usr/bin/bash
dataset=$1
run_id=$2
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${dataset}_taxonomy_2023.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/people/svekut/cami2_urog_out_32_667/results_taxonomy_predictor.csv
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${da... |
0e1f2dde97c486f97d6b35ff26983f02d6b026a771bc30aa93221d123bdd0111 | Shell | 1,720 | 60 | #!/bin/bash
# Ultralytics YOLO 🚀, GPL-3.0 license
# Download COCO 2017 dataset http://cocodataset.org
# Example usage: bash data/scripts/get_coco.sh
# parent
# ├── yolov5
# └── datasets
# └── coco ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_coco.sh --train --val --test --segments
if [ "$... |
5dbd35b35ba2adfe17759420c520395451ffbfb7c269cac87fda151f61c9590e | Shell | 1,725 | 36 | #!/usr/bin/bash
dataset=$1
annotator=$2
thres=$3
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${dataset}_taxonomy_2023.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/people/svekut/cami2_urog_out_32_667/results_taxonomy_predictor.csv
# --taxonomy /home/projects/cpr_10006/people/svekut... |
aaadb331ea90fc9c31c70c84c103340f44a07e9b4a8de4457e62efb6ac3449d2 | Shell | 1,726 | 17 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/intron_matcher/AFTER/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/intron_matcher/AFTER/
echo ../../Intron-Matcher/build/intron_ma... |
e3ead80d78909e2f01c835989c0fe82c0815f80d60369d6c384e3c917d5832d4 | Shell | 1,729 | 50 | #!/usr/bin/env bash
# Get modules for major cell types using scdemon:
# TODO: At some point, put up as an array job instead
# ---------------------------------------------------
pconf -t DEVTRAJ -s multiRegion -g b37
MBDIR=${SBINDIR}/modules
conda activate scanpy_env
# Overall runs, with defaults (5% cut, z=4.5)
# -... |
14b95392a71ab1c447bb06d497d1fd693668e5f07a462ee5f8ad42e1c2bb7023 | Shell | 1,732 | 33 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
#... |
baf378bebb3d088449cda4c163fd23b2ae5fc46508cbbf2d055f4013dfcbd96d | Shell | 1,738 | 25 | # for OUTPUTFILE in "./dataset/pos" "./dataset/neg_1" "./dataset/neg_random"
for OUTPUTFILE in "/ccb/cybertron/khchao/splam-analysis-results/train/results/tool_benchmark/"
do
for TARGET in "splam" "spliceai"
# for TARGET in "spliceai"
do
if [[ $TARGET == "splam" ]]
then
echo "bed... |
b6aea81e420539c5fcd011da802a3225857be8c67e7a7caf377891d9778ec92b | Shell | 1,743 | 55 | #!/bin/bash -e
if [ $# -ne 4 ]; then
echo "usage v1: rampage_idr.sh <peaks_a_bed> <peaks_b_bed> <chrom_sizes> <idr_root>"
echo "Compares two sets of peaks and generates an Irreproducible Discovery Rate report. Is independent of DX and encodeD."
exit -1;
fi
peaks_a_bed=$1 # First peaks .bed file to compar... |
df89f04b68f24ccc97f41bb7a0a4cabe980bd74553f1cb09b623ab64e92616c4 | Shell | 1,750 | 39 | #!/usr/bin/bash
dataset=$1
run_id=$2
keyword=$3
# --taxonomy /home/projects/cpr_10006/people/svekut/mmseq2/${dataset}_taxonomy_2023.tsv \
# --taxonomy_predictions /home/projects/cpr_10006/people/svekut/cami2_urog_out_32_667/results_taxonomy_predictor.csv
# --taxonomy /home/projects/cpr_10006/people/svekut/... |
8a6730dc2b67e7365a1e2dd115357ff02b6bfb30ebb649da7944052d6f544dde | Shell | 1,752 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
4dbdc4ad454766a78b4f74ef7c4c239655b3082649131082872f08f75f9da90e | Shell | 1,753 | 39 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
c4bb1ab7f3ede094cd1560cd231396fbf6440ddd86f740ec85656d3b81272b26 | Shell | 1,755 | 60 | #!/bin/bash
#
# Current date and time.
#
NOW=`date '+%Y%m%d.%H%M%S'`
#
# Path to the Nextflow processing run configuration file.
#
PWD=`pwd`
CONFIG_FILE="$PWD/experiment.config"
#
# Nextflow executable and pipeline script locations.
#
NEXTFLOW="/net/trapnell/vol1/home/readdf/nextflow"
NF_ANALYZE="/net/trapnell/vol1/... |
26090407a2daabf085b2081f7bfd259b3a158e00c70cac5b9b075f80f24b8282 | Shell | 1,761 | 37 | #!/bin/bash
#SBATCH -c 1
#SBATCH -p normal
#SBATCH --mem=12g
#SBATCH --time=12:00:00
source /com/extra/ucsc/2015-04-21/load.sh
# bedtools v2.27.1 fails due to a bug in BEDtools merge (not reporting strand after merge)
source /com/extra/bedtools/2.25.0/load.sh
# change directory to the local scratch-directory, and ru... |
7294043a80fab2f2a711b993a19a0d7c237ca1108c55005e0c2d28e0fb63c267 | Shell | 1,767 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=64000 # Memory pool for all cores (see also... |
d855365179f3af26041555be858606deecee55f96c78e4cefdac2e15d06ef543 | Shell | 1,767 | 19 | #!/bin/bash
set -euxo pipefail
#HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
./hippunfold/run.py test_data/bids_singleT2w test_out participant -np --modality T2w
./hippunfold/run.py test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
./hippunfold/run.py test_data/bids_singleT2w test_out part... |
a54d89daf002008b23fbe8b3561903002859696ed2c656a8127a8d5e8f19ccd4 | Shell | 1,768 | 56 | #!/bin/bash
#SBATCH -J mastwx_res
#SBATCH -N 1
#SBATCH -n 32
#SBATCH -p kellis
#SBATCH --time=48:00:00
#SBATCH --mem=90G
#SBATCH --output=/home/cboix/data/DEVTRAJ/db/out/mastwx_res_%j.log
#SBATCH --export=ALL
#SBATCH --requeue
#SBATCH --array=2-668
# Run as:
# sbatch --time=48:00:00 --array=1-667 $SBINDIR/diffe... |
9a5961d3ffb3c50c5403aa8edb45e3d72e7903aada4018244993520acc4d78a9 | Shell | 1,770 | 39 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=144:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1... |
0d41c4008067bcff7798869dc48a534961b0d547d1344d448493eee49a7cc835 | Shell | 1,773 | 34 | #!/usr/bin/bash
annotator=$1
thres=$2
# --taxonomy_predictions /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/vaevaeout/results_taxonomy_predictor.csv \
vamb bin taxvamb \
--outdir /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/vaevae_${annotator}_predictor_${thres} \
--f... |
f45107c15142d2f82b19d55debf9c3e942a55e0f7ad63e4307ddba7ae8bf9186 | Shell | 1,774 | 31 | #!/bin/csh -f
set top_dir = top_dir/
cd ${top_dir}/ClusterOverlapMap/3dMerge
set filename = 'all70_phononeighden_clusters_70subj_6ghits'
# Phonological Neighborhood Density individual participant cluster heatmap, just the cerebellum
# Trying to create a cluster overlap map wherein at least 6 subjects have to have shar... |
b1160ad66cf2206f97646a2ac05dc6815e71789194b87b6d243813e3e37ad497 | Shell | 1,779 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
3918279b2e2471e801163edb5059dd806fef4400699fe71716517ede2c4ceb77 | Shell | 1,780 | 36 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=00:10:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
b2ecfabe26a5ba25cfff8147f0131f55e774712c048896182f9d7f817b5867d5 | Shell | 1,781 | 31 | #!/bin/csh -f
set top_dir = top_dir/
cd ${top_dir}/ClusterOverlapMap/3dMerge
set filename = 'all71_lexicalfrequency_clusters_71subj_6ghits'
# Lexical Frequency individual participant cluster heatmap, just the cerebellum
# Trying to create a cluster overlap map wherein at least 6 subjects have to have shared voxels for... |
41a41e846fdf9edbbac31610c143e682acbca82e033deb24e7f53b534b5bcc36 | Shell | 1,793 | 55 | #!/bin/bash
set -e
# shellcheck disable=SC2139
alias pip="$HOME/anaconda3/bin/pip"
sudo apt-get update \
&& sudo apt-get install -y gcc \
cmake \
libgtk2.0-dev \
libgl1-mesa-dev \
libgl1-mesa-glx \
libosmesa6 \
libosmesa6-dev \
libglfw3 \
unzip \
... |
9f53c0e28804bf2b9fcc3ce8e8a236351c5651e7da3373dbd316345ce295ce05 | Shell | 1,799 | 59 | #!/bin/bash
#
# Path to the Nextflow processing run configuration file.
#
WORKING_DIR="/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_01_11_Dana_and_HM11_nobackup"
CONFIG_FILE="$WORKING_DIR/experiment.config"
#
module load java/1.8.0
cd $WORKING_DIR
# cp /net/trapnell/vol1/home/readdf/trapLabDir/fib... |
20c362f8932480a0b236e53e5ca019d392456a1f2d2d23d9eec9bf44fd62dc54 | Shell | 1,802 | 52 | #!/bin/bash -e
if [ $# -lt 4 ] || [ $# -gt 5 ]; then
echo "usage v1: srna_index.sh <ref_fasta_gz> <annotation_gtf_gz> <annotation_version> <genome> [<gender>]"
echo "Creates STAR index of reference genome and annotation for small-RNA-seq. Is independent of DX and encodeD."
exit -1;
fi
ref_fasta_gz=$1 # Re... |
732c67ba103b1a6fd3ca6d79492c56b9a7642a572dc0bcd2760b7ea9947020b0 | Shell | 1,805 | 48 | #!/bin/bash
# SpinalLearning_2020_MotionOutliers is the helper function you will need here.
#1. find motion outliers in mocoed blocks
echo "detecting motion outliers for refined moco, CombinedRuns"
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%0... |
1eade48a85dc151a3158149f9e4ae81ef45154c9e71db4e7a510d744f3b4b77c | Shell | 1,807 | 59 | #!/bin/bash
source 00_global_variables.sh
inDelimiter=tab
SelectedColumns='SNP MAF A1 A2 Effect SE Pval'
RenamedColumns='SNP MAF A1 A2 EFFECT SE P'
outDelimiter=tab
outFileDeco=.REFORMAT4ldsc.GWAS
outExtension=txt
outDIR=./reformatted/
mkdir -p ${outDIR}
for i in ${!Phenotypes[@]}; do
phenotype=${Phenotypes[$i]}... |
5dc61ad830ed71fe80e7ff34740deaece2de0c511cfe0dbddf4ea4429606a3b5 | Shell | 1,815 | 15 | #!/bin/csh -f
# Maps the cluster overlaps between individual cluster masks for lexical frequency and phonological neighborhood density
# FOR EACH PERSON
# The masks are thresholded at an individual level of: p <0.01, alpha of < 0.05, and cluster threshold of 77.6
# Removed 12 participants because they either: had no s... |
a9a119a0437ee4bfe968ce3f5c671a740ea60cf80c361287c04119cc55dbfec4 | Shell | 1,815 | 79 | #!/bin/bash
# Performs QC on a non-RD metadata matrix (e.g. PE/SR/RD) generated by module 00
set -e
#Usage statement
usage(){
cat <<EOF
usage: nonRD_matrix_QC.sh [-h] [-d DISTANCE] MATRIX GENOME OUTFILE
Performs QC on a PE, SR, or BAF metadata matrix
Positional arguments:
MATRIX full path to matrix to be QCed... |
3dea6ccea47b29514a2925c6bc40f7a8540b7b5d657443a0a1615a9a81891100 | Shell | 1,833 | 48 | #!/bin/bash
# 02_ExtractStatsDHR.sh
#on subject level we need:
#peak zstat & cope, #avg zstat & cope, all values in respective ROI zstat & cope
#rois:only c6, dh left, ventral horn right and respective dilated version
#we dont need group level extraction as this code will only check for changes in reliability, not sp... |
727d5293d20a074e11dab262f11646fbf6d39347dec26fdb5ff098b4a7a809ac | Shell | 1,833 | 37 | #!/bin/bash
set -ex
# Delete the existing bazel and replace it with bazelisk.
powershell ci/ray_ci/windows/install_bazelisk.ps1
# Install uv
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/0.13.4/install.ps1 | iex"
conda init
# TODO(ci): Remove once conda fixes the splitext bug in delete.py (conda/c... |
558eeb59f732463d0b4b166bda9933655902c0fe53ff960745d69c396b586814 | Shell | 1,835 | 54 | #!/bin/bash
set -eu -o pipefail
# Filter input $VCF by passing its records through $RECORDS_FILTER_CMD, keeping the header intact
# Store the result in file named $FILTERED_VCF_NAME
# #### IMPORTANT NOTE ####
# If using a filter command that may return non-zero in normal operation (e.g. grep returning no records)
# y... |
09eeae0e0304bf78c61e11544f8b887f86dfa76abdbefa826eb184adb6e96c42 | Shell | 1,837 | 25 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/chess/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord... |
c008daca18e941a034c02c32a32fb0c1f82d33cb166d0272bc4b19ad7cd711f2 | Shell | 1,842 | 47 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
6adf4d84451bb8c8779dfaec30c3ffee46f019e9a04d5effa8866050fcd9e82a | Shell | 1,844 | 41 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=1:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
fa16b21cf5b39b82b477f28f4f4de0a30b0396c6887a0c25b172ef6ed4bbff55 | Shell | 1,853 | 51 | #run SKATO for genes
#variant group directory name
groupdir=PTV.01NA_I.1;
R_file=/mnt/analysis-psp/users/timchang/v3/pc/2211/code/R/SKAT/run_gene.Rscript;
bed_dir=/mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/hwe/id/plink/;
bed_head=r3.bm.;
bed_tail=.PspNhwCon.id;
dat_dir=/mnt/analysis-psp/users/timch... |
9135be1dda1f82d090b3723cbdb0966d3f6f2c3faa848c8d2c6337042da16a4c | Shell | 1,855 | 55 | #!/bin/bash -e
if [ $# -ne 6 ]; then
echo "usage v1: lrna_rsem_quantification.sh <rsem_index.tgz> <anno_bam> <paired_end> <read_strand> <rnd_seed> <ncpus>"
echo "Align single-end reads with STAR. Is independent of DX and encodeD."
exit -1;
fi
rsem_index_tgz=$1 # RSEM Index archive.
anno_bam=$2 # ... |
17fb180008fb8ab6340af74118e6bd7f2d21e97233b8efe712e17ec98ca51134 | Shell | 1,862 | 48 | #!/bin/bash
# 02_ExtractStatsDHR.sh
#on subject level we need:
#peak zstat & cope, #avg zstat & cope, all values in respective ROI zstat & cope
#rois:only c6, dh left, ventral horn right and respective dilated version
#we dont need group level extraction as this code will only check for changes in reliability, not sp... |
ed01f5f2c85901509b6b767c71ee7208ed2a0ef63015cc9f681d4bb494ed51fc | Shell | 1,862 | 48 | #!/bin/bash
# small-rna-signals.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.2a)
#(cd STAR; make)
#wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.1.0.tar.gz
# If a... |
04923f20c3107f7cea956786365bd62837142a353090d77c3cd86111f415fde8 | Shell | 1,867 | 48 | #!/bin/bash
# bam-to-bigwig-stranded.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.1.0.tar.gz
#... |
a7b9ae05e337c592a04f8c955e07b2de39cf6ab633c3b15a288f3ab6d2f7c564 | Shell | 1,872 | 49 | #!/usr/bin/env bash
# SETUP EXPERIMENT DIRECTORIES ----------------------------------------------
# Prepare experiment directories with necessary input files for DeepRVAT running
# Replace `[path_to_deeprvat]` with the path to your clone of the repository.
# Activate your virt-env before running script. i.e. $ mamba a... |
c49d6b5288047af2fd7f16d4db57532eb1bf50a04aee75723dfd628149557777 | Shell | 1,873 | 54 | #Main pipeline steps for rare SNV/InDel analysis
#see subdirectories for code used
##Processing##
#==biallelic
#norm indel, annotate. (note set missing DP<10 or GQ<20 by Wan-Ping)
qsub /mnt/analysis-psp/users/timchang/v3/pc/2211/code/bcftools/sampNormAnn.sh
#==multiallelic
#psp/con, remove mono
qsub /mnt/analysis-psp... |
b28b53a94faec01fe48e1a41e17a026f488e7588ec04392cba470744cf6a61e4 | Shell | 1,876 | 50 | #!/bin/bash
############################### subject ROI loop script ###################################
# Purpose: Create mask for individual subjects based on individual brain size and register that mask to individual subject space.
# Prior to running script, point masks should be created based on desired coordina... |
e5c660177c139b60841fa19144b3ce8cc09e54e6585ea8205b4c4884921b6d01 | Shell | 1,878 | 32 | #!/bin/bash
##-------------------------------------------------------------------------
#************************************* Run TappAS on Knight
ISO_DIFF_DIR=/gpfs/mrc0/projects/Research_Project-MRC148213/sl693/rTg4510/A_IsoSeq_Whole/3_differential/1_Input/A_IsoSeq_solo
HYBRID_DIFF_DIR=/gpfs/mrc0/projects/Research... |
0db1d6bd97502acc784ef02a038b0b2f34512f258f44d8659aa64cd1fe951c87 | Shell | 1,883 | 33 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=128000 # Memory pool for all cores (see als... |
ed2b4e2ffb22c71a7c0d0ba467c6bd23e82b10257ad685ab25d78f3a311b46a6 | Shell | 1,893 | 74 | #!/bin/bash
# file: update-mak.sh
# description: Helper script to update Makefile.mak
# author: Andrea Vedaldi
# AUTORIGHTS
# This script updates Makefile.mak based on the current source tree
# and version in vl/generic.h. It saves the new version to
# Makefile.mak.new.
function make
{
# sed below re... |
446ee8ebf4a27647fa5e58aad184b7c8d6486c90d3f746d042ecff082d667f6f | Shell | 1,895 | 37 | # pull out RSIDs and p-values from some full studies that I downloaded (each of which has its own unique format)
# Note that I am trying to get N in some cases and for one or two studies it is a little tricky but fine for most part
module unload python
module load python/2.7.3
mkdir -p ldsc_sumstats_files
# N taken f... |
6ffeb0c083d7086ec3bca48a337bbf622b0bddb3b015d7db0baa2b194b22974d | Shell | 1,909 | 48 | #!/bin/bash
# SpinalLearning_2020_MotionOutliers is the helper function you will need here.
#1. find motion outliers in mocoed blocks
echo "detecting motion outliers for refined moco, reliability run"
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub ... |
ad9c30754ed6f38aa73b3651704e74bfd4437b36ab89e3cb44c89fe1e3129455 | Shell | 1,914 | 51 | #!/bin/bash -l
# run this script from adrd_tool/
conda activate adrd
pip install .
# install the package
# cd adrd_tool
# pip install -e .
# define the variables
prefix="."
data_path="${prefix}/data/training_cohorts/new_nacc_revised_selection.csv"
train_path="${prefix}/data/train_vld_test_split_updated/demo_train.c... |
c9291efbea99ae313c730c849c55e368ca7ae9862eca6e910ec9a8d19d6c3af7 | Shell | 1,923 | 46 | #!/bin/bash
#######################################################################################
#RNA QuantSeq Analysis: https://www.lexogen.com/quantseq-data-analysis/
#######################################################################################
#install if don't have:
#http://bioinf.wehi.edu.au/feature... |
351fe77454c27e752560400b9a995e83176879586d7d052a65d5be45784590c7 | Shell | 1,929 | 25 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/gencode/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoo... |
6cc481e1cfcc04d092c6d65fe85b3a1aa17e5f73518e01a8949c7ae7fdea1503 | Shell | 1,932 | 62 | #!/bin/bash
# registers the current experiment as a job to the OAR scheduler
##########################
# Parameters
NUM_PROCESSES=$EU_PRJ_GRICAD_DEFAULT_NUM_PROCESSES
WALLTIME=$EU_PRJ_GRICAD_DEFAULT_WALLTIME
PROJECT=$EU_PRJ_GRICAD_DEFAULT_PROJECT
RUN_REPETITION_SCRIPT=$EU_PRJ_DEFAULT_RUN_REPETITION_SCRIPT
ARGUMENTS... |
452b3ebf11ae210975074b653068056b0bf930f669017efcb8265eb7b4d3ae7f | Shell | 1,934 | 68 | #!/bin/bash
#-------------------------------------------------------------------------------
# This script performs a test of the program a impute-md-som.py
# in a Linux environment.
#
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Recu... |
8585d771840bded4a7d697619e46b9439acebdbb1e72ff0f17e23058bd80c4c2 | Shell | 1,936 | 71 | #!/bin/bash
set -exuo pipefail
# Host user UID/GID
HOST_UID=${HOST_UID:-$(id -u)}
HOST_GID=${HOST_GID:-$(id -g)}
if [ "$EUID" -eq 0 ]; then
# Install sudo
yum -y install sudo
# Create group and user
groupadd -g "$HOST_GID" builduser
useradd -m -u "$HOST_UID" -g "$HOST_GID" -d /ray builduser
# Give sud... |
45e8440b79bb2c04fbb904d8c957500298933263245e3978977ce2d658a465fd | Shell | 1,941 | 46 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
e5b61461ae71a5bfc09a28a1de2c5bc5a3095a7ac6290e60a5efeef032ba5416 | Shell | 1,946 | 33 |
/usr/bin/bowtie2-build -f data/ref/female.hg19.fa,data/ref/ENCFF001RTP.fasta data/female.spikeins.hg19
#- /archive/TGCapps_data/bowtie2_indexes/male.spikeins.hg19
#bowtie2-build -f /path/to/male.hg19.fa,/path/to/human_spike_ins.fa /archive/TGCapps_data/bowtie2_indexes/male.spikeins.hg19
#Generate transcriptome ... |
7bcb8d2b30e312b2ad75d2c8b6a6f9f95868d137fa0d7c455436754a130b225c | Shell | 1,958 | 58 | #run SKAT by module
#choose a group
groupdir=PTV.01NA_I.1
R_file=/mnt/analysis-psp/users/timchang/v3/pc/2211/code/R/SKAT/run_mod.Rscript;
bed_dir=/mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/hwe/id/plink/${groupdir}/;
bed_head=r3.bm.chr;
chr='ALLauto'; #used for weight, nonbeta
bed_tail=.PspNhwCon.id... |
6ba282edb0f26205cbfb605d44c65669379118fd8aa2380e8aac51f0edb8a077 | Shell | 1,959 | 24 | #!/bin/tcsh -f
# Calculates the cluster overlaps between the Lexical Frequency AmpMod Cluster 1 (832 voxels; left cerebellum VII/Crus II) and the Phonological Neighborhood Density Cluster 2 (64 voxels; left cerebellum crus II)
# The masks are thresholded at: p <0.001, alpha of < 0.01, and cluster threshold of 31.5
# Th... |
b2d42d7268ba2e40b8415f99bc6dfed8ca5495ad96b1c0bf523f2e4324ca8387 | Shell | 1,960 | 46 | #!/usr/bin/env bash
set -e
set -x
cd "$(dirname "$0")"
(cd .. && bazel build //java:all_tests_bin_deploy.jar)
function generate_one()
{
file=${2//./_}.h
javac -h ./ "$1" -classpath ../bazel-bin/java/all_tests_bin_deploy.jar -d runtime/target/
clang-format -i "$file"
cat <<EOF > ../src/ray/core_worker/lib/j... |
5d1c3086d5f9f73310621261136042b4b1c9f50cc488212171ff4f7750c66e3b | Shell | 1,969 | 67 | #!/bin/bash
#
# Current date and time.
#
NOW=`date '+%Y%m%d.%H%M%S'`
#
# Path to the Nextflow processing run configuration file.
#
# PWD=`pwd`
PWD="/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_03_24_reprocessHeartAlone_nobackup"
CONFIG_FILE="$PWD/experiment.config"
#
# Nextflow executable and pipeli... |
d27a19d7df96dd19e41b4761a850a16d9ce48b500d64bd1c4f79f651f5ea14c4 | Shell | 1,969 | 24 | #!/bin/tcsh -f
# Calculates the cluster overlaps between the Lexical Frequency AmpMod Cluster 2 (606 voxels; RIGHT cerebellum VII/Crus II) and the Phonological Neighborhood Density Cluster 1 (404 voxels; RIGHT cerebellum crus II)
# The masks are thresholded at: p <0.001, alpha of < 0.01, and cluster threshold of 31.5
#... |
0e25966cd45299e062d38283b9f1432b95264a168cf541381dc102369ae41f49 | Shell | 1,979 | 89 | #!/bin/bash
# Wrapper to manage external SV benchmarking plotting from output tarball
set -e
###USAGE
usage(){
cat <<EOF
usage: plotQC_external_benchmarking.helper.sh [-h] TARBALL PREFIX
Wrapper to manage external SV benchmarking plotting from output tarball
Positional arguments:
TARBALL .tar.gz file co... |
2c9e3449aca7304331ac738c6d3d1701a16665f34b093fe0fe3d42dd5210e0a0 | Shell | 1,984 | 29 | #!/bin/csh -f
set top_dir = top_dir/
foreach subject(S0056INA1 S0105LIA1 S0125HAN1 S0162JRG1 S0212QLT1 S0313QWR1 S0522GSR1 S0706OPY1 S0717JHH1 S0734IDQ1 S0776SSB1 S0835TAV1 S0984XGH1 S1747WTT1 S2104WGB1 S2234RGC1 S2236QMA1 S2309MVT1 S2329JLY1 S2432UIE1 S2470AHE1 S2594GTY1 S2662UVC1 S2686ROL1 S2845UBH1 S2871WKK1 S3027... |
bec07855e448cd75ac467f388de3dc5257b2f89d35f5a87f829aa0560b3694c7 | Shell | 2,010 | 12 | sudo -u rstudio Rscript -e "setwd('/home/rstudio')" -e "rmarkdown::render('S1_CustomArraySequences.R')" 2>&1 | tee logs/S1_CustomArraySequences_runLog.txt &
wait; sudo -u rstudio Rscript -e "setwd('/home/rstudio')" -e "rmarkdown::render('S2_AAV-lib_libraryExtraction.R')" 2>&1 | tee logs/S2_AAV-lib_libraryExtraction_run... |
ec9c1f69bb1bdadaa33b2ee024527e8a86c9b830cce12679c877be23de8ac299 | Shell | 2,012 | 43 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
1c71de044770533406ca7b39a27ca599a65480a4e1bb9b7e95cbd6152400e95f | Shell | 2,025 | 59 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
cd3f44e5f28df7ef60f6259fc56db58aea4331b318de8643dc6346b71b68c454 | Shell | 2,025 | 25 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/gffcompare/refseq_ucsc/
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedB... |
2d15bd4e8443c68825cdf01bf4811f88d70ef5b28a972b44f413bc102d27030f | Shell | 2,031 | 72 | #!/bin/bash
set -euo pipefail
set -x
# TODO(#54047): Python 3.13 is skipped due to the bug
# we should re-enable it when the bug is fixed.
PYTHON_VERSIONS=("3.10" "3.11" "3.12")
BAZELISK_VERSION="v1.16.0"
# Sets RAY_VERSION and RAY_COMMIT
source .buildkite/release-automation/set-ray-version.sh
install_bazel() {
... |
e917d5c6b507d4dbc977826ee16557595bf5a26bf78b8c00798f42d53fe2a3a8 | Shell | 2,033 | 68 | #!/usr/bin/env bash
set -Eeuo pipefail
#######################################################################
# conda environment
#######################################################################
__conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)"
eval "$__conda_setup"
unset __conda_setup
###########... |
f63eddc996340e52d5a966330f13958cd5c9c0dce1fc998aa8a293ae1b3e686e | Shell | 2,034 | 99 | #!/bin/sh
USERNAME=$1
CONDA_ENV=$2
WHEEL=$3
RAY_HEAD_IP=$4
TYPE=$5
echo "Installing wheel..."
sudo -u "$USERNAME" -i /bin/bash -l -c "conda init bash"
sudo -u "$USERNAME" -i /bin/bash -l -c "conda activate $CONDA_ENV; pip install $WHEEL"
echo "Setting up service scripts..."
cat > /home/"$USERNAME"/ray-head.sh << EOM... |
a9767427a93d5fb410bfa60c332bfe0630a9669d213d0a1ff985cebb11343228 | Shell | 2,037 | 42 | #This script use a container to do automated tumor segmention of multi-contrast MRI images
#It operates on an input folder (one subject) that contains four MRI images
# cpu or GPU can be used. Details as follows:
#######################################
## set your input folder containing four Nifty files, with the f... |
69e04cbead4c1dab508077b749f0a088a422577235d7161ac411faf284f9d476 | Shell | 2,038 | 49 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
56ab1537880602dd2e2e53370528bffb9a42ebe777e058a53c4767ab98037c5e | Shell | 2,042 | 54 | #!/bin/bash
#######################################################################################
#RNA QuantSeq Analysis: https://www.lexogen.com/quantseq-data-analysis/
#######################################################################################
#install STAR
#https://github.com/alexdobin/STAR
#git clo... |
20a61a5ff234d700e9131cddd9161f635baa1714e4895fa45b705d1692669bc4 | Shell | 2,045 | 73 | #!/usr/bin/env bash
set -eu
set -o pipefail
PYTORCH_VERSION=${PYTORCH_VERSION:-""}
PYTHON_VERSION="3.13"
TWINE_VERSION=">3,<4.0.0dev"
CONDA_ENV="skorch-deploy"
if [[ $# -gt 1 ]] || [[ $1 != "live" && $1 != "stage" ]]; then
echo "Usage $0 [live|stage]" >&2
exit 1
fi
if [ -z "$PYTORCH_VERSION" ]; then
echo "Set a P... |
192af1a4400aa5cadafc2bc0dfd253bb0d50d759446f1cafd01d3b2c9ea309c8 | Shell | 2,056 | 68 | #!/usr/bin/env bash
set -Eeuo pipefail
#######################################################################
# conda environment
#######################################################################
__conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)"
eval "$__conda_setup"
unset __conda_setup
###########... |
26e4454748e77865b2293aa4e86f4f7c21eee9136c3e967e136c1f5514e6198a | Shell | 2,056 | 23 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/intron_matcher
mkdir ../results/polyA_STAR/$sample.bamAligned.sortedByCoord.out/intron_matcher
echo mkdir ../results/polyA_STAR/$sample.bamAligned.sor... |
9509c6f088ccdbb83d2da3efc5f527445e6d9e371fafdeef42602b813c2c46e4 | Shell | 2,056 | 60 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
288932c013c3c582904983db7751ec6141a9ab405feae8935e9557ed4bff43d9 | Shell | 2,061 | 46 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
ccddfaaaae0568d9e3e9165a8dc3e4f89b398618b3c15b954b273f4d3375d96f | Shell | 2,069 | 49 | #!/bin/bash
# 06_Normalization.sh
# What shall be done?
#normalization of T2w can be found in github/pain-reliability-spinalcord/1_preprocessing/06_Normalization.sh first part, no need to repeat here :)
normalize_epi=1
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
... |
411bea3a2239ae266233419321a19ad68a55b5715eec72ee0644b8c6c224634c | Shell | 2,075 | 68 | #!/usr/bin/env bash
set -Eeuo pipefail
#######################################################################
# conda environment
#######################################################################
__conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)"
eval "$__conda_setup"
unset __conda_setup
###########... |
7599efb4f6e4fc8f0958d896910889f495f63b29272f85e3f8d6a1f678ea9dd2 | Shell | 2,076 | 42 | geneList="fp_transcript_all_gene.txt"
geneID=( $(cut -d ',' -f1 ${geneList} ) )
genotype="R57C10_1"
mkdir "190919_Neuro_Glia/all_transcript_new_${genotype}"
for id in ${geneID[@]}
do
echo "fp-transcript -o 190919_Neuro_Glia/all_transcript_new_${genotype}/${id}.txt -b 190919_Neuro_Glia/genome/dm6_ensemble.bed -a 1909... |
bb187990b9174691d3ebad46f1325d1b4eb3441e0ebbd2b9ae8b97dc9e8d6387 | Shell | 2,076 | 43 | #SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=0:10:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 # specify num... |
7d3b2b57a748cb57bb801a313725fe265ec4bc37b5fdbb809841ef3fc3424c26 | Shell | 2,081 | 52 | #!/bin/bash
set -Ceu
outdir=$(mktemp -d)
gpu="$1"
storage="sqlite:///${outdir}/tmp.db"
# optuna/dqn_obs1d/NopPruner
study="optuna-pfrl-test-nop"
optuna create-study --study-name "${study}" --storage "${storage}" --direction maximize
python examples/optuna/optuna_dqn_obs1d.py \
--env "CartPole-v0" \
--optuna-st... |
1d267328b211567e73b25137c8cb7411376f4dd495d36c3b886ec9a9a34b0ece | Shell | 2,102 | 57 | #!/bin/bash
# comp-signals-se 0.0.2
#set -x
#set +e
main() {
echo "*****"
echo "* Running: comp-signals-se.sh"
echo "* Using: awk, tee, alexAwkBg.sh"
echo "*****"
# TODO: at some point the bam-to-bw scripts will stop uploading the bedGraphs.
# When that happens, this compare routine can... |
7b2a15360970898d89107a707a222db5b23c9358b0371f11a559de0f5892d54a | Shell | 2,109 | 49 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
de1ae8d5da1fb1c35b02415cf6b4c7a384aa5aa20ac132a06cd2db8e43677dde | Shell | 2,115 | 54 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
885ca47f71409bd3805f4d39baaa21e40213d643b447184e40cbd4fa701230f7 | Shell | 2,117 | 90 | #!/bin/bash
# Performs QC on an RD metadata matrix generated by module 00
set -e
#Usage statement
usage(){
cat <<EOF
usage: RD_matrix_QC.sh [-h] [-d DISTANCE] MATRIX GENOME OUTFILE
Performs QC on an RD metadata matrix
Positional arguments:
MATRIX full path to matrix to be QCed
GENOME full path to genome f... |
aab07a6b16682a0368e34c3693c1ad5009a7b8a89f19177d8c7e0ba65ad183c9 | Shell | 2,125 | 79 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Evaluate flashed reconstructions with MS-SSIM and LPIPS
Assumes that reconstructions have been previously produced using the
flash_reconstruct_grid_and_generate.sh shell script, and are
in the corresponding locations produced by that script
SYNOPS... |
6dd1cc8837d0811e2bc88a059b9bfdb157a8dcb91c33be46bbe186bd3a738309 | Shell | 2,127 | 70 | #!/bin/bash
module load cluster/R/4.2.1
file=$1
ID=$(echo $file | cut -d "/" -f 6)
if [ $ID == "5397-JL-0001" ]; then
rep="1224"
else
rep="1230"
fi
tmp=$(echo $file | cut -d "/" -f 8)
EXP=$(echo $tmp | cut -d "." -f 1)
# START
## step3: Intersect SNPs
mkdir -p ${rep}/intersect/
python ~/software/WASP/m... |
b78d63d6f04d12465d4b15375562e6bde75deb7cf8fe318ae40b8fc7ddbf6bba | Shell | 2,131 | 49 | #!/bin/bash
#
# WARNING: The script is overwriting the original images and labels in the `imagesTr` and `labelsTr` directories. Make
# sure you are working on a copy of the data.
#
# Crop lumbar data around the spinal cord
# The script iterates over all the images in the current directory (`imagesTr`) and:
# 1. Segme... |
d17d3ae0edf7ca9ece3c59d194d9caa7dac21543c4a36bde3006324f1ac91324 | Shell | 2,131 | 58 | #!/bin/bash -e
if [ $# -lt 2 ] || [ $# -gt 3 ]; then
echo "usage v1: lrna_bam_to_stranded_signals.sh <bam_file> <chrom_sizes> [<stranded:T/F>]"
echo "Converts BAMs from alignments from stranded or unstranded libraries to bigwig format. Is independent of DX and encodeD."
exit -1;
fi
bam_file=$1 # ... |
fa7ec062745be5283dc22cdb4b6b95343fa13467284d0b0af97e6d6057315709 | Shell | 2,148 | 48 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
a0a4426ad3f85d62aa48a6e9f458a70fdf3ba14775b5044ed9711e7289b8c719 | Shell | 2,149 | 75 | #!/bin/bash
# We actually want the full path to scripts
scripts=$(cd $(dirname $0) && pwd)
# Where are the read files at?
reads_by_sample=$1
if [ -z "$reads_by_sample" ]
then
echo "Please give me the location to the directory that holds all reads by sample"
exit 1
fi
# Where is the sample/reference mapping f... |
c60a87854dee77382fcf22a27dd5f75f5a3bd60ad055f389c7e9fbca6fc180f3 | Shell | 2,149 | 62 | #!/bin/bash
source 00_global_variables.sh
OUTdir_for_munge=./munged
mkdir -p $OUTdir_for_munge
OUTdir_for_heritability=./heritability
mkdir -p $OUTdir_for_heritability
for i in ${!Phenotypes[@]}; do
phenotype=${Phenotypes[$i]}
SUMSTAT=${reformated_sumstat_for_LDSC[$i]}
EffN=${SampleSize[$i]}
MungeN... |
331a25938711796b4da587b425c75a7f856fd62ec42cba6ecf69ac72c2b10c2a | Shell | 2,156 | 52 | data_path='dwar'
MASTER_PORT=10090
task_name="dwar-iBond"
head_name='chembl'
weight_path='pretrain_save/checkpoint_best.pt'
n_gpu=1
save_dir='finetune_save'
# train params
seed=0
nfolds=5
cv_seed=42
task_num=1
loss_func="finetune_mse"
dict_name='dict.txt'
charge_dict_name='dict_charge.txt'
only_polar=-1
conf_size=11
l... |
c15dcf4ea8f95883ccdc57b550690f9fddb4861e9b0578a0e6a50a8944a3420e | Shell | 2,158 | 78 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -s <scriptDir> -p <spmDir>... |
f6b9585cb52ca7bc5be75f41289a1965967838773ae3a6a5639e91ce1de3fd89 | Shell | 2,163 | 69 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/GatherSampleEvidence.wdl
# Task: RealignSoftClippedReads
set -Exeuo pipefail
sample_id=${1}
reads_path=${2}
reads_index=${3}
scramble_table=${4}
is_bam=${5}
reference_fasta=${6}
reference_index=${7}
reference_bw... |
6d7c02278fb104bc1a79dc00f97b877f76dfab11fd905acf08fd5e273a9b1e93 | Shell | 2,169 | 49 | #!/bin/bash
#$ -S /bin/bash
#$ -N vep
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/none/vep/vep.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=8G,h_rt=48:00:00
#$ -hold_jid ann
#$ -t 1:22
chr=($(seq 1 1 22) X Y M)
echo ${chr[${SGE_TASK_ID}-1]}
indir=/mnt/analysis-psp/users/timchang/v3/pc/... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.