sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
21a08112706e2abd871b36a3e057f972b91724c2fed46d87258b27c6e1242707 | Shell | 1,037 | 27 | #!/bin/bash
#Purpose: Create SNR maps using fslmaths.
#Input: CBIG2016 preproc output.
#Output: SNR maps.
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2023
#PATHS:
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/HCPD_analysis/tSNR/ALL
PREPROC_DIR=/fslgroup/fslg_HBN_preproc/compute/HCP... |
32d7ff127aba22f3cd3d49500795db9d3d610d6409fceddfe821e03e2ec7736d | Shell | 1,038 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
ee358be8d09d712e934527bfb933bacf8e93c9c47d24aab2f060bb01bd8fa6e9 | Shell | 1,038 | 26 | #!/bin/bash
# $1 usr_name for server
# $2 ip_addr for server
# $3 is upload folder from your pc in elasticai.creator/build folder
# $4 is download folder to your device
# Clear auto_build folder
ssh $1@$2 "rm -rf /home/$1/.autobuild/*;exit;"
# Copy build folder from your device to server
scp -r $3 $1@$2:/home/$1/.aut... |
40e8a6a8615b04a230f1ee29d874bc535a87f8baf3c99ae46ae3b2830cca655d | Shell | 1,042 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f5cabf88c352d346bed307cbb8be032039507769d596aac59467e2a255594d54 | Shell | 1,043 | 35 |
# prep SAIGE results for METAL meta-analysis
nacc_res_dir=./output/gwas/adc/saige
rosmap_res_dir=./output/gwas/rosmap/saige
act_res_dir=./output/gwas/act/saige
metal_input_dir=./output/gwas/metal/input
for pheno in hs microinf grossinf
do
nacc_results="$nacc_res_dir"/"$pheno"_saige_results.txt
rosmap_resul... |
834a03d054d448fec01d14c80ca62bd3d3343fc46e0d9e9fbf1a4633c6577a66 | Shell | 1,047 | 22 | #!/bin/bash
# get sampling distributions for disease and subject effects for each split
# user-defined parameters for defining distributions are defined within this python code.
# this script drops "bins" containing too few items to be stratified. may need to
# guess + check on original number of samples (TOTAL_... |
9890db78eb0abfc5427b53fe6d30aea5f28fd0c60d776a064d09ac68f622a5ba | Shell | 1,048 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
fdd6597257ca5e0a54158bd9945984e022534bdcb2225b31de7384bcd823643d | Shell | 1,048 | 26 | #! /bin/bash
# Train the model using 5-fold validation on train dataset
# and run the trained models on the test dataset (no explanation).
python lib/train_meta_kfold.py --k_fold 5 \
--data_path Dataset/train_relative_abundance.csv \
--metadata_path Dataset/train_metadata.csv \
--edge_list train_output/NetworkInput/E... |
ef2a86b081202822d0be4d63fa7e562cb958d44c5c69d8c34f635cba162aa721 | Shell | 1,050 | 37 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --nodes=1
#SBATCH --ntasks=1 #--cup-per-task=1
#SBATCH --time=00:40:00
#SBATCH --mem-per-cpu=8G
#SBATCH --job-name=4/13
#SBATCH --array=1-150
main_dir=/data/g****/a***/****/model_training/
#1. model training
ml GCC/8.2.0 OpenMPI/3.1.4 R/3.6.0
module load PLINK/1.9b_5.2
... |
889feaf00fbc59a94c9e17e4f0af88b5ee20799b47f55ec5e4f87bbc3bcae634 | Shell | 1,051 | 26 | #!/bin/bash -ex
# This script adds the kerberos only configs to relevant hadoop config files. For example,
# if there are core-site.xml and core-site.xml.part files in ${HADOOP_CONF_DIR}, the content of
# core-site.xml.part is appended to core-site.xml. The process is following:
# 1. remove the closing configuration... |
3b66cab0a7338fec9dd4f25ee58304ae8266df52d9211f3ffbd4348002e596c9 | Shell | 1,055 | 51 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_ccle_nn_dropout_range_2
ERRORS_DIR=./tcga_ccle_nn_errors
mkdir -p $ERRORS_DIR
# number of features to "preselect" to by mean ab... |
bd90ced11cebf1dec1aa52f822c795b6629cab9160eabc598262af824d5b4b98 | Shell | 1,055 | 23 | #! user/bin/bash
subject=$1
origpath=/m/cs/project/networks-pm/mri/fast_prepro_bids
path=/m/cs/scratch/networks-pm/pm
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
cp -R ${origpath}/${subject} ${path}/${subject}
fslroi ${path}/${subject}/func/${subject}_task-pvt_bold.nii ${path}/${subject}/func/${subject}_task-... |
d17fb386c19c697d08b6d52b54ae718b1367244826a2069bd46aaa3817f735c7 | Shell | 1,057 | 32 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
f67c4154985579923c0ad64f0556edb91b8a1fcc3fbd54b60b852514ec702d9c | Shell | 1,057 | 43 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
NCOLS=640
# 1e6 causes out-of-memory
for n in 1e4 0.2e5 0.4e5 0.6e5 0.8e5 1e5; do
echo "===== sqrt-bsxfun-dist2(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-sqrt-bsxfun-dis... |
491a485e5781a54eb9ca4ed4815c14ae19a87a2dff030bd547f0c3b894a115ed | Shell | 1,060 | 62 | #!/bin/bash
set -e
echo "
Started annotation workflow ...
"
Rscript R_demo.R
echo "
Finished annotation workflow, check figures in Results directory
"
cd Transitions
echo "
Started celltype transitions workflow ...
"
Rscript -e "rmarkdown::render(input = '01_Integration.Rmd', output_dir = '../Results', clean = T... |
ce657d066ea90b0ffb3c3b4b623bde2876bef54dd9dac662e60561a08501fc8a | Shell | 1,061 | 26 | #!/bin/bash
#
# Gokberk Alagoz
#
# This script will reformat dys and rhy_imp sumstats for
# local genetic correlations analysis with LAVA.
#-----
# PATHS
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
# Dyslexia
awk 'NR>1 {print $19, $25, $24, $8, $4, $3}' ${sumstats}dyslexia.filtered.2_lambdaG... |
5343a5969ebf48ff75d255e6ae99fcae3eafca8b69142b8884ea8c2245c1f3d3 | Shell | 1,062 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
b9a5ea26be46428b4a638925212cc7fb0b233d074f74a66ce944e121f8b5dd47 | Shell | 1,062 | 15 | #!/bin/sh
python eval_multilabel.py --results-dir "/mnt/ds3lab-scratch/webermau/rey-figure/spaceml-results/1000-data_232x300-seed_1/final-3_scores/rey-multilabel-classifier/"
python eval_multilabel.py --results-dir "/mnt/ds3lab-scratch/webermau/rey-figure/spaceml-results/1000-data_232x300-seed_1/final-aug-3_scores/rey... |
2fa425971e949711a28511bd199a2c9cf0220a6ba1c8dfed66b7d6251bbad6e3 | Shell | 1,063 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
5a1a70dc0020a77249a4549738759614f6f92f3a0d4e2d6cb4f67b8481d76761 | Shell | 1,065 | 49 | #!/bin/bash
## default data/grna.fa
gfile=$1
mis=$2
gname=${gfile##*/}
## Creating the index structure for genome sequences.
# risearch2.x -c /data/genome/fasta/hg19.fa -o CRISPRoff/hg19.suf
## off-target prediction
if [ ! -d "CRISPRoff/data/" ];then
mkdir CRISPRoff/data
fi
cp $gfile CRISPRoff/data/
cd CRISPRoff/
... |
250f8f0ab0add5255e55944c7e0b709639508c6abeee0eb4b1f27f0953277860 | Shell | 1,066 | 27 | #!/bin/bash
#run full model pipeline
exps=(experiment_name1 experiment_name2 experiment_name3)
arrs=(TP TN)
for exp in "${exps[@]}"
do
echo training model for $exp
python model_3d.py --expname $exp #train model
echo evaluating $exp
python evaluate_3d.py --exp_name $exp #evaluate model
... |
04df8bef6b8a4b7d90831df30aff6590f9159bacf23b3c8b1af2e6c71e354a89 | Shell | 1,067 | 40 | #!/bin/bash
## 1. receive arguments from run_bayescenv_chtc.sub
chr=$1
env_var=$2
num=$3
in_snp=$4
in_env=$5
pr_pref=$6
## 2. set paths
wd_abs=$(pwd)
bayscnenv=biosoft/bayescenv-1.1/bin/linux64/bayescenv
prefix=$env_var\_$chr\_$num
out_stat=$prefix\_fst.txt
out_acc=$prefix\_AccRte.txt
out_sel=$prefix.sel
out_verif=$... |
0919fd04f204cbb02cbd3365e9038a106339ff2ae6dbf843233f87e8a2b1a6a9 | Shell | 1,068 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
0d5b8d894301b1ca77791bcc8d615d8b8c29f8ec88947768f92026275c49294b | Shell | 1,070 | 33 | #!/bin/bash
#SBATCH --time=45:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16384M # memory per CPU core
#SBATCH -J "utah_FS" # job name
# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fsl... |
c1a5d5b13fbcdce987de38b6289520763afe573e66b89f01c6a1e2cd9d383429 | Shell | 1,072 | 54 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_ccle_nn_weight_decay_range
ERRORS_DIR=./tcga_ccle_nn_errors
mkdir -p $ERRORS_DIR
# number of features to "preselect" to by mean... |
20d2863287f62808ba0ec0ab7d2bba9f7239450f82858585a5fe96c0582a32a5 | Shell | 1,076 | 35 | #!/bin/bash
path2scripts=/hpc/hub_oudenaarden/aalemany/bin/mapandgo2
if [ $# -ne 2 ]
then
echo "Please, give: "
echo "1) input root to fastq files"
echo "2) protocol [celseq1, celseq2, nla, scscar]"
exit
fi
outfq=$1
protocol=$2
if [ $protocol == 'celseq1' ]
then
python ${path2scripts}/concatenat... |
d6375383f2852c6096b2e82b010ca44f24ac0fb3e39cc419c8e7a6a6d0910015 | Shell | 1,078 | 33 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
e3bd796a1118a9323ec1e0694ad1a49d827c6832d830c197fedc53a69929d4cd | Shell | 1,078 | 29 | #!/bin/bash
# Get the parent directory containing subfolders (relative path)
parent_dir="."
# Iterate over each subfolder
for folder_name in "$parent_dir"/*/; do
# Check if the folder is actually a directory
if [ -d "$folder_name" ]; then
# Find the zip file in the current subfolder
zip_file=$... |
01710b386f2411cc9c822d2b66ceb4a92f08b4ce3fea313071a7c9bc448541e0 | Shell | 1,079 | 25 | #!/bin/sh
# Last successfully run on Dec 17th, 2019
# Written by Gia H. Ngo and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
... |
1ca2417114eaf10b8c30d8aa903115a1a9f53f2cbd79c5c619ad3e4982bb514a | Shell | 1,081 | 40 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 <brainDir>
- brainDir Directory ... |
49da06d00466967af9708d94a9b1a6c296dcc6c95c1d28ad13006cddf78f7e30 | Shell | 1,081 | 21 | #!/bin/sh
# https://stackoverflow.com/questions/30747469/how-to-add-initial-users-when-starting-a-rabbitmq-docker-container
# Create Rabbitmq user
( rabbitmqctl wait --timeout 60 $RABBITMQ_PID_FILE ; \
rabbitmqctl add_user $RABBITMQ_USER $RABBITMQ_PASSWORD 2>/dev/null ; \
rabbitmqctl set_user_tags $RABBITMQ_USER admin... |
4a2331a768d84bb0d69261fce613c3179fca53331d21553c9972b5ac3584c882 | Shell | 1,081 | 61 | # fba; percentile
fba extract \
-1 $READ1 \
-2 $READ2 \
-w $BARCODES \
-f $FEATURE_REF \
-o feature_barcoding_output.tsv.gz \
-cb_m 1 \
-fb_m 1 \
-cb_n 3 \
-fb_n 3 \
-r1_coords 0,16 \
-r2_coords 0,6
fba count \
-i feature_barcoding_output.tsv.gz \
-o matrix_featureco... |
ad8623452e89e09adfca55ca1d437fb9c2eb5c86d5258b4ca1d7e1edec37a112 | Shell | 1,081 | 31 | #!/bin/bash -l
#SBATCH --time=04:30:00
#SBATCH --mem-per-cpu=45G
#SBATCH -o /m/cs/scratch/networks-pm/jobs/denoise-%j.out
subject=$1
task=$2
strategy=$3
FWHM=2.5532 #This number is FWHM/2.35
denoisepath=/m/cs/scratch/networks-pm/pm_denoise
module load matlab
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
module l... |
f41317673147c6c723b46186a7e617e2b25ad7c6feb26b9519a131cdafee6801 | Shell | 1,084 | 17 | #!/bin/bash
#Assign variables to be built into the inputs json
PROJ="<project_name>"
FLOC="<path/to/general/project/folder/${PROJ}"
OUT="${PROJ}_<suffix>"
READ1="${FLOC}/fastq/${PROJ}_read1.fastq.gz"
READ2="${FLOC}/fastq/${PROJ}_read2.fastq.gz"
FASTA="${FLOC}/setup/${PROJ}_reference.fasta.gz"
WORK="<path/to/MPRA_oli... |
176c61235a75ef4160b920c6207e841599bc9c3dfbc78fffd74306c86552e157 | Shell | 1,088 | 39 | #!/bin/bash
#******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fr... |
62ee7ebb8dc04dfb539b0b384464fbf53c4f8b409f09fa3bc1d8052d52075e8e | Shell | 1,088 | 37 | #!/bin/bash
# Make .annot and l2.ldscore files for all chromosomes and annotations.
# Run this on grid as "bash run_make_annot_l2.sh"
# Variables
inDir="/data/workspaces/lag/workspaces/lg-genlang/Working/23andMe/Dyslexia2/Evolution/dys_rhy_pleiotropy/resources/beds"
# Run LD Score Estimation
mkdir $inDir/scripts
f... |
332933a0ab620d5cd4a2940b6e0c032bd84b4d25f24f76abc7329f29d326d517 | Shell | 1,089 | 26 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure3/Results/"
#file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro/HCP/* | cut -f... |
184735f34e1541b17d361f1c7a125b924a96164484fe927869b6140ae54c9c8d | Shell | 1,090 | 29 | #!/bin/bash -ex
VERSION=$1
REPO_VERSION=$2
USERNAME=$3
PASSWORD=$4
case ${VERSION} in
5*)
echo -e "# Packages for Cloudera's Distribution of Hadoop, Version 5\n\
deb [arch=amd64] http://archive.cloudera.com/cdh5/ubuntu/trusty/amd64/cdh trusty-cdh${VERSION} contrib\n\
deb-src http://archive.cloudera.com/cdh5/ubu... |
77b6aab8308edb84471ab46df1f651e79fbf7ad1fa2a3f64fdaadf2732767503 | Shell | 1,090 | 37 | #!/bin/sh
#SBATCH --job-name=dcm2nii
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=02:00:00
#SBATCH --output=/home/intoumanis/sugar/code/logs/dcm2nifti.out
#SBATCH --error=/home/intoumanis/sugar/code/logs/dcm2nifti.err
# The user changes only the variable "participant", which correspon... |
a839cc7e7216a0b0692c5e02c0428cf93244736b402bafb3fd525568613493e0 | Shell | 1,090 | 35 | #!/bin/bash
path2scripts=/hpc/hub_oudenaarden/aalemany/bin/mapandgo2
if [ $# -ne 2 ]
then
echo "Please, give: "
echo "1) input root to fastq files"
echo "2) protocol [celseq1, celseq2, scscar, nla]"
exit
fi
outfq=$1
protocol=$2
if [ $protocol == 'celseq1' ]
then
python3 ${path2scripts}/concatena... |
bde050e5a4be33c8d25e004480c2bcaa13bfcff1fecabdd997c9c6ac56f9effc | Shell | 1,090 | 39 | #!/bin/bash
## 1. receive arguments from run_bayescenv_chtc.sub
env_var=$1
BatchNum=$2
script=$3
in_outlier_prefix=$4
## 2. set paths
wd_abs=$(pwd)
# PermutationReps=1000
PermutationReps=100000 # try more permutation reps to get a more precise P value
script=$(basename $script)
in_outlier_prefix=$(basename $in_outli... |
b42e31c3b63e8b8b3f55e8572a9b7a98253bcc1ad758563aa582ab86989d6258 | Shell | 1,100 | 35 | #!/usr/bin/env bash
cd ../bin/BRB-seqTools/releases/
InputDir=${1}
OutputDir=${1}/demultiplexed
mkdir -p ${OutputDir}
#BarcodeFile=../../../data/fastq/barcodes/barcodes_96_V4C_brb.txt
BarcodeFile=${2}
UMILength=${3}
ls ${InputDir}/*_R1.fastq.gz
for Library in ${InputDir}/*_R1.fastq.gz
do
LibraryFile=${Library##*... |
ce70003beb7ce15b3a9e79a4ce8184205e412a235f24c61990c4f6fa3fb7e374 | Shell | 1,103 | 29 | #!/bin/bash
###############################
# Speech processing pipeline #
###############################
eval "$(conda shell.bash hook)"
conda activate neuro
# 1. Run the Python script `get_stimuli_transcripts.py` to generate .txt-files for the MFA from file `stimumatrix_sentences.xlsx`
python get_stimuli_transc... |
e924b764bf88eebdee56880aaa07c42a238bce5a57e28033a4fb7b0b793529f2 | Shell | 1,103 | 31 | #/bin/bash
# -------------------------------------------------------------------------------------------------
# -- Simple admin view of all analyses currently running on the server
# -------------------------------------------------------------------------------------------------
n=0;
for SAMPLE in $(ps aux | grep "... |
75c60d8704e48cc2d5d14f99c754bd25184726661fddc6ef9166e7a757cb75c7 | Shell | 1,104 | 39 | VFC_BACKENDS="libinterflop_mca.so" python -c "
import torch
import pickle
N_SAMPLES = 30
torch.manual_seed(0)
a = torch.rand(5, 5)
b = torch.rand(5, 5)
res = []
for _ in range(N_SAMPLES):
res.append(a @ b)
with open('fuzzy-pytorch_mca_results.pickle', 'wb') as file:
pickle.dump(torch.stack(res), file)
"
VFC_BAC... |
2bb3c705de18c35e4f6ee5c0ae331a5756a3ebf7e7eb7183b9d631f4fd8b0301 | Shell | 1,106 | 43 | #!/bin/bash
# Script to run simulate_k.ipynb for several different sets of simulation
# parameters using papermill, writing the resulting plots to the
# simulation_plots directory.
cd /home/jake/research/pancancer-evaluation/09_simulations/
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_nbs"
mkdir -... |
ed7f52f456dc78afe60ff184b673d34100f00babe13626e3782cc989daff55c7 | Shell | 1,106 | 31 | #!/bin/bash -l
export TPU_LOAD_LIBRARY=0
export TPU_NAME=$1
export ZONE=$2
python3 train_model.py \
--tpu_name="pod1" \
--tpu_zone="europe-west4-a" \
--wandb_project="enformer_atac_ft" \
--wandb_user="njaved" \
--wandb_sweep_name="enformer_atac_ft" \
... |
fbffb4819fe4f5ee99b295c1b8ba10d6d36c29ede4ca14eb12828a8edb76b376 | Shell | 1,107 | 46 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=imwarp
SIZE_Z=250
for n in 1000 2000 3000 4000 5000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z}.log
if [ -f ${... |
38cafd8e95c634162c41f0b2ff06b83eaff54bcc8193b229cb9ac9d06652c67d | Shell | 1,113 | 22 | #!/bin/bash
################################################################################
# Analyze CSDP on target pattern database
################################################################################
GPU_ID=$1
## analyze a saved model on test-set of MNIST database & produce a tSNE plot
## of its saved... |
dee8d890bc0621cd8a6909f6c999f774c2cc7d3a50fe47dd806be7187e352005 | Shell | 1,113 | 34 | #!/bin/bash
# Function to train the wavelet-curvelet combined model
train_wavelet_curvelet() {
echo "Training Wavelet-Curvelet model with $1 train observations per class, $2 test observations per class, and alignment processing: $3..."
python3 Alpha_emp.py --train "$1" --test "$2" --alignment "$3"
}
# Check for t... |
c65c2cd673986402242d3be4ebb421f961dd4364116b4be71475a40d241a2845 | Shell | 1,115 | 33 | #!/bin/bash
#SBATCH --time=45:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16384M # memory per CPU core
#SBATCH -J "NSD_FS" # job name
# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fsla... |
f8c7bafaed1a52643e9724114413c5724c57d9fa184286902d998535dbc1ab5e | Shell | 1,116 | 36 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
set -x
ExtractDir=$CBIG_CODE_DIR/data/templates/surface/
SubjectDir=$1
SubjList=$2
ResamplingMethod='BARYCENTRIC -largest'
for Subject in $SubjList
do
for Hemisphere in L R
do
MetricIn=$SubjectDir/"$... |
7b0fff84d2c41e0d22ae8d2082e511ca70373637f8adce1c77584a177a84b3ec | Shell | 1,117 | 24 | #!/bin/bash
#SBATCH --time=04:00:00
#SBATCH --mem=20G
#SBATCH --array=1-24
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/glm-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" variants.txt`
IFS=' ' read -a array <<< "$variants"
cd /m/cs/scratch/networks-pm/effects_externalfactors_on_fun... |
a28fb5b2e9c6383510f8793082955672aa465955af62628de302fc7642ed6f83 | Shell | 1,117 | 34 | #!/bin/bash
#SBATCH --time=45:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16384M # memory per CPU core
#SBATCH -J "HCPD_FS" # job name
# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fsl... |
62ea770f06929c1bc6f6df7e27821828a04245fd969692029a17f174be075b68 | Shell | 1,122 | 18 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# call from ./107/fmri as ./scripts/regressNuissance.sh
3dDeconvolve -input ./processed/pb02.SUBJ.r??.volreg+orig.HEAD \
-polort 6 \
-mask ./processed/full_mask.SUBJ+orig ... |
d597e7d1c83d67126f624d745281b6164805aeb20180b0b3828f143fe138e8af | Shell | 1,126 | 47 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
ef2b2eccb5f21c81cbdc821d4fc6c35854b1c11ef3a79482c2e4c0b625f5cd56 | Shell | 1,126 | 23 | export CARLA_ROOT=${1:-/home/kchitta/Documents/CARLA_0.9.10.1}
export WORK_DIR=${2:-/home/kchitta/Documents/misc/transfuser}
export CARLA_SERVER=${CARLA_ROOT}/CarlaUE4.sh
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI/carla
export PYTHONPATH=$PYTHONPATH:$CAR... |
26f58a8649df8be23f1175a5de2ac1e6e7a42a2397fcf96917be71292c247517 | Shell | 1,127 | 41 | #!/bin/bash
# Script to run lasso_range_gene.ipynb for all genes in Vogelstein dataset
# using papermill, writing the results to the output directory in the script.
# Note that this must be run from the parent directory
# {repo_root}/08_cell_line_prediction.
kernel_name="pc-eval"
papermill_output_dir="./papermill_o... |
a0bcedb5fdc861ba08abbb60e571dccd48e5dd7b55a4922e5237e48280cd8722 | Shell | 1,127 | 38 | #!/bin/bash
set -e
#infiles
#$1 <- fasta file
#$2 <- outdir
#$3 <- num trials
#$4<- minlen orf orfs (multiple of 3)
#example bash run_benchmarks.sh ../testdata/testseq.fa b1 5 30
#run benchmark
python benchmark.py $1 $2 $3 $4
#test all sequences match
#echo "Comparing nucleotide sequences"
#python compare_fasta_file... |
dc48b9b3a641930d68fc2b17aed203113310362e5a91836f40917af05ff28b03 | Shell | 1,127 | 35 | #MOLGENIS walltime=01:59:00 mem=1gb ppn=1
#string callrateDir
#string Project
#string intermediateDir
#string genderCheckDir
#string logsDir
set -e
set -u
set -o pipefail
mkdir -p "${genderCheckDir}"
# remove header from the callrate file before comparing the genders
sed -e 1d "${callrateDir}/Callrates_${Project}.t... |
f6d7571b026816d94a489a5c2f4a77690f82bc7bb58ea9b38d6692c59f91b498 | Shell | 1,127 | 34 | #!/bin/bash
##################VARIABLES##################
#ASSEMBLY (name of assembly used - i.e. hg19)
#############################################
export SGE_JSV_TIMEOUT=120
: <<'COMMENT'
#Make list of all fasta files
echo "Step (1/7): Building Chrom List"
ls | grep ^chr | grep ".fa" | awk -F ".fa" '{print $1}'... |
0b5c6ae3af7ea923a82fac7d23d598bd92def92b17aeab1d1daf5fa9a45cb2d0 | Shell | 1,129 | 30 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_filter_pdb test_inputs/5edw.pdb is_not_water"
./ap_filter_pdb test_inputs/5edw.pdb is_not_water
echo -e "# Running ./ap_filter_pdb test_inputs/5edw.pdb is_water"
./ap_filter_pdb test_inputs/5edw.pdb is_water
echo -e "# Running ./... |
694ee1fd51fedd0234191d430a87fc13b9eb4699729b9852bc01a3535b9abfb8 | Shell | 1,129 | 29 | #!/bin/bash -l
python3 train_model.py \
--tpu_name="node-1" \
--tpu_zone="us-central1-a" \
--wandb_project="enformer_rampage_ft" \
--wandb_user="njaved" \
--wandb_sweep_name="enformer_rampage_ft" \
--gcs_project="picard-testing-176520" \
... |
30b2e5c7469fb73ad04bcf773b4ee517824a364593976d6030b829e04aa31167 | Shell | 1,133 | 52 | #!/bin/bash
download_file() {
local url=$1
local output_file=$2
wget --progress=dot "$url" -O "$output_file" 2>&1 | \
grep --line-buffered "%" | \
sed -u -e "s,\.,,g" | awk '{printf("\rDownloading %s: %s", "'$output_file'", $2)}'
echo " Done."
}
extract_tar_gz() {
local tar_file=$1
local output_dir=$2... |
03a437fe45604c4465b7eb64449c8a8ea99b7f9d11e3598c0b5fa8ba230a53e3 | Shell | 1,135 | 26 | # Uncomment the next 3 lines if not using modules
module load modules/0-traditional
module load gcc/9.3.0
module load matlab
# Set FMM3D download directory here
FMM_PATH=/mnt/home/mrachh/git/FMM3D
# Set fmm3dbie download directory here
FMMBIE_PATH=/mnt/home/mrachh/git/fmm3dbie
# Set install directory here
INSTALL_DIR=/... |
df1560da18931dd7e29694cd3cce4a381ed66fc1e1fa6508c421759ca3d364b3 | Shell | 1,136 | 33 | #!/bin/bash
# update
sudo apt update
# install packages
sudo apt install python3-pip -y
sudo apt install python3-pyqtgraph python3-pyqt5 -y
sudo apt install python3-pyqt5.qtsvg
# clone the repo
sudo apt-get install git -y
cd ~/Desktop
git clone https://github.com/hongquanli/octopi-research.git
cd octopi-research/sof... |
b4091deb6f9a4bc2ffd526fb957580c9b7fd8832ad1129048078e129a34cf32a | Shell | 1,137 | 44 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
NCOLS=3
N2ROWS=1.4e5
# 1e6 causes out-of-memory
for n1rows in 1e3 0.2e4 0.4e4 0.6e4 0.8e4 1e4; do
echo "===== pdist2(): n1rows = $n1rows"
TOP_LOG=${TOP_LOG_DIR}/top-... |
08948ba74ace4808f1766d79afa3f9b327450612528d89fb974060797a80920a | Shell | 1,138 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
b8fc50206ab3794a749f73d40c94760d05502b3d855afdea0345909bc8eae590 | Shell | 1,140 | 25 | #! /bin/sh
# Last successfully run on December 13th, 2019
# Written by Csaba Orban and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_en... |
fc838939230a8b96522c4f2e3b83cdc2b0aba34056d1354a357a7193e233e0ea | Shell | 1,140 | 42 | #!/bin/bash
#=====================================
# prep for PC-AiR on related data set
#=====================================
prefix=act
prefix_out="$prefix"_np
# keep only european subjects
plink \
--bfile tmp/"$prefix"_qc1.tmp \
--keep tmp/"$prefix"_qced.txt \
--make-bed \
--out tmp/"$prefix"_qc3.tmp
# on... |
ef66a169178ed3c3dd8bd3f75456087a936823e4ba3e89d1c3416a6e6fbd2960 | Shell | 1,142 | 32 | #!/bin/bash
#==========================================
# basic QC
#==========================================
bfile=data/act/act
prefix=act
#--------------------------------
# identify duplicates
#--------------------------------
plink --bfile "$bfile" --maf 0.05 --make-bed --out tmp/"$prefix"_maf05
king -b tmp/"... |
6c31f70a06fbe80dc96da7a0ded9c71369eb7d7cf5117b925a8578ae4944600f | Shell | 1,144 | 23 | ##make directories
mkdir corhot1
mkdir corhot2
#Make gene.tab files
cat Gene.ID | parallel -j 10 "cat EUR.nopermute.all | grep {} | awk 'BEGIN{print \"SNP A1 A2 P Effect N\"}\$1==\"{}\"{split(\$8,a,\"_\");print \$8,a[3],a[4],\$12,\$13,397}' > cohort2/{}.tab"
cat Gene.ID | parallel -j 10 "cat EAS.nopermute.a... |
59b5cf62380db39c9b7f92bc9ff14218c6a9ade626dbfeb21e43c659cd792868 | Shell | 1,146 | 37 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
set -x
ExtractDir=$CBIG_CODE_DIR/data/templates/surface/
SubjectDir=$1
SubjList=$2
ResamplingMethod=BARYCENTRIC
for Subject in $SubjList
do
for Hemisphere in L R
do
MetricIn=$SubjectDir/"$Subject".$He... |
c4807ee950f176a5dfcca36d8df3cd2fd56cfac5510e82f52478f345cba33717 | Shell | 1,151 | 47 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
76f4dee93e33fdd15f947dbd5f0d5217992f09b4c81036647866df2924edc5e2 | Shell | 1,152 | 43 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -v <4DVolume> -s <sigma> -o <outD... |
00a0ca1a4ececec27d7e64d138d0bebb70329d2a67ce4d8da141a94b1b2dd0e5 | Shell | 1,153 | 24 | #!/bin/bash
#Purpose: Create label files in fs6 space - from GROUP parcellation files
#Inputs: parc2annot annotation files
#Outputs: .label.gii parcellation files
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS- ODD RUNS
HOME=/fslgroup/grp_hcp/compute
OUTDIR=${HOME}/HCP_analy... |
0ce0b2110e31083b76812f9ee459056d67bc13ef48b4716c24792887c418ddbe | Shell | 1,153 | 33 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
window_len=$3
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/ML_tree/results/mincount_10_no_se_auto_X_over10/winlen_$window_len\_mincov_$mincov\_mincount_$min_count
sd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/ML_tree/scripts
script=$sd/prep_input_forTreeMix_... |
da98a8aca7178ab899569f839c8ea5950c28a8b156d33b941fad8ce8d212df6c | Shell | 1,159 | 42 | #!/bin/bash
# This will start H2o backgrounded, and automatically consume 90% available memory
# If you want S3 support create a core-site.xml file and place it in $HOME/.ec2/
# Assumes the h2o.jar you want is in /opt
set -e
d=`dirname $0`
# Use 90% of RAM for H2O.
memTotalKb=`cat /proc/meminfo | grep MemTotal | ... |
db5d9359b369fc76d43d28cfca9838a9c24fbe693826676e409ce761d3e80462 | Shell | 1,159 | 11 | #Add an annotation column(eSNPs or sSNPs) in baseline model
for i in {1..22}; do zcat ~/database/LDSR/EUR_baseline_2.2/baselineLD."$i".annot.gz | awk 'BEGIN{OFS="\t"}NR==FNR{a[$9""$10]=0}NR>FNR&&FNR==1{print $0,"robust_eQTL"}NR>FNR&&FNR>=2{if($1""$2 in a){print $0,1}else{print $0,0}}' nominal_eQTL.txt - | gzip >~/datab... |
71fd92dd2ec6b4b8db4845bba64075c4ca147c09de33342be3b0731a8c24fc30 | Shell | 1,160 | 34 | ntrials=18
folders="cumul_prob cumul_step independent"
for folder in $folders; do
if [ ! -d $folder ]; then
echo Creating dir ... $folder
mkdir $folder
fi
$subdir = "$folder/ntrials_$ntrials" # $folder/ntrials_16"
for s in $subdir; do
if [ ! -d $s ]; then
echo Creat... |
71391560d71777e9871fd48c459df57f8ade58399be01da86877b1ae533c5ffe | Shell | 1,161 | 49 | #!/usr/bin/env Rscript
#
# This script will parallelize Overlap Analysis
# jobs over annotations.
# The R script works only with R version >4.0.3.
# Thus, run this script on gridportal1 instead of
# gridmaster.
#
# Gokberk Alagoz
# Created on: 02.07.2021
#--------------------------------------------------#
# VARIABLES... |
b262ca4c6290d1208646f54bda2c8238c52d11eda812008b3bdd34941a91c359 | Shell | 1,163 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
c77118651de0f1c60f699c6306421242e08cdd44169a6a16bf2a099a87c8309e | Shell | 1,163 | 48 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
0044ecb94072dae2c27d14560304a2eb6227145fb18f1d2e2addd4d882af5115 | Shell | 1,164 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
2acf37934a434e5eec2dd8fe8c6c1dfee03c5fb557892b79d0149f00ba4a9d48 | Shell | 1,164 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
2fb70f6dd107034843fd2c139737d08bd3fee9709ea8edc44160978a4a1c9fd3 | Shell | 1,164 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
620d0ddd573a6c641eff1b5b81517971b4b64caf1a97bf2f9351ed35965bf68c | Shell | 1,164 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
f3bdf2f98d758269d243aec9bbf89bea2da001e55f0da85f21568b6bfbb6912f | Shell | 1,164 | 34 | #!/usr/bin/env bash
# Configure below, then run: ./scripts/run_check_tumor_data.sh (paths are relative to your cwd)
# Run this BEFORE run_tumor_tracking.sh.
SEG_DIR="tumor_volume"
FILENAME_PATTERN='(?P<date>\d{4}[-_]\d{2})\.nii\.gz$'
CONNECTIVITY=26 # should match run_tumor_tracking.sh
... |
8380ef2559de450ad23c071c268ac7848232ce667e5c12b36dc207ebb3614784 | Shell | 1,165 | 41 |
mkdir output/gwas/adni/polmm
phenos=$(cat data/mega/adni_np_ord.pheno | \
cut -d " " -f 3- | \
awk 'NR == 1{print}')
for pheno in $phenos
do
# # output top clumped SNPs from NACC analysis to SnpMatrix
# snps=tmp/"$pheno"_nacc_snps.txt
# cat output/gwas/adc/polmm/"$pheno"_polmm_results.clump... |
80ad99743f9025b4ac18eff5d902bc1dac03902e9d085738b8b77dc20ee63882 | Shell | 1,167 | 43 | #!/bin/bash
NUM_NODES=1
NUM_GPUS_PER_NODE=2
NODE_RANK=0
BATCH_SIZE=64
ACCUM_STEP=1
MASTER_PORT=$(shuf -n 1 -i 10000-65535)
DATESTR=$(date +"%m-%d-%H-%M")
SAVE_PATH=/
mkdir -p ${SAVE_PATH}
set -x
torchrun \
--nproc_per_node=$NUM_GPUS_PER_NODE --nnodes=$NUM_NODES --node_rank $NODE_RANK --master_addr localhost --... |
923a51268481b561a1a7d4c6b57dd1e8ac888e338abc8056a829ae1a8d769604 | Shell | 1,167 | 58 | #MOLGENIS walltime=02:00:00 mem=2gb ppn=1
#string intermediateDir
#string logsDir
#string Project
#list arrayFinalReport
#string finalReport
set -e
set -u
set -o pipefail
#Function to check if array contains value
array_contains () {
local array="${1}[@]"
local seeking="${2}"
local in='no'
for element in "${!arr... |
c8efbeaec1cde3a8825eba9393a2e42d78f2506f50ab21a06e5d0d425b51b61a | Shell | 1,167 | 36 | #!/bin/bash
set -e
set -o pipefail
set -o verbose
#General description:
# https://wiki.dnanexus.com/scientific-notes/human-genome
#Description of decoy sequences:
# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707
src=`pwd`/../src/
root... |
7e105f4daa5b093f17fc58e10fb30bb28bce86d66796fa21ee8e0a43193ac113 | Shell | 1,169 | 48 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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 ... |
5a6ee01deb941d441c58afa8d4035c8e540170080c33a6f4421d021a032b4eca | Shell | 1,171 | 38 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Dxy/mincov_$mincov\_mincount_$min_count
dir_snp=/home/siyuan/jobs/suzukii_WGS/call_snp/amb/updated_poolsnp/paratest/test_maxcov/call_snp_maxcov_99/mincov_$mincov\_mincount_$min_count
dir_mpileup=/home/siyuan/jobs/... |
59a47d2faad99940fea3bf371bf4f6fcfb8c0e22a404ef4b6437451ecc5a6634 | Shell | 1,174 | 27 | #! /bin/bash
config_file_expert=$1
config_file_mclust=$2
# Rscript get_genex_data_from_rds_ST_data.R ${config_file_expert}
python st_data_to_matrix_representation_converter.py --params ${config_file_mclust}
echo "========================================"
echo "Data convertend in matrix representation"
python autoscri... |
0cde3a1aab51eedb4a235dd2a7950a3b3981665f182b6a053c734c5a4671180d | Shell | 1,176 | 38 | #!/bin/bash
#SBATCH --time=5:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=505000M # memory per CPU core
#SBATCH -J "avg_FC" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= ppn... |
12e2c18cd2da498c2fe4ce4250a0d77548dc1e73230b916c846a387b04be01dc | Shell | 1,176 | 27 | #! /bin/bash
config_file_expert=$1
config_file_mclust=$2
# Rscript get_genex_data_from_10x_h5.R ${config_file_expert}
python visium_data_to_matrix_representation_converter.py --params ${config_file_mclust}
echo "========================================"
echo "Data convertend in matrix representation"
python autoscrib... |
4e85b73f5f20c780ffd6ece8715ca5c89f276fc8430479966474cb12cc0279d9 | Shell | 1,176 | 43 | #!/bin/bash
# Script to run simulate_add_domains.ipynb for several different
# sets of simulation parameters using papermill, writing the resulting
# plots to the simulation_plots directory.
cd /home/jake/research/pancancer-evaluation/09_simulations/
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_nb... |
35d2f3f978c9e2f3771241df70947560e1007f9bd75e7cd85815aae3a724513c | Shell | 1,178 | 55 | #list SentrixBarcode_A
#list SentrixPosition_A
#string GTCprmDataDir
#string GTCtmpDataDir
#string prmHost
#string ateambotUser
#string Project
#string logsDir
set -e
set -u
set -o pipefail
#Function to check if array contains value
array_contains () {
local array="${1}[@]"
local seeking="${2}"
local in='no'
for ... |
2ff3cb22159152b5317eeb7e254a06d703e898152443e5b5404bb1e7624f23b7 | Shell | 1,180 | 23 |
VGGMODEL10="vgg19/18112020/10push0.9506.pth/"
VGGMODEL20="vgg19/18112020/20push0.9489.pth/"
VGGMODEL30="vgg19/18112020/30push0.9483.pth/"
RESMODEL10="resnet152/19112020/10push0.8167.pth/"
RESMODEL20="resnet152/19112020/20push0.9678.pth/"
DENSMODEL10="densenet161/25012021/10push0.9800.pth/"
DENSMODEL20="densenet161/25... |
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