sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
eda831fa2835fb83ad110e2bc5a1e246c65b8dad85eadfee4d66165c5e74fe72 | Shell | 2,484 | 14 | #! /usr/bin/env bash
# cd /workspace/datasets/ISBI2021/BF-C2DL-HSC/ && python /opt/elephant/script/generate_seg_labels.py --sparse /opt/elephant/script/generate_seg_labels_configs/BF-C2DL-HSC_sparse.json .
# cd /workspace/datasets/ISBI2021/BF-C2DL-MuSC/ && python /opt/elephant/script/generate_seg_labels.py --sparse /op... |
8368d571a1f2ad4812d60d79ee028fb98ad909aa4a6cb9e27745977b81b01fe7 | Shell | 2,488 | 69 | #!/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 -b <brainList> -t <tmp> -s <sigma... |
e67adf548afdb712f5aee526bef9e285d64dfaeae1270599e5a53de30b394d96 | Shell | 2,517 | 52 | #!/bin/bash
#
# This script runs GCTB SBayesS on the dyslexia & rhythm impairment
# meta-analysis results.
module load gctb/2.02
genSEM="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/"
outDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/GCTB/"
# Run SBayesS on GWAMA, dys and rhy_imp s... |
2dc0a5fce053878d9a65c8f2a1ac9dd746ef5406c23f52d89bfef7a26f7fca22 | Shell | 2,522 | 72 | #!/bin/bash
# 1. receive essential arguments from dag input
sequencing_run=$1
sample=$2
outdir_staging=$3
outdir_home=$4
indir_home=$5
dir_scripts=$6
genome=$7
split_lines=$8
bwa_index_squid=$9
conda_pack_align_squid=${10}
job_parent=${11}
job=${12}
# 2. set paths
path_splitFastq=/home/sfeng77/biosoft/fastq-tools/bin... |
d459ebfe37c026ec23541c67c4780f9517c3d321fb6ae5e82a17ea3fdd9f93a2 | Shell | 2,525 | 89 | #!/bin/bash
## 1. receive arguments from 03sort.sub
sequencing_run=$1
outdir_staging=$2
conda_pack_squid=$3
genome_seq_squid=$4
job_parent=$5
job=$6
## 2. configure the conda enviroment
set -e
workdir_pac=$(basename $conda_pack_squid)
ENVNAME=$(basename $conda_pack_squid .tar.gz)
ENVDIR=$ENVNAME
# these lines handl... |
2e6f3f9f5d1c92b7997656ea0ac620adfce63e6617438de5e193c148781ad129 | Shell | 2,530 | 87 | #!/bin/bash
# Some quick shortcuts to ease running Syncopy's testing pipeline
# First and foremost, check if `srun` is available
_useSLURM=$(command -v srun)
# Stuff only relevant in here
_self=$(basename "$BASH_SOURCE")
_selfie="${_self%.*}"
_ppname="<$_selfie>"
# Brief help message explaining script usage
usage()
... |
2667ebcc836733d094cc8b8fdd9dac3fbd345c9d843002c8a972f91e859e1aad | Shell | 2,539 | 72 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
45f4f86aa6b81c9f3c3acc04b05b9f8b79ea961ac63652b3d60c16d20485350f | Shell | 2,543 | 66 | #!/bin/bash
#SLURM_ARRAY_TASK_ID=1 #1 to N
#main_dir=${your_dir}/predixcan
#step 1. model training
#ml GCC OpenMPI R
#Rscript ${main_dir}/src/predixcan_r.r \
# --model_training \
# --main_dir ${main_dir} \
# --plink_file_name ${main_dir}/chr22/chr22 \
# --expression_file_name ${main_dir... |
6d941a687b98f2ef6d353e50633c50e3c8640236b6064e0655bb2fd01a5d7192 | Shell | 2,545 | 85 | #!/bin/bash
#PBS -N deeph_band
#PBS -l nodes=1:ppn=24
#PBS -l Qlist=n24
# calculate bands from band_i to band_f
# submit num_tasks tasks simultaneously
# place under same directory with hamiltonians_pred.h5, overlaps.h5
# == basic information ==
fermi_level=-3.9143371779349274
lowest_band=-3.1
num_band=100
band_i=1 #... |
1d25b13e24b5778c4f74ad24b95baa384ea8a5260f0247bf17d18b2ccf6ec7aa | Shell | 2,548 | 66 | #!/bin/bash
# Purpose: Generate text files to create individual vertex-to-vertex FC matrices.
# Inputs: Surface-projected timeseries (rsfMRI)
# Outputs: Vertex-to-vertex FC matrices for each individual
# Written by M. Peterson, Nielsen Brain and Behavior Lab under MITT License 2022
##########################
# Specif... |
0aa741c25e9296b4d6ee71e2b5193a91f8d1eb1b9d2d1b5f9758f23c1cbd21b8 | Shell | 2,550 | 73 | ###############################################################################
# Help #
################################################################################
Help()
{
# Display Help
echo "Prepare the cafemol input file"
echo
... |
5bc2001e7e23068e8befb403a97b6bac7d6764dd0ecc4e0d48fad633a07778cf | Shell | 2,554 | 32 | #!/bin/bash
#Purpose: Convert 32k fs_LR surface to fsaverage6 surface
#Inputs: HCP COPE4 STORY-MATH task activation zstats files in 32k fs_LR space.
#Outputs: HCP task activation tstats files in fsaverage6 space.
#Software: wb_command (HCP), freesurfer
#32k and fsaverage templates: https://github.com/Washington-Univer... |
b88648edc2afbfdfccc25b71135bd0a83b99f58c4282e9d96b8a8e2da12de639 | Shell | 2,570 | 90 | #!/bin/bash
outswcfolder=$1
markerfile=$2
brainpath=$3
Vaa3dPath=$4
if [ $# -ge 6 ];then
threadNum=$6
elif [ $# -lt 6 ];then
echo "Input error: not enough parameters"
exit 0
else
threadNum=30
fi
#multi-thread
tempfifo="dendrite_Complete_fulltrace_fifo"
mkfifo ${tempfifo}
exec 6<>${tempfifo}
rm -f ${te... |
68e6c8882ef27593f8a81fce0780b959c02681344088d10e81621659c9d10c67 | Shell | 2,576 | 77 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This function projects x, y, z index files of a single subject (which contains coordinates in fsaverage projected to subject's surface space) to the subject's T1 space, using FreeSurfer'... |
3f39ba2261ac7e942f6f46527f5791fa1feb14528f7518d906427f221a5db726 | Shell | 2,583 | 88 |
# prep POLMM results for METAL meta-analysis
nacc_res_dir=./output/gwas/adc/polmm
rosmap_res_dir=./output/gwas/rosmap/polmm
act_res_dir=./output/gwas/act/polmm
nacc_bim=./data/adc/adc_np.bim
rosmap_bim=./data/rosmap/rosmap_np.bim
act_bim=./data/act/act_np.bim
metal_input_dir=./output/gwas/metal/input
for pheno in d... |
558e9e799938c6a3546412623d0404faa61440e9f22b1be742c242f8da2bac1a | Shell | 2,592 | 80 |
mkdir output/gwas/adc/polmm
# create SNPMatrix
mkdir data/adc/SNPMatrix
./code/gwas/ordinal/polmm_create_SnpMatrix.R \
--bim data/adc/adc_np.bim \
--out data/adc/SNPMatrix/
phenos=$(cat data/mega/nacc_np.pheno | \
cut -d " " -f 3- | \
awk 'NR == 1{print}')
# main regression model
for pheno in ... |
67a03004f4aed76bf52a4fe42eb02f98811c43becaa4eaec5dec2eafa8145ce9 | Shell | 2,594 | 84 | #!/bin/bash
# Load necessary modules
module purge
module load gcc/8.2.0
module load python/anaconda3.10-2022.10
source activate deeptools
# Define constants/paths
WINDOW_SIZE=10
# Define Paths for Sox2CR
SOX2_BAM_DIR="/ix1/ialdiri/CR-ChIP/nfcore_runs/Sox2CR/results/02_alignment/bowtie2/target/dedup"
SOX2_BIGWIG_DIR=... |
a189f67d85d720d040f70096e4032931a8105a616d9a008869959c59b513a05a | Shell | 2,599 | 61 | #### GIN fine-tuning
runseed=$1
device=$2
split=scaffold
### for GIN
for dataset in bace bbbp clintox hiv muv sider tox21 toxcast
do
for unsup in contextpred infomax edgepred masking
do
model_file=${unsup}
python finetune.py --input_model_file model_gin/${model_file}.pth --split $split --filename ${dataset}/gin_${mode... |
862d620897a62b75d42e004dc8ac89049c4e45f84f05034af9242addc80f5bb8 | Shell | 2,606 | 80 | #!/bin/bash
#==============================================================
# basic QC
#==============================================================
prefix=act
#--------------------------------------------------------------
# make plink fileset of only those with autopsy data
#---------------------------------------... |
60ee2c842eb69405939f075f03d14a19d58ca9ad1423776afb1c4ae9256b4808 | Shell | 2,638 | 79 | #!/bin/bash
# Run feature selection experiments for prediction of mutation status, with
# all cancer types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/ccle_mutation_ridge
ERRORS_DIR=./ccle_mutation_ridge_errors
# number of features to "preselect" to
# -1 == no preselection... |
ec7ef1ffe7baabe3f6d28ae3eb45f79e636b64042c2a59cb0fdaf59c49fd2fbc | Shell | 2,648 | 113 | #!/bin/bash
# file: tests/test-runPipeline.sh
if [ ! -f tests/test-helper.sh ]; then
echo "test-helper.sh not exist"
exit
fi
. tests/test-helper.sh
SHUNIT2_SRC_DIR=~/works/shunit2
INPUT_IMAGE_DIR=/mp/nas1/share/ExSEQ/AutoSeq2/test-data/xy01/1_deconvolution-links
DECONVOLUTION_DIR=1_deconvolution
TEMP_DIR=./t... |
baa2b2e4a3fd9056a7c128c92b76114784e2220c08a6f09091f83797a4f178f3 | Shell | 2,652 | 79 | #!/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 ... |
52e984fb9649fcb3bac1717aed4d9493270c5093d71327e851f5a68c08112774 | Shell | 2,666 | 66 | #!/bin/bash -ex
if [ -z "$TRINOTATE_HOME" ]; then
TRINOTATE_HOME=`pwd`/..
fi
sqlite_db=myTrinotate.sqlite
trinotate_data_dir=`pwd`/TRINOTATE_DATA_DIR
#################################################################
## Load Expression info and DE analysis results for Trinotate-web
############################... |
b95c853dddac31744880f4d44608bfdcba2662e072946f30148f2c72c68d22c5 | Shell | 2,675 | 70 | #!/bin/bash
# Written by Minh Nguyen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
ROOTDIR=`readlink -f $0 | xargs dirname`/../
export PYTHONPATH=$PYTHONPATH:$ROOTDIR
mkdir -p output
echo Generate 10 cross-validation folds
python -m cbig.Nguyen2020.gen_cv_fold \
--spreads... |
d26a81c81ccb9790658e6a94c0cbbebd15f3fe1c40e752834829a15ec6c7aeb3 | Shell | 2,681 | 84 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
87a2a5cdd0ffe2b09171fa032b399a992d2a1e3c8863c15456795f1bfe50017d | Shell | 2,686 | 67 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
ca060a2a8e6e56c91558e377e2ef18ac10f26490f9ec0fa3fcd9683867044859 | Shell | 2,696 | 91 | #!/usr/bin/env bash
set -euo pipefail
ENV_NAME=${ENV_NAME:-modeller_env}
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
if ! command -v conda >/dev/null 2>&1; then
if [[ -x "$HOME/miniforge3/bin/conda" ]]; then
export PATH="$HOME/miniforge3/bin:$PATH"
fi
fi
if ! command -v conda >/dev/null 2>&1... |
e6b7004645c254d37350872fcc010d3eefa0e2589516e72a6ffda64797ebacbf | Shell | 2,701 | 92 | #!/bin/bash
# author : sjn
# date : Aug 25, 2022
# Histogram of per read length/#nucleosomes (bin sz=1, range 0-2000bp)
# Collapse all reads > 2000 to 2000
# Vertical line at median value between 0-300 bp/nuc
# Can you actually make this with xlim 0-1500, and say on the chart the % of fibers in the bin >1500
# Get %... |
0094a1e1abf537b6e427ff999931fb47af5f7b6307a4fefd49c97b3f4a179d3a | Shell | 2,728 | 91 | #!/bin/bash
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
4f1e47d8bd3665327306025615d0fb43da36107b4afc5b0cc459eb56bd8f9e3a | Shell | 2,745 | 67 | #!/bin/bash
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
#
# This bash script comprises the full analysis pipeline associated with the following paper:
#
#
# -------------------------------------------------... |
0367aa9afd5e0fb02e7c039f07e8e769deea617dca85ba79701532aed1f27a39 | Shell | 2,746 | 80 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with either liquid or solid cancers held out
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_binary_liquid_or_solid
ERRORS_DIR=./drug_response_binary_liquid_or_solid_errors
# number of features to ... |
92b81e1bc10f7d9bbd264010f8dc84586b06166cfc3ec38c5358e1d188122735 | Shell | 2,746 | 81 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with all cancer types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_binary_drop_liquid
ERRORS_DIR=./drug_response_binary_drop_liquid_errors
# number of f... |
d63c91989e28804dcc3ebf0d374bb80786c2acf1b8640c8fd710cff12e82d3ca | Shell | 2,773 | 62 | #!/bin/bash
# how to write it out: ./masking_out_eeg.sh -n racsleep08
# nina fultz may 2021: contact nfultz@mgh.harvard.edu if you run into any problems
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script... |
b8f2ad95d9d86e907951ae8e3f5fa3c1c6574130b7a7dc7a51cc4db86b3e5aa1 | Shell | 2,778 | 113 | #!/bin/bash -efx
# author : sjn
# date : Aug 22, 2022
# histogram of per read #nucleosomes
# add a line and values for the median, 10%ile and 90%ile
set -euo pipefail
if [ $# != 4 ]; then
printf "Expect $0 <sample-name> <input-file> <output-pdf> <output-stat.txt>\n"
exit 1
fi
samplenm=$1
inp=$2 # fiber-all-... |
adcb130a737602a25351fa8a8a95c6178af27b592593b65718284bcaf328bd60 | Shell | 2,782 | 82 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
##########################... |
067eb28e524c19a64477782f2a043d4f626139ba64611c451c971d79d5c4fdab | Shell | 2,783 | 85 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
########################... |
947c5a1ed30ec053a242f95234169acca5a4e7433d9fea872852eaa10d9090e9 | Shell | 2,790 | 82 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
##########################... |
b2fbc18f22ba020ad2d6a7073f322fa1a4bc999320c909c2b76ba7a9ab493bd0 | Shell | 2,790 | 82 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
##########################... |
650190fb3ccfc51245b79cef99e0350ae5eeb5db9aa7770a2c428a1fb2032ef8 | Shell | 2,793 | 119 | #!/bin/bash
#2019-02-15 lizhe
#$1 Dir
#$2 ID
#$3 VOI Center Coordinates
#######MT#########
Dir='/mnt/v_share/data/D007/MT/T1/'
ID='D007_mt'
Anat=${Dir}${ID}'.nii.gz'
voi_center=(-40.3 -13.2 -30.8) #MRS VOI center coordinates (mm) -L -P -F
voi_size=(20 20 20) #MRS VOI size (mm)
echo ${ID}>>log.txt
echo `date +"%Y-%m-... |
d9cf3360dfcb6c4adc31c6f9159ba5921d2bf0b37a9280f0b13a839640db1f18 | Shell | 2,797 | 85 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
########################... |
a3e8f4347b8acf49b0608ee169176a81520e02f5dc102845c98ca636ea3fb07e | Shell | 2,800 | 85 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
########################... |
0d208e9c5a70cbb476e58dd51cf9a325e4d3d085d849e506c36edb86c65d2807 | Shell | 2,811 | 61 | #!/usr/bin/env bash
# output to a log file rather than stdout
#!/bin/sh
# exec >> negbio_log_file
# exec 2>&1
BASE_FOLDER=$1
NEGBIO_PATH=$2
if [ -z "$BASE_FOLDER" ]
then
echo "You must call this script as: ./run_negbio.sh FOLDER_WITH_DATA_CSVS NEGBIO_GIT_PATH"
exit 1
else
echo "Source of data: $BASE_FOLD... |
7bd296f9a93199575269de1dffd0ff2b177d81e53a8889028bd28f5ee4e85ff0 | Shell | 2,815 | 83 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
06475b7c5c71b28b797c7bdcfa7806d03849dababd270294efe103b69b044f21 | Shell | 2,823 | 83 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
ae6b41d44184742c1a08f4dbc1eb1f0aa139466a84928c42079376109d7acc94 | Shell | 2,823 | 83 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
a5909e9d262992e94a644d16d131a9a7cb515d5055e151169588111090425743 | Shell | 2,830 | 88 | #!/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> -d <idList> -r <reorientSa... |
f56cebda5b37865229472c25561366e86e32d77890314d88bc311bfa3daf6d12 | Shell | 2,838 | 93 | #!/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 ... |
e5e881fea5c94de45d115957c349a2a3db9e44e77e04ef23e13c5612aff2fc48 | Shell | 2,847 | 114 | #!/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... |
dced8a6f5d9d9304089b6f8d6877681db9d347170d39c61fa3cb44f4c6133b55 | Shell | 2,854 | 41 | #!/bin/bash
#
# This script will reformat dyslexia, rhythm impairment and
# Genomic SEM common factor sumstats for FUMA.
#
# All columns need for FUMA are already there, you just need
# to add the total N column to each file.
#####
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
genSEM="/data/clus... |
d91f0359d886cec2b427c9e7bacfbba1681afaa8510bd8a23b0bd9dcf69f51dc | Shell | 2,855 | 83 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with either liquid or solid cancers held out
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_regression_liquid_or_solid
ERRORS_DIR=./drug_response_regression_liquid_or_solid_errors
# number of feat... |
0ed98c73c960f9f0637a4ccd21fc61c4edfae930cafb7acb1568f567b649c39d | Shell | 2,857 | 109 | #!/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 ... |
221bb7bad0c259ff2ce023c1ed4328ca5e134509ed5a848504671441cc06cc42 | Shell | 2,861 | 84 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with all cancer types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_regression_drop_liquid
ERRORS_DIR=./drug_response_regression_drop_liquid_errors
# num... |
e94b6a81eff7308a0167f8584f817034d41797181f8f26134c51d2b68d321322 | Shell | 2,864 | 88 | #!/bin/bash
# Run feature selection experiments across a few genes
RESULTS_DIR=./01_stratified_classification/results/univariate_fs_big
ERRORS_DIR=./stratified_fs_errors
# number of features to use as 'upper bound' model by variance selection
# this should be larger than the actual experimental methods
# -1 means th... |
f7ab0387ddf2aa794c39be8d7ddf5dd52073bd5e72ff52bcea87a1f10e119b3c | Shell | 2,870 | 82 | #!/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 ... |
5afb713779e7b2a69c9a216fd35b5838f05549f2ea252e37d531ce54987e113a | Shell | 2,872 | 90 | #!/bin/bash
# This is Step 2.5, which will generate the profile lists for Step 3
##########################
# Specify output directory
##########################
HOME=/fslgroup/fslg_spec_networks/compute
HOME_D=/fslgroup/fslg_fun_conn/compute
out_dir=${HOME_D}/NSD_analysis/parc_output_fs6_NSD_ALL_REST
preproc_output... |
6fbf3f097f5b9a90f95c89f42eab61cc431c5088e599564c5cdbe4fc3a72c7b7 | Shell | 2,884 | 57 | #!/bin/sh
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Li2019_GSR
# remove useless stable projects
rm -r Standalone_Li2019_GSR/stable_projects/brain_parcellation/Kong2019_MSHBM
rm -r Standalone_... |
0b81cbd6fc64a3ec9e767485b21ceec8cec0ef193e158594ef2bd768e94930a2 | Shell | 2,886 | 93 | echo
echo "### setup/set env started"
echo
SETUP_DIR=$(dirname ${BASH_SOURCE[0]})
if command -v module &> /dev/null
then
module purge
module load unstable git python gcc hpe-mpi py-mpi4py petsc py-petsc4py
else
if command -v conda &> /dev/null
then
if conda env list | grep bfs_env >/dev/null ... |
8467195ae8470ebbfaa3234a7e4275cc2234187550726007247bbfcc185cb39d | Shell | 2,930 | 98 | #!/bin/bash
#
# Gokberk Alagoz, March 2022 - last update Feb 2023
#-----
# PATHS
mungedDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged"
ldscores="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/resources/eur_w_ld_chr/"
outDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gencor"
f... |
3769af907f80548e5f4d5bede787333817d751a19424307613a99ec6df0820d8 | Shell | 2,935 | 120 | #!/bin/bash
TAG_COLOR="\e[95m"
END_COLOR="\e[0m"
TAG_NAME="Bioemum build"
TAG="[$TAG_COLOR$TAG_NAME$END_COLOR]"
# Define environment variable for BIOEMUM_PATH if not already set
if [ -z "$BIOEMUM_PATH" ]; then
echo -e "$TAG Error: BIOEMUM_PATH is not set"
exit 1
fi
# Determine target architecture
if [ "$BIOE... |
bcc104fcc8e28132945aeef8fc9ae3834827567969ff696db8f3220b1c71c251 | Shell | 2,935 | 90 | #!/bin/bash
# Don't forget to copy over 40 sub HCP priors to /generate_individual_parcellations/priors or generate your own priors in Step 2
# This is Step 2.5, which will generate the profile lists for Step 3
##########################
# Specify output directory
##########################
HOME=/fslgroup/fslg_spec_... |
5292e4d5653da06fca091d3c89ebaa43917526851d08a91cc420073ddad7e3a6 | Shell | 2,939 | 90 | #!/bin/bash
# Don't forget to copy over 40 sub HCP priors to /generate_individual_parcellations/priors or generate your own priors in Step 2
# This is Step 2.5, which will generate the profile lists for Step 3
##########################
# Specify output directory
##########################
HOME=/fslgroup/fslg_spec_... |
f6d66c71643e00c9a145cd632dc27546db2ccfb0c79eb9c66ebe3a6c904f5820 | Shell | 2,939 | 90 | #!/bin/bash
# Don't forget to copy over 40 sub HCP priors to /generate_individual_parcellations/priors or generate your own priors in Step 2
# This is Step 2.5, which will generate the profile lists for Step 3
##########################
# Specify output directory
##########################
HOME=/fslgroup/fslg_spec_... |
02abca91e5133e6915ffc290eecc794d2cc034b8bda384bf5d651a76113f9bed | Shell | 2,940 | 90 | #!/bin/sh
# This function replicate the linear ridge regression results in the GSP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(pwd... |
91d7de7581fa1221cce436413d13bf7b54e9a5fa54dae72662509b602a8663b3 | Shell | 2,942 | 98 | #!/usr/bin/env bash
## deploy.sh: run during a CI build to deploy manuscript outputs to the output and gh-pages branches on GitHub.
# Set options for extra caution & debugging
set -o errexit \
-o nounset \
-o pipefail
# set environment variables for GitHub Actions
REPO_SLUG=${GITHUB_REPOSITORY}
COMMIT=${GITH... |
b4d10e003db1c1aca7d4b2930c6c8676feae7312756d677aec7fae1e2ec07049 | Shell | 2,945 | 82 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function script warps an input volume to FreeSurfer's nonlinear volumetric space, and then to the target volume, using talairach.m3z transform file from recon-all results of the in... |
ea7a483a83246482fa6757215fdb221583617d2cf15f9d5b305f42ba1b501faf | Shell | 2,945 | 88 | #!/bin/bash
set -e
set -u
function showHelp() {
#
# Display commandline help on STDOUT.
#
cat <<EOH
===============================================================================================================
Script to run the research workflow (incl opticall)
Usage:
$(basename "${0}") OPTIONS
Options:
-h ... |
e3f33dff8c9397b83c58cef9f8969caea02c8959a6e1d563bee8e1df5f324c90 | Shell | 2,957 | 60 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
project_dir=${1} # output directory
data_type=${2} # data_type = metric/label.
version=${3} # version = 20160827 or 20170508
fsLR_surface_dir=$CBIG_CODE_DIR/data/templates/surface
######################... |
af926d5d7f206a1d8c3eba8cca4e41ebc22bca0781f948280e65efd211a26e65 | Shell | 2,961 | 104 | #list SentrixBarcode_A
#list SentrixPosition_A
#string GTCtmpDataDir
#string intermediateDir
#string ateambotUser
#string Project
#string logsDir
#list Sample_ID
set -e
set -u
set -o pipefail
array_contains () {
local array="$1[@]"
local seeking="${2}"
local in=1
for element in "${!array-}"; do
if [[ "${element... |
38ccfa82e7bb48a13a0a986dfcb618dc77c016aa3a1841b2698b67c3554e67c8 | Shell | 2,962 | 89 | #! /bin/bash
# Train the model using 5-fold validation, and
# inference on the whole dataset (no explanation).
# python lib/train_meta_kfold.py --k_fold 5 \
# --data_path Dataset/relative_abundance.csv \
# --metadata_path Dataset/metadata.csv \
# --edge_list output/NetworkInput/EdgeList.csv \
# --output output/ \
# ... |
2962cb54011eae8cb5f40d972f8b26bae5e24fea18f4d4ca19cfb2bbc932903d | Shell | 2,965 | 128 | #!/bin/bash
### [0] Set the env (generated w/ chatgpt)
current_dir=$(pwd)
while [ "$current_dir" != "/" ]; do
if [ -f "$current_dir/.env" ]; then
echo "Running .env file in directory: $current_dir"
source "$current_dir/.env"
break
fi
current_dir=$(dirname "$current_dir")
done
### [1] Parse the argu... |
0e110e0989d6a36adea7ac309f3f6ffe71ed00a02fc6d683e033e3e3203a0b5d | Shell | 2,967 | 68 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
project_dir=${1} # output directory
data_type=${2} # data_type = metric/label.
fsLR_mesh=${3}
version=${4} # version = 20160827 or 20170508
fsLR_surface_dir=$CBIG_CODE_DIR/data/templates/surface
######... |
9560dab4b0f9a415c0c4dd13aaa6c8a38ed87403d15b3e855fffb6a01219e495 | Shell | 2,976 | 110 | #!/bin/bash
#
# Gokberk Alagoz, March 2022 - last updated Jan 2023
#
#-----
#PATHS
mungedDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/"
ldscores="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/resources/eur_w_ld_chr/"
outDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gencor/s... |
f30dc54271bfd628fe92acf1da68ce88c9961fa47e72d39c28d9c729ce44d707 | Shell | 2,986 | 112 | #!/bin/bash
## 1. receive arguments from 01qc.sub
sequencing_run=$1
read1=$2
read2=$3
outdir_staging=$4
indir_staging=$5
job=$6
conda_pack_squid=$7
## 2. configure the conda enviroment
set -e
workdir_pac=$(basename $conda_pack_squid)
ENVNAME=$(basename $conda_pack_squid .tar.gz)
ENVDIR=$ENVNAME
# these lines handle... |
39ffb0963cced6f208785c11d53b485fda2ddc251802035d1a8dccb0917970ad | Shell | 3,001 | 53 | #!/bin/sh
set -x
apt-get update
apt-get install curl gnupg debian-keyring debian-archive-keyring apt-transport-https --no-install-recommends --no-install-suggests -y
## Ignore warnings
export APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1
## Team RabbitMQ's main signing key
curl -1sLf "https://keys.openpgp.org/vks/v1/by-fin... |
6e57c230e0f8098a0773096ca856cfe6ade08cd90bcd4c9e1c8bd3a4061bd855 | Shell | 3,029 | 50 | #!/bin/bash
QUPATH_EXPERT_LAYERS_ANNOTATED_PROJECT_PATH="../ProjectQuPath_for_test/Ground_truth.qpproj"
QUPATH_PROJECT_PATH="../ProjectQuPath_for_test/ProjectQuPath_for_test.qpproj"
RESULT_PATH="/arch_results"
FIGURE_PATH="/arch_results/Figures"
FOR_PREDICTION_PATH="/arch_results/prediction"
FOR_TRAINING_PATH="/arch_... |
cb9a67e06eae864c0b252803dd9ea4cf8efd6cb8a9e463457d6461a36f2a7961 | Shell | 3,031 | 79 | #!/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 ... |
de4092a045920e274e9423142c5cbd4e692684c86d4081ea947519b3b6943675 | Shell | 3,033 | 24 | # tumor growth dataset
## zero-shot transfer/data-efficient transfer/standard supervised learning
## zero-shot transfer metrics: dst-zero-shot-encoder_test_rmse_last, dst-zero-shot-decoder_test_rmse_[2-6]-step
## data-efficient transfer metrics: dst-encoder_test_rmse_last, dst-decoder_test_rmse_[2-6]-step
## standard s... |
669247d233eedf1228c86e43e1abdbdbaf70af78ae3bb43fb1bfced0af4a9e18 | Shell | 3,036 | 54 | #!/bin/bash
#
# This script will reformat GWAS sumstats for
# GCTB analysis.
# Paths
inDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
genSEM="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/"
# 1) Dyslexia
# dose.b column is allele frequency of alleleB, which is the effect allele.
#aw... |
367cee0d76bb0d8308213de0ac24b46e120eb93c7f6f4c6c73fdcac8e385a78c | Shell | 3,057 | 57 | #!/bin/bash
mkdir ./projects_folder
touch ./bin/settings.ini
echo "ngsd_host = \"127.0.0.1\"" >> ./bin/settings.ini
echo "ngsd_port = 3306" >> ./bin/settings.ini
echo "ngsd_name = \"test_db\"" >> ./bin/settings.ini
echo "ngsd_user = \"test_user\"" >> ./bin/settings.ini
echo "ngsd_pass = \"password\"" >> ./bin/settings.... |
92685018b12f0e71f0ddc69cc5cfea4c7b5fe0b01510ddca8229a8e34fe6c47d | Shell | 3,067 | 40 | #!/bin/bash
#
# This script will reformat dyslexia, rhythm impairment and
# Genomic SEM sumstats for LocusZoom:
# i) add a marker column
# ii) sort by chr and pos
#####
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
genSEM="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/"
module... |
3a41aead628cc64cfd69994f9f72ffd1f13e666a2382cede62d1c26a4fc1740b | Shell | 3,069 | 51 | #!/usr/bin/env bash
# Regenerate Phase-3 (v1.x --ffs) byte-identity goldens from the repo's Perl
# coverage2cytosine (v0.25.1, self-contained). Run from this directory
# (tests/data/phase3_ffs). Creates the tiny fixtures AND the per-mode Perl
# golden output dirs under ./gold/ — full provenance.
#
# --ffs --gzip has NO... |
43c4d04229d87cb707fff87d73c121a372f226831f3a9e4ef8b0bca7e5469ad8 | Shell | 3,072 | 87 | #!/bin/bash
set -ex
mkdir -p /opt/cache/bin
mkdir -p /opt/cache/lib
sed -e 's|PATH="\(.*\)"|PATH="/opt/cache/bin:\1"|g' -i /etc/environment
export PATH="/opt/cache/bin:$PATH"
# Setup compiler cache
if [ -n "$ROCM_VERSION" ]; then
curl --retry 3 http://repo.radeon.com/misc/.sccache_amd/sccache -o /opt/cache/bin/scc... |
9527f53732015f9f86a01f1db3ad4fd4d6429e53f9f654c7d33b527ff6181c64 | Shell | 3,078 | 102 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./02_cancer_type_classification/results/univariate_fs
ERRORS_DIR=./cancer_type_fs_errors
# number of features to "preselect" to
# -1 == no preselection
NUM_FEATURES_L... |
e4c7123eff893e7382c80bf83580320dd99ec19ec707b0ff74d8a13d188d577e | Shell | 3,080 | 86 | #!/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 ... |
8e982dc755f4a0a3b03c4c6d321ffc0ab4d6472d091764d5f1eba2bbe74da380 | Shell | 3,084 | 93 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This function script projects a single volume to fsaverage space using MNIsurf approach. It is required to finish running the recon-all results before running this function.
###########... |
ba5a7c6d98bbc49912743b70c6e926bb779320658f33649262862dc7869d6f37 | Shell | 3,086 | 121 | #!/bin/bash
## 1. receive arguments from 07callsnp.sub
outdir_staging=$1
conda_pack_squid=$2
genome_seq_squid=$3
job_parent=$4
job=$5
## 2. configure the conda enviroment
set -e
workdir_pac=$(basename $conda_pack_squid)
ENVNAME=$(basename $conda_pack_squid .tar.gz)
ENVDIR=$ENVNAME
# these lines handle setting up the... |
29f8354ec5bb41a4e14d7c75fedf0034b2478df7f30711b04b077a0448b5004b | Shell | 3,091 | 38 | # Group the sub-trajectories into the main trajectories.
# Enhancers.
cat enhancer_10000_imputation_traj_peak_peaksplit.bed enhancer_11000_imputation_traj_peak_peaksplit.bed enhancer_11100_imputation_traj_peak_peaksplit.bed\
enhancer_11110_imputation_traj_peak_peaksplit.bed > enhancer_early_imputation_traj_peak_peakspl... |
114a35267e9720fb16020631a01a9987ab2da3820327099cdca592491f72d88c | Shell | 3,102 | 94 | #!/bin/bash
# Run feature selection experiments for prediction of tumor purity, with
# all cancer types held out (either partially or completely)
# For now we're just making this into a binary classification problem,
# above/below the mean for each sample.
RESULTS_DIR=./08_cell_line_prediction/results/ccle_mutation_... |
c68c9ffb90725c5816770620aad4a4bc87239c4fefae5e4e19715c233048409a | Shell | 3,127 | 75 | #!/bin/bash
#
# This script will extract phyloP and phastCons
# scores of SNPs in the genSEM CPM results.
#
# Gokberk Alagoz, 07.12.22
#
module load bedtools/2.29.2
##########################
# PATHS
input="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/evo_results/GenomicSEM_multivarGWAS_CPM_dys_rh... |
f5630aeae6fda685bd13685a6c77781e575c72906b16e0d8f6278bc92e6bb858 | Shell | 3,142 | 104 | #!/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 ... |
232287c9bceb84b8a4a01218b283a263b0529237a243ebdf9be78f931c768b0a | Shell | 3,155 | 93 |
#!/bin/bash
# This downloads and installs a pinned version of miniforge
# and sets up the base environment
set -ex
cd $(dirname $0)
MINIFORGE_VERSION=4.9.2-2
MAMBA_VERSION=0.7.4
# SHA256 for installers can be obtained from https://github.com/conda-forge/miniforge/releases
SHA256SUM="7a7bfaff87680298304a97ba69bcf92f6... |
629955e056839eb6c540a18a7720105aff1f1216b693477565ef9bcfb7bcc86f | Shell | 3,162 | 106 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
e917aa4e8357fcc3008bc2cced486d297f61560a539c62a872c4fbc069a7d4e3 | Shell | 3,167 | 77 | #!/bin/bash
rm -r collapsed_bam_H1_20230102
mkdir collapsed_bam_H1_20230102
mkdir dedupped_bam_H1_20230102
mkdir AEI_H1_v1
mkdir AEI_H1_v1/tmp_20230518
mkdir AEI_H1_v1/log_20230518
mkdir AEI_H1_v1/output_index_20230518
mkdir AEI_H1_v1/output_mpileup_20230518
for FILE in cb_listsH1/v4/*
do
ter_id="$(echo $FILE | cut... |
0b46763d825c392b9b28f702594be1d9180d4e5ba8d09607ee5a77d827808263 | Shell | 3,175 | 38 | perl -ne 'print "chr$_";' hg38_promoters_cage_corrected.bed >hg38_promoters_cage_corrected_withChr.bed
liftOver -bedPlus=6 hg38_promoters_cage_corrected_withChr.bed hg38ToHg19.over.chain hg19_promoters_cage_corrected_withChr.bed unmapped
./supplement_ids.pl >hg19_promoters_cage_corrected_withChr_andOthers.bed
grep -... |
898235436e6d7bc04eeb7c7e32ada9fcbe4ab295144a403dd1959fcbbbf6b5f5 | Shell | 3,201 | 103 | #!/bin/bash
apt-get -y update
apt-get install -y \
curl \
wget \
unzip
apt-utils \
software-properties-common \
python-software-properties
echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --exp... |
8e416a41301762b5a670df9ac2b2b7d6d7e84cfdeaa63a859982326ae0541bf8 | Shell | 3,212 | 70 | # Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
42ffbe733d265ca2689151a16a6867fb098dcda18d9ee158d8d4bcb3520868a1 | Shell | 3,224 | 90 | #!/bin/bash
set -e
set -o pipefail
set -o verbose
root=`dirname $(pwd)`
# Path to your settings file
SETTINGS_FILE=$root/settings.ini
if [ ! -f "$SETTINGS_FILE" ]; then
SETTINGS_FILE="$root/settings.ini.default"
fi
# Extract container_folder from the settings file
CONTAINER_FOLDER=$(grep -E "^container_folder" ... |
cb529d41dd20aa90a302262c3156c2beec79d484de2d3c2d65d8780ecab7574e | Shell | 3,226 | 87 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This warpper script runs CBIG_RF_MNICoord2fsaverageVertex.m and CBIG_RF_fsaverageVertex2MNICoord.m for an example
if [ "$(uname)" == "Linux" ]; then
SCRIPT_DIR=$(dirname "$(readlink ... |
a6652a89bf0f934f050bca39d7516524f642409e42c95ef032a9790b0d0209c6 | Shell | 3,242 | 133 | #!/bin/bash
# author : sjn
# date : Aug 22, 2022
set -euox pipefail
if [[ $# != 4 ]]; then
printf "Expect $0 <sample-name> <input-file> <output-pdf> <output-stat.txt>\n"
exit 1
fi
samplenm=$1
inp=$2 # fiber-all-table.tbl.gz
outpdf=$3
outstat=$4
ftype=msp
tmpd=/tmp/$(whoami)/$$
if [ ! -s $inp ]; then
pr... |
4c4f919e9ee238d5fc357e2a5946fe7efb0ae5f0ea33dd5afddf06d3e01c4e6a | Shell | 3,243 | 120 | #!/bin/bash
# author : sjn
# date : Aug 22, 2022
set -euo pipefail
if [[ $# != 4 ]]; then
printf "Expect $0 <sample-name> <input-file> <output-pdf> <output-stat.txt>\n"
exit 1
fi
samplenm=$1
inp=$2 # fiber-all-table.tbl.gz
outpdf=$3
outstat=$4
ftype=readlengths
tmpd=/tmp/$(whoami)/$$
if [ ! -s $inp ]; then... |
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