sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4e09cf991c7c0df2df6407705bccb727e9bfcf37ef890faed3d5c8257c95ef2f | Shell | 2,323 | 92 | #!/bin/bash
# Harvests basic info for all task and rest data sets
if [[ ! $QC_CODE_ROOT ]]
then
echo "Cannot find QC_CODE_ROOT"
echo "Please set manually or source an environment variable script."
exit 1
fi
if [[ ! $QC_META_ROOT ]]
then
echo "Cannot find QC_META_ROOT"
echo "Please set manually or... |
e9c2224891ca3bd1fdf28395f6eb9e6ee443db66a059c254589d2b7370226537 | Shell | 2,323 | 25 | #!/bin/bash
ORGAN=$1; shift
TopFile=$1; shift
#
RESULT=`cat $TopFile \
| grep -a -e "irus B19 " -e "irus_B19_" -e " B19V " -e "B19 virus" -e "B19_virus" -e "parvovirus B19" -e "Parvovirus B19" -e "erythrovirus V9" -e "Erythrovirus V9" -e "AY386330.1" -e "AY661661" -e "AY028237.1" -e "AY504945.1" -e "KM393163.1" -e "KM3... |
639cc68d1c5daaf23326bfa54c4b51b099ec33a412b91ede5c2265c86e74771a | Shell | 2,358 | 57 | #!/bin/bash
#
# EXAMPLE: ./TRACES_multiorgan_consensus.sh B19 B19.fa B19-multiorgans.fa 8
#
# ==============================================================================
#
FIELD="$1";
REFERENCE="$2";
SCAFFOLDS="$3";
THREADS="$4";
#
# ==============================================================================
#
if... |
3e0ce7e63c0b4c52472c7d091971c5e9b689d50051f43be65868ca060d4778cf | Shell | 2,399 | 64 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
d14574761cef24ae8f41ef053947c5c6c3c2535e3e7f3119d419aa7d274584a4 | Shell | 2,400 | 68 | #!/usr/bin/env bash
set -euo pipefail
cd /raid/mbrown/simplemind
SMCORE_BIN="/raid/mbrown/.micromamba/envs/smcore/bin"
ARTIFACT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATASET_CSV="/raid/mbrown/simplemind/artifacts/design/bb-memory/phase5_step5_kidney_ct40_parent_preprocessing_20260717_164031/kidney_ct_im... |
8def14da36bc9d63ec2ab1b5ccf7af5a962d471013fae36d86c27517fceeb7a8 | Shell | 2,410 | 86 | #!/bin/bash
ap_loc=$(which afni_proc.py)
if [[ $? != 0 ]]
then
echo "Cannot find afni_proc.py; is it installed?"
exit 1
fi
if [[ ! $QC_FS_ROOT ]]
then
echo "QC_FS_ROOT is not set."
echo "Please set this manually or source a setup file."
exit 1
fi
sid=$1
if [[ ! $sid ]]
then
echo "You must p... |
393e7a033c5f0ee81bb95c7f0463e9c894b4a1382584e6d91fd5b1ee1080edec | Shell | 2,412 | 85 | #!/bin/bash
#This script is intended to pass over a vcf file and remove conflicting variants
#The choice is made first by higher quality, then by VCF order
#Confilicting alleles are snps at the same position as an insertion
# and other variants which appear in the region covered by a deletion
#If there are multiple va... |
bfee8c4e64ce675e41a4bf805e4b1d88ef50d2dd2eadccf7cf0d626794933d3c | Shell | 2,433 | 26 | rm Vertebrate*.fa
# Chicken
wget -qO- ftp://ftp.ensembl.org/pub/release-78/fasta/gallus_gallus/dna/Gallus_gallus.Galgal4.dna_sm.toplevel.fa.gz | gunzip -c | sed "s/>/>Vertebrate:Gallus_gallus:/" >> Vertebrate1.fa
# Cod
wget -qO- ftp://ftp.ensembl.org/pub/release-78/fasta/gadus_morhua/dna/Gadus_morhua.gadMor1.dna_sm.top... |
ce9a4edb867167933da7e2801ab094004f804ec4d1fe7f96014ea143e0e83f89 | Shell | 2,440 | 68 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
799eff44efef50397909794ac6d4d58b56fd927a58c9131989a605f6ca38bbd8 | Shell | 2,445 | 56 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
7beec8bbfd561229e955138560169da484afc8dc7d73f9a0659eea704016c846 | Shell | 2,445 | 54 | #!/bin/bash
#
# moreFilters: http://samtools.github.io/bcftools/howtos/variant-calling.html
# MITOCHONDRIAL SNIPS DATABASE: http://www.mtdb.igp.uu.se/
#
Reference=$1; # EXAMPLE: mtDNA.fa
Alignments=$2; # EXAMPLE: mt_aligned_sorted-heart.bam
Organ=$3; # Example: heart
Label="mt"; # MT
#
echo "Usin... |
2e825a2fe280d29e9474a9b78aa03279930294965a67b75a281e42d65e023f30 | Shell | 2,446 | 87 | #!/bin/bash
ap_loc=$(which afni_proc.py)
if [[ $? != 0 ]]
then
echo "Cannot find afni_proc.py; is it installed?"
exit 1
fi
if [[ ! $QC_FS_ROOT ]]
then
echo "QC_FS_ROOT is not set."
echo "Please set this manually or source a setup file."
exit 1
fi
sid=$1
if [[ ! $sid ]]
then
echo "You must p... |
2ed4c79bcf1244ce8110caeba0f448d9c3c88717f800a36149d7877347913de1 | Shell | 2,509 | 57 | #!/bin/bash
#
# moreFilters: http://samtools.github.io/bcftools/howtos/variant-calling.html
#
Reference=$1; # EXAMPLE: TTV.fa
Alignments=$2; # EXAMPLE: ttv_aligned_sorted-heart.bam
Organ=$3; # Example: heart
Label=$4; # Example: TTV
#
echo "Using Reference : $Reference";
echo "Using Alignments ... |
c96f604f5114c7d116918aa9ec1dc6a8d2dcebc0a1535daefefa1fc4b6df885e | Shell | 2,545 | 74 | #!/bin/bash
#
THREADS="$3";
OUTPUT="../output_data/TRACES_specific_diff";
#
# ==============================================================================
#
CHECK_FILE () {
if [ ! -f $1 ];
then
echo -e "\e[34m[TRACESPipe]\e[31m ERROR: file $1 not found!\e[0m"
echo -e "\e[34m[TRACESPipe]\e[33m For additi... |
111bd7ffb20e9e16dcc9b86755b6ea851f2c301ad8ed2380e70b9f5f5cbe50ef | Shell | 2,553 | 44 | #!/bin/bash
#
# ==============================================================================
#
echo -e "\e[34m[TRACESPipe]\e[32m Extracting programs versions ... \e[0m";
#
#BEGIN AUTO-GENERATED SECTION - VersionCmds : DO NOT MODIFY
#==================================================
#This code snippet generated on Th... |
289da3c5ecc81936bf042f5846e7053070237d39d586a19a8688101d199580ac | Shell | 2,558 | 72 | #!/bin/bash
#
declare -a VIRUSES=("B19V" "BuV" "CuV" "HBoV" "AAV" "BKPyV" "JCPyV" "KIPyV"
"WUPyV" "MCPyV" "HPyV6" "HPyV7" "TSPyV" "HPyV9" "MWPyV"
"STLPyV" "HPyV12" "NJPyV" "LIPyV" "SV40" "TTV" "TTVmid"
"TTVmin" "HAV" "HBV" "HCV" "HDV" "HEV" "SENV" "HPV2"
"HPV6" "HPV... |
7a9076deb77002da27c665b313c71ffbd45b099c47fbfa85b2941ce0a3f5333c | Shell | 2,603 | 53 | #!/bin/bash
#
VIRUS="$3";
ORGAN="$4";
THREADS="$5";
#
if [ ! -f "$1" ] || [ ! -f "$2" ];
then
echo -e "\e[38;5;208mWARNING: $1 or $2 consensus file not found!\e[0m"
echo "TIP: before this, run: ./TRACESPipe.sh --run-meta --run-all-v-alig --run-de-novo"
echo -e "\e[38;5;198mDon't panic! This warning may be cause... |
aa5cc26218c1b1917853e01fa233c55e9677f64d97e3ad25986c2eeb6a8c8731 | Shell | 2,629 | 91 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for deta... |
89d124887d754573e357598d427a65316e2a7debac39a17eb8a1752bab2850ab | Shell | 2,639 | 56 | #!/bin/bash
#
VIRUS="$3";
ORGAN="$4";
THREADS="$5";
#
if [ ! -f "$1" ] || [ ! -f "$2" ];
then
echo -e "\e[38;5;208mWARNING: $1 or $2 consensus file not found!\e[0m"
echo "TIP: before this, run: ./TRACESPipe.sh --run-meta --run-all-v-alig --run-de-novo --run-hybrid"
echo -e "\e[38;5;198mDon't panic! This warning... |
aac03d5bfca7f3e9c8e092ab9b0f4365dfec9a3bfd5315f74b49b74155a1f429 | Shell | 2,666 | 31 | #!/bin/sh
### Job name
#PBS -N indexBacteria
### Number of nodes
#PBS -l nodes=1:ppn=64
#PBS -q bigmem
#PBS -j oe
cd /home/rrk24/scratch_grace/ANNOTATIONS/Genomes_BacteriaFungiMammalPlantProtistVirus
STAR="/gpfs/scratch/fas/gerstein/rrk24/bin/STAR_2.4.0d/STAR"
mkdir STAR_GENOME_BACTERIA1
$STAR --runMode genomeGenera... |
f4fcb9b6ecb3058ae93db70b39b2455f0e88c42e8c8cedd79fcbd037089754c4 | Shell | 2,688 | 94 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
ae4be16b531e9ed75d0d16ac71fa3175b908f9ae021bd52dd29d874960dae857 | Shell | 2,689 | 74 | #!/bin/bash
#
# INSTALLATION DEPENDENCIES:
#
# sudo apt-get install libopenblas-base
# conda install -c 'bioconda' art
# conda install -c 'bioconda' mummer4
#
RUN_ALL=1;
RUN_TRACES=1;
#
zcat MINIDB.fa.gz > ../src/VDB.fa
cd ../src/
#
if [[ "$RUN_ALL" -eq "1" ]];
then
./TRACESPipe.sh --get-all-aux
#
gto_fasta_ext... |
85580b8c51cae727f1a5021086483b4cc34b2fcbd9aa1b163064928c050a2440 | Shell | 2,690 | 78 | #!/bin/bash
# The script launches a docker container to run ASV benchmarks. We use the same docker
# image as our CI (i.e., dgllib/dgl-ci-gpu:conda). It performs the following steps:
#
# 1. Start a docker container of the given machine name. The machine name will be
# displayed on the generated website.
# 2. ... |
667b43708f8c023bd923ed9df549b15a922a67e4eeebd0381b5aac1fb3473db2 | Shell | 2,762 | 95 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
82071c8a298df473c71ed7ee8028a87e22aae8946f546114919638b672bfb321 | Shell | 2,857 | 100 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
7a90e796be191ce198c8273c1d8bd34b987116806fa11205bb2ff4c8a440a03d | Shell | 2,874 | 88 | #!/bin/sh
## Program: VMTK
## Module: Anaconda Distribution
## Language: Python
## Date: January 30, 2018
##
## Copyright (c) Richard Izzo, Luca Antiga, David Steinman. All rights reserved.
## See LICENSE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## t... |
d51bafe28bca39396cbf38ec2a90b12fdd24a065be0d67c5667f3121079ea0be | Shell | 2,875 | 60 | #!/usr/bin/env bash
# Reproduce every result and figure in this folder.
#
# Builds harmonypy twice (tag v2.0.2 and PR #56 as merged) into throwaway
# venvs, builds R harmony from the harmony2 branch with LAPACK enabled, runs
# all three on the same inputs, then plots.
#
# Needs: git, uv, a C++ toolchain, and R with dat... |
8143ad997546e64e5848a3272db22ede518168d713c9a5dfde50dc13db39bb33 | Shell | 2,942 | 93 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
fe6e9b63ab53c292f76966f999f8332af1a50665af992efbd3d4a1a79ac012b5 | Shell | 2,954 | 101 | #!/bin/bash
# -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024
# qsub_power_analysis.sh - Submit power analysis jobs (one job per subject/session)
# -----------------------------------------------------------------------------
basedir=/bcbl/home/public/Gar... |
f9426f923ea3b3ee925f27b4a026b90526f8b73629e2a8f6d182892c23288faf | Shell | 2,967 | 91 | #!/bin/bash
# Default base directory
DEFAULT_BASE_DIR="collections/faiss/"
BASE_DIR=${1:-$DEFAULT_BASE_DIR}
# Shift the arguments if a base directory is passed
if [ "$BASE_DIR" != "$DEFAULT_BASE_DIR" ]; then
shift
fi
# Check if the --all flag is passed
if [ "$1" == "--all" ]; then
# Get all subdirectories in the... |
1e2ab8307646e40a1e2d0d360a7a68642d2afcb8676f74c1e544c3ddabf9caff | Shell | 2,974 | 31 | #!/bin/bash
scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_pilot_31/*.fastq.gz .
zcat MT18021B_S1_L001_R1_001.fastq.gz MT18021B_S1_L002_R1_001.fastq.gz > MT18021B_S1_R1_001.fastq.gz
zcat MT18021C_S2_L001_R1_001.fastq.gz MT18021C_S2_L002_R1_001.fastq.gz > MT18021C_S2_R1_001.fastq.gz
zcat M... |
36941144c9da06b994665887f5937ea8403b6a7a3adef17fa87197318643d3af | Shell | 2,982 | 110 | # Please note that we can make no guarantees regarding the use of this patch
# and provide no warranties, explicit or implied.
# It has been tested for pixman version 0.38 in Ubuntu 18.04 and 20.04
#
# Preparation:
# 1. ensure a deb-src source is uncommented
# sudo nano /etc/apt/sources.list
if grep -q ^deb-src /etc/ap... |
fd35d065595b6474ed5f0d5bd0c85659be89c8b08afdedb1c0f721e984e78f8d | Shell | 2,990 | 65 | mkdir Fastq
## Public1NOSN (GSM4157068, Sample_6_N3)
mkdir Fastq/Public1NOSN
# SRR10433204
cp SRA/SRR10433204.1_1.fastq.gz Fastq/Public1NOSN/Public1NOSN_S1_L001_R1_001.fastq.gz
cp SRA/SRR10433204.1_2.fastq.gz Fastq/Public1NOSN/Public1NOSN_S1_L001_R2_001.fastq.gz
# SRR10433205
cp SRA/SRR10433205.1_1... |
2e25087f7f94509e8f278672687535a18b51871565d576dc5235dee7315f4319 | Shell | 3,010 | 95 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
basedir=/bcbl/home/public/Gari/VOTCLOC/main_exp
codedir=/bcbl/home/public/... |
36f597ee8b7237d8c6158464c782b37b0b81c5c83b61b07473fa463787c365ae | Shell | 3,025 | 89 | #!/bin/sh
# there is a problem when activating python3 envs from a shell script when using sh.
# the solution is to either run the script with bash (adding the #!/bin/bash shebang line) or use "source install.sh"
# or replace "source" with "." in the script, as I have done
# make working folder
mkdir ../../packages
... |
fc50f8f8a0da58b647df60268fe935a37af1197f8006e3049351bc0e5893820c | Shell | 3,032 | 105 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
a008906dd9a2fb46364082f5c566548beb2dae42c51da0dce15f49a8f67d29b4 | Shell | 3,034 | 94 | #!/usr/bin/env bash
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
nordic_modality="dwi"
script_dir=/export/home/tlei/tlei/soft/launchcontainers/MR_pipelines/01_prepare_nifti/prepare_dwi
TB_PAT... |
65d0b05a6506a3759e008b0b08dc0bb59b637019aa473e82f79642b5fc377465 | Shell | 3,074 | 91 | #!/bin/bash
#Function that tries to use awk's inplace editing to insert a code snippet
#Note that this requires a GenerateSnippet function to exist in the environment
#Inputs - a Target File
# - a Section Label
# - an option number of max insertions, defaulting to 1
# if there are multiple AUTO-s... |
a8e27d9cfd23985336684c7be8ae9da9f1cca4752109b4320d97d950a9f990d9 | Shell | 3,092 | 42 | #!/bin/bash
zcat MT18021B_S1_L001_R1_001.fastq.gz MT18021B_S1_L002_R1_001.fastq.gz | gzip > MT18021B_S1_R1_001.fastq.gz
zcat MT18021B_S1_L001_R2_001.fastq.gz MT18021B_S1_L002_R2_001.fastq.gz | gzip > MT18021B_S1_R2_001.fastq.gz
#
zcat MT18021C_S2_L001_R1_001.fastq.gz MT18021C_S2_L002_R1_001.fastq.gz | gzip > MT18021C_S... |
3eaf1fce681e37e4c3ca7adfe09ef7c3a858a8ca51166257782d625463a71f7d | Shell | 3,128 | 109 | #!/bin/bash
# Check for duplicate DICOM files by comparing pixel data MD5 hash
# Requires: AFNI tools (dicom_hdr, to3d)
# Usage: ./check_duplicate_dcm_md5.sh <dcm_folder>
if [ $# -eq 0 ]; then
echo "Usage: $0 <dcm_folder>"
exit 1
fi
DCM_FOLDER="$1"
if [ ! -d "$DCM_FOLDER" ]; then
echo "Error: Directory ... |
a7727c22d2aa521d7e97bbeca03728961e4c7e1c1a83e52dc404bbeeb9c2776e | Shell | 3,146 | 109 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for deta... |
68893a35c6b5b93fda2624ecc15930b4d049662942c0c273f5b1012eec69ce61 | Shell | 3,166 | 104 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
script_dir=$(dirname "$(realpath "$0")")
tbPath=/export/home/tlei/tlei/to... |
644abfe26ff782d4f65442691bd99bed62d51f1f54a8d6ce72e8db3687031663 | Shell | 3,184 | 79 | #!/bin/bash
#This script autogenerates the conda install commands for TRACES_install.sh
# based on the dependencies in the dependencies.yml file
#It attempts to modify the target in place, with a backup which is either
# deleted or restored depending on the success of the modification
#This script requires yq (a CLI... |
8d6fc757ad837249ea79543a098bcf170a110a94aaf83e8cdffe0f61cc125311 | Shell | 3,185 | 100 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
project=VOTCLOC
basedir=/bcbl/home/public/Gari/$project/Japan_27ses_dp
ou... |
09ae28baf96d68a39511dd34c1fd8f98605653d4e84eed9fd5cf1d56e035f000 | Shell | 3,373 | 94 | #!/usr/bin/env bash
# Refresh every cached inference column + every downstream eval/figure/table
# using the current model checkpoints. Intended to keep the manuscript's
# tables, figures, and inline numbers internally consistent after any change
# to the trained-model checkpoints in data/pd_channel_cache/, data/hemi_c... |
b8716ed9d132db20b2c84b07acd3fe39aba7b082d514fcc15ebf53f756532973 | Shell | 3,413 | 107 | #!/bin/bash
#SBATCH -p steinlab
#SBATCH -n 1
#SBATCH --mem=10g
#SBATCH -t 3:00:00
#Generate list of snps for specific chromosomes, and filter out snps with missing any of the subjects
module add plink;
for i in {1..22}
do
#eQTL
plink --bfile /proj/steinlab/projects/R00/atac-qtl/EMMAXResult/Genotype_Hg38/${i}.dose.R... |
2c17af32396ac3e79f0732f15540740b3346b5a7529eb8aef9acf7ab0c28144e | Shell | 3,443 | 124 | #!/bin/bash
# Check for duplicate DICOM files with detailed information
# Usage: ./check_duplicate_dcm.sh <dcm_folder>
if [ $# -eq 0 ]; then
echo "Usage: $0 <dcm_folder>"
exit 1
fi
DCM_FOLDER="$1"
if [ ! -d "$DCM_FOLDER" ]; then
echo "Error: Directory $DCM_FOLDER does not exist"
exit 1
fi
if ! comm... |
78543763c28d1a677725f24e936d715646f6856199b03bdb4f92a35c9d0e0b5f | Shell | 3,453 | 107 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
project=votcloc
basedir=/bcbl/home/public/Gari/VOTCLOC/main_exp
codedir=/b... |
fee7c8fadf44bbd8296c8780dfe9f118e3eab6ee540e27798846f0b9af3c4569 | Shell | 3,470 | 40 | #!/bin/bash
set -e
cd ..
# for debugging use `dryrun`, otherwise use `run`
WANDB_MODE=run
ENV=adrian-exodus
GROUP=$1
ARCH=$2
EPOCHS=50
BATCH_SIZE=512
CONFIG=configs/model_configs/$ARCH.yaml
if [ -n "$1" ]
then
GROUP=$1
fi
# FROM SCRATCH RECOGNITION CASIA
python main.py --config_file $CONFIG --name $ARCH-scr... |
5ec4d3e87e415b53db0fabcfcc9361d010a501fb988c6926211267f257ac0950 | Shell | 3,502 | 92 | #!/bin/bash
# Function to check if a package is installed
check_package() {
package_name="$1"
print_output="$2"
if dpkg-query -W -f='${Status}' "$package_name" 2>/dev/null | grep -q "install ok installed"; then
if "$print_output"; then
echo -e "\e[32mPackage '$package_name' is install... |
84477aacf36302c3d6bb105373f1da3b57a2f06a7080abf42ffe64f14bab8bc1 | Shell | 3,623 | 58 | # Run notebooks and Rscripts to create the figures
# conda activate figure_env
# bash run_notebooks.sh TestFigs/
# ### Prep data & annotations ####
# jupyter nbconvert --to pdf --execute notebooks/Prep_filter_lowExp.ipynb --output-dir $1
# jupyter nbconvert --to pdf --execute notebooks/Prep_rate_SDs.ipynb --output-dir... |
38110c26dd6538fd43dd5260197d382f81f702392e6f2788cc04a7af34808e29 | Shell | 3,643 | 102 | #!/bin/bash
#
# ==============================================================================
# | |
# | THIS PROGRAM COMPUTES COMPLEXITY PROFILES |
# | ========================================= ... |
d88a056728a4c7cdb76801b76ff9f236f03a21b7bafa2262aba818d16b43cfd2 | Shell | 3,731 | 122 | #!/usr/bin/env bash
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
script_dir=$(dirname "$(realpath "$0")")
TB_PATH="/export/home/tlei/tlei/toolboxes"
# nordic parameters (must match your MATLA... |
2c161ade54373994a133a5ddd3f8161f3a1e684496d03708c042c872d304fc37 | Shell | 3,744 | 102 | #!/bin/bash
#
# 1 -> TURNS THE RESPECTIVE COMPUTATION ON
# 0 -> IGNORES THE RESPECTIVE ACTION
#
GET_UTILS=0;
INSTALL_PIPELINE=1;
#
# ==============================================================================
# ################################# FUNCTIONS ##################################
# =========================... |
9f54149d519872dfdd4cf137794b33657e90a97ec0d3ef86ece9dfb790153406 | Shell | 3,762 | 106 | #!/usr/bin/env bash
set -euo pipefail
# The repo tracks `data` as a symlink to `../example_data`. A fresh CI checkout
# has the symlink, but not the target directory, so hydrate the documented
# example datasets and weights on demand.
repo_root="$(pwd)"
LOCAL_EXAMPLE_DATA_ROOT="${SM_CI_LOCAL_EXAMPLE_DATA_ROOT:-/home/... |
869d1da4fbd2a299faa9095dbbb397f28a078cd0e79932f1c1f0a5959cc2fad8 | Shell | 3,769 | 125 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
baseP="/scratch/tlei/VOTCLOC"
script_dir="$(cd "$(dirname "${BASH_SOURCE[0... |
6720c35fbca71009bc50d68e64fe950b18dcf8918afd49dc30884da776c034c1 | Shell | 3,797 | 90 | #!/bin/bash
#
#USAGE: TRACES_overall.sh reftype pattern organ [maxdepth=1000]
# RefType is one of viral, specific, cy, mtdna and defines the type of reference we are calculating stats for
# Pattern defines the specific reference used
# for cy and mtdna this should be cy and mt respectively
# for specifi... |
872ad16934074e8c7f41aa217db2277d38cc2c7c7518eb9460eeb74e075cfda4 | Shell | 3,879 | 143 | #!/bin/bash
output_dir=$1
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
train_fast5_links="${SCRIPT_DIR}/links_wick_data_train.txt"
test_fast5_links="${SCRIPT_DIR}/links_wick_data_test.txt"
basecalls_links="${SCRIPT_DIR}/links_wick_basecalls_test.txt"
references_links_general="${SCRIPT... |
bccc606f73bac6eff0a6962484528228f8dad709a9204938f770325c44b2e472 | Shell | 3,915 | 122 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ===========================================================================
# NOTE: prfresult container only works on the BCBL server, NOT on DIPC.
# Do not submit this script on DIPC — the container will fail.
# Use the equivalent ... |
62f3fe446a2f9ca55cd5ae58ab2331009d7c77b0a3ad9fed2b09aadbc91318a3 | Shell | 3,951 | 94 | #!/bin/bash
# Run the benchmark: one process per configuration, results appended to
# results.jsonl, progress to stdout. Within each dataset the two builds run
# back to back, so a change in the server's load affects both. A lock keeps
# two invocations from running at once.
#
# usage: ./run.sh [stage ...]
# core ... |
b91014db46bf8e949f5c40369d1c218ae9d32d47242e70d4da343d6b8e59e687 | Shell | 3,968 | 121 | #!/bin/bash
function ConstructOutPath {
path=$1; shift
echo "$(dirname "$path")/DN-$(basename "$path")"
}
function CreateLink {
path=$1; shift
ln -s "$(readlink -f "$path")" "$(ConstructOutPath "$path")";
}
#Taken from stackoverflow question 1527049
# Answer from user Nicholas Sushkin
function JoinBy... |
d8fabb5d5932ba35eac0c3cdb674c78e1fc4e2ad374da1dbfe74af7f1f48eaaa | Shell | 4,007 | 107 | #!/bin/bash
#
EMAIL="$1";
TOP_SIZE=500;
#
declare -a INDIVIDUALS1=('I1' 'I3' 'I4' 'I6' 'I7' 'I8' 'I12' 'I14' 'I15' 'I16' 'I18' 'I19' 'I29' 'I30')
declare -a INDIVIDUALS2=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I... |
e32e0fcf474049565fdda446b724ebae699d23f5d8d7cf11c25e28134822c5e7 | Shell | 4,055 | 107 | #!/bin/bash
#
EMAIL="$1";
TOP_SIZE=500;
#
declare -a INDIVIDUALS1=('I1' 'I3' 'I4' 'I6' 'I7' 'I8' 'I12' 'I14' 'I15' 'I16' 'I18' 'I19' 'I29' 'I30')
declare -a INDIVIDUALS2=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I... |
1b48ac34480a6c366557b0b909005a547318086379e63d56c0ef7423f24f95d2 | Shell | 4,096 | 38 | wget ftp://ftp.ensemblgenomes.org/pub/plants/release-24/fasta/aegilops_tauschii/dna/*.dna_sm.toplevel.fa.gz
wget ftp://ftp.ensemblgenomes.org/pub/plants/release-24/fasta/amborella_trichopoda/dna/*.dna_sm.toplevel.fa.gz
wget ftp://ftp.ensemblgenomes.org/pub/plants/release-24/fasta/arabidopsis_lyrata/dna/*.dna_sm.topleve... |
4dae33cd4ef2349d13ce67eb8967b1b567d1cc388c4e9d8605df032c859a13aa | Shell | 4,097 | 90 | #!/bin/bash
mkdir hilander_checkpoint
####################### ITER 0 #######################
# iter 0 (supervised baseline) - train Smooth-AP
CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7
python Smooth_AP/src/main.py \
--dataset Inaturalist --lr 1e-5 --fc_lr_mul 1 \
--n_epochs 400 --bs 384 \
--source_path "../../data/" --embe... |
792c036138abefc090a5f066b613b0a549add9d92ecf6aab81e1dc0675da8f53 | Shell | 4,127 | 57 | #!/bin/bash
# Create the collections folder if it doesn't exist
mkdir -p collections
# Array of URLs to download
urls=(
"https://rgw.cs.uwaterloo.ca/pyserini/indexes/faiss/faiss-flat.beir-v1.0.0-arguana.bge-base-en-v1.5.20240107.tar.gz"
"https://rgw.cs.uwaterloo.ca/pyserini/indexes/faiss/faiss-flat.beir-v1.0.... |
457cb011db151a93bb5d4d83009f075504715cb5fd74f244c655c88acfa308b2 | Shell | 4,144 | 134 | #!/bin/bash
#==============================================================================
# Universal PRF analysis run script
# Handles: prfprepare, prfanalyze-vista, prfresult
# Auto-detects cluster (DIPC or BCBL) and adjusts bindings accordingly
# Determines step from script name or STEP environment variable
#====... |
a34dbc45fd9b0295a1ee552da576b35357709496b20b24c524c5a093d40dd2cb | Shell | 4,242 | 99 | #!/bin/bash -e
MMSEQS="$1"
QUERY="$2"
BASE="$4"
DB1="$5"
DB2="$6"
DB3="$7"
USE_ENV="$8"
USE_TEMPLATES="$9"
FILTER="${10}"
TAXONOMY="${11}"
EXPAND_EVAL=inf
ALIGN_EVAL=10
DIFF=3000
QSC=-20.0
MAX_ACCEPT=1000000
if [ "${FILTER}" = "1" ]; then
# 0.1 was not used in benchmarks due to POSIX shell bug in line above
# EXPAND_E... |
562e10470111cb0b73932bb4f9b82b39c3b9aed3d996666063de1613c0c91b34 | Shell | 4,253 | 123 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
script_dir=$(dirname "$(realpath "${BASH_SOURCE[0]}")")
fp_version=25.2.5... |
b2d8c5ed89f533cfc949bd5c12e73e565f8683b36088e89fa053a096e5bc9d86 | Shell | 4,286 | 184 | #!/bin/bash
readonly CUDA_VERSIONS="11.8,12.1,12.4"
readonly TORCH_VERSION="2.1.0"
readonly PYTHON_VERSION="3.10"
usage() {
cat << EOF
usage: bash $0 OPTIONS
examples:
bash $0 -c
bash $0 -g 12.1
bash $0 -g 12.1 -p 3.10
bash $0 -g 12.1 -p 3.10 -t 2.1.0
bash $0 -c -n dgl-dev-cpu
Create a developement environ... |
61a3eb24cf364da66115eac0becce051fbccda0383f9833ee748c873fdb7506f | Shell | 4,304 | 156 | #!/bin/bash
output_dir=$1
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
train_fast5_links="${SCRIPT_DIR}/links_wick_data_train.txt"
test_fast5_links="${SCRIPT_DIR}/links_wick_data_test.txt"
basecalls_links="${SCRIPT_DIR}/links_wick_basecalls_test.txt"
references_links_general="${SCRIPT... |
4dbcb9f1d64194e0b050cd8a84eb5c7a68e9e6cb5462a1b3fca0814342fc26e6 | Shell | 4,426 | 56 | cd /gpfs/scratch/fas/gerstein/rrk24/ANNOTATIONS/Genomes_BacteriaFungiMammalPlantProtistVirus/PlantGenomes_fasta
rm Plant*.fa
## Extract
gunzip *.fa.gz
## Fix missing chromosome number in first sequence of Solanum_lycopersicum.SL2.40.24.dna_sm.toplevel.fa
cat Solanum_lycopersicum.SL2.40.24.dna_sm.toplevel.fa | sed 's... |
5d3b56e95b29d11c6f87a87647e4c0ab6d4a7d688da43f1fa99a2297f49ac091 | Shell | 4,605 | 148 |
echo "Script to run in configuration folder "
##############INPUT DESCRIPTOR PARAMETERS########
#################################################
programtouse=op_comp_3bcc
rc_radial=1.9
rc_triplets=1.8
number_of_particles=1000
nf=1 #number of frames of the dataset (train+test)
seed=12345 #to select frames
#######... |
b64345371f3f333f72a085adf4df1aeb37fe11cc199f209b4e45ac05f9c6265a | Shell | 4,636 | 132 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2020-2023 Garikoitz Lerma-Usabiaga
# Copyright (c) 2022-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
basedir="/bcbl/home/pub... |
63ecbfd0b8d8919013bd73cb9400eb62608aa043521b925ecac1945baf172e18 | Shell | 4,672 | 119 | #!/bin/bash
# executable modules
uTR=../uTR
uTR_param="-stda"
gen_units=gendata/gen
check_uTR=check_uTR/acc
checkTRF=checkTRF/checkTRF
tmp=tmp
mkdir $tmp
num_TRs=1000
listError=(0.0 0.01 0.03 0.05 0.1 0.15)
listPattern=("AC_AG" "ACC_GTT" "AAG_AG" "AAG_AGG" "AAAG_AG" "AAAG_AG_AAAG" "AAAG_AG_AGGG_AG_AAAG" "AGGGG_AAA... |
db456f27d9f643d22c4c093cbf590024563c3e1d0e80ad4aca9c15c335ff70a1 | Shell | 4,777 | 126 | #!/usr/bin/env bash
# Phase 1 from-scratch retrain launcher.
#
# Runs every model training sequentially under conda env morgoth, writing per-step
# logs into results/retrain_v1/. Use `tail -f` on individual logs to monitor;
# when the chain completes, $RUNDIR/COMPLETE will exist with the final exit code.
#
# Total expe... |
55428eac29406664edfdafe8fea53fdb71849225f6cc72f85967364b3bba76bc | Shell | 4,835 | 125 | #!/bin/bash
#
# sudo apt-get install libopenblas-base
# conda install -c 'bioconda' art
#
RUN_ALL=1;
zcat MINIDB.fa.gz > ../src/VDB.fa
cd ../src/
#
if [[ "$RUN_ALL" -eq "1" ]];
then
./TRACESPipe.sh --get-all-aux
#
gto_fasta_extract_read_by_pattern -p "AY386330.1" < VDB.fa > B19.fa
gto_fasta_extract_read_by_patt... |
28e2d88b1e5cd96212bcc2f39e8c842eb11de7fd85ad8812f7244453bd769b69 | Shell | 4,892 | 137 | #!/usr/bin/env bash
## build.sh: compile manuscript outputs from content using Manubot and Pandoc
set -o errexit \
-o nounset \
-o pipefail
# Set timezone used by Python for setting the manuscript's date
export TZ=Etc/UTC
# Default Python to read/write text files using UTF-8 encoding
export LC_ALL=en_US.UTF-... |
2f7d56fdbc8121fee6e9eeab144cab29773a45c8b441ffd6949bee7cf1cf4a2e | Shell | 4,897 | 129 | #!/bin/bash
CURRENT_DIR=$(dirname "$0")
RESET_PARAMS=false
SKIP_TRIAL_GEN=false
SEED1=$1
SEED2=$2
shift 2
while [[ "$#" -gt 0 ]]; do
case $1 in
--skip-trial-gen) SKIP_TRIAL_GEN=true ;;
--reset-params) RESET_PARAMS=true ;;
*) echo "Unknown parameter passed: $1"; exit 1 ;;
esac
shi... |
c632e12ac50b6814f04368223a354c8811337cb143518fa5ba17a64e971cf746 | Shell | 4,902 | 140 | ####1 TF Footprint analysis
##prepare files
#extrat peaks
perl -p -i -e 's/,/\t/g' *csv
perl -p -i -e 's/\"//g' *.csv
perl -p -i -e 's/^M//g' *csv
awk '{print $2"\t"$3"\t"$4"\t"$11"\t"$14"\t"$15}' ground.meristem.csv >ground.meristem.bed
awk '{print $2"\t"$3"\t"$4"\t"$11"\t"$13"\t"$14}' epidermis.csv >epidermis.bed
#ex... |
fb4454924219a5bde34bb09fe4502947209c2fa68a333658e7c0ebc35e4083e2 | Shell | 4,965 | 106 | #!/usr/bin/env bash
# Paired source-only documentation regression; no SM runtime execution.
set -euo pipefail
cd "$(git rev-parse --show-toplevel)"
prepare_only=false
if [[ ${1:-} == --prepare-only ]]; then
prepare_only=true
shift
fi
tasks=("$@")
if (( ${#tasks[@]} == 0 )); then
tasks=(C01 C02 C03 C04 C05 C06 N42... |
f26065f53539783fce313cf7ac3035b2f9b62bca09a9354b06d34c7a3d6a18ac | Shell | 5,065 | 177 |
echo "Script to run in configuration folder "
##############INPUT DESCRIPTOR PARAMETERS########
#################################################
programtouse=/home/francegm/Scrivania/CoarseGraining/alpha_nes_mixture/descriptors_utility/distangoli/bin/op_comp_3bcc
path_ut=/home/francegm/Scrivania/CoarseGraining/alpha... |
dae404052dfcbda6bc6ff5251223c54a58973df840eed2a06433178c36272202 | Shell | 5,207 | 121 | #!/usr/bin/env bash
# ------------------------------------------------------------------------
# test-ensure-dotnet.sh - guards the contract of ensure-dotnet.sh.
#
# Runs in well under a second, needs no network and no real .NET SDK: a stub
# dotnet on PATH mimics the agent image (8.0.423 only, so any 10.x pin fails).
... |
d1e181717583024fe7d8176aabd1d39f448aa7e3f2e2b1ea9df89bc6a6c6424e | Shell | 5,351 | 109 | mkdir Fastq
##=====================================================================================================================
#### Public1NOSN
cp -r /home/ajl1213/Projects/PD/SciAdv_Data/snRNAseq/00b_GetPublicData/Fastq/Public1NOSN Fastq/
#### Public2_1NOSN
cp -r /home/ajl1213/Projects/PD/SciAdv_Data/snRNAseq/... |
d0e687b92bc713710c9caee19681caff2de1824cb62d326092565b3c945f9a23 | Shell | 5,359 | 163 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration — IPS / BCBL
# ---------------------------------------------------------------------------
baseP="/bcbl/home/public/Gari/VOTCLOC/main_exp"
codedir="$bas... |
8e56869930e83664baa14d9b2b9066897f84ff24d91c26111d8c21dd8e283b48 | Shell | 5,409 | 51 | #!/bin/bash
set -e
cd ../
# for debugging use `dryrun`, otherwise use `run`
WANDB_MODE=run
ENV=adrian-exodus
GROUP=$1
ARCH=$2
DATASET=$3
EPOCHS=50
BATCH_SIZE=512
CONFIG=configs/model_configs/$ARCH.yaml
CHECKPOINT="$GROUP:$ARCH-$DATASET"
############################################################################... |
9248f8c5bf2593afb690ae303f1e7cf98cf43a2ca29ecb3a04bd72b892806f45 | Shell | 5,420 | 130 | #!/bin/bash
ValidTypes=("viral" "specific" "mtdna" "cy");
ViralNamesFile="viral_names.txt"
MetaFile="../meta_data/meta_info.txt"
ResultsDir="../output_data/TRACES_results"
SpecAlnDir="../output_data/TRACES_specific_alignments"
#Assumes existence of Mapping files, Breadth and Depth statistics files, and Top files
#Cre... |
0c9d462c472425eccccc39c8d317e55a25683a49414a8bdc42fb24a7cc2ac070 | Shell | 5,452 | 106 | #!/bin/bash
# TeamCity entry point: Linux counterpart of tcbuild.bat. Builds + tests Osprey with
# TeamCity service messages, then packages the redistributable so it is published as an
# artifact of this per-commit config.
#
# The real work is in build.ps1 / package.ps1, which are cross-platform: pwsh is the
# project ... |
2896e4fe8c6ceb429683b4a6ba654a7c40605e94e6ce78d32ba3e6fbfbcafc58 | Shell | 5,618 | 145 | #/bin/bash
set -x
pths=`cygpath -a -u ${WORKSPACE}/EXAMPLES_test`
pths_matlab=`cygpath -a -w ${WORKSPACE}/EXAMPLES_test`
wksp_matlab=`cygpath -a -w ${WORKSPACE}`
pth_fsda=`cygpath -a -w ${WORKSPACE}/FSDA`
/usr/bin/find $pths -name "*.m" >flist
# cat flist
# MATLAB R2009b
rm -f test_runner2009b.m
rm -f execution_log... |
cc9201c99bb85e35bf746bac076aab6efae7d0445d00f38956b5027f8dded8bb | Shell | 5,632 | 102 | #!/usr/bin/bash
function secure_file {
if test -f $1.orig; then
rm $1
cp $1.orig $1
else
cp $1 $1.orig
fi
}
echo "Starting daemons"
systemctl enable kafka.service zookeeper@kafka.service
systemctl start kafka.service zookeeper@kafka.service
#echo "Removing previous partitions"
#ka... |
7d25f18c14aed4cf89de09f7ae9d792492562ce6fb6efe02f458f4770c328173 | Shell | 5,640 | 64 |
#### X4870NOSN
mkdir Fastq/X4870NOSN
## /home/CBFG/20210623_Nextseq (SW213)
cp /home/CBFG/20210623_Nextseq/SW213_1_S1_R1_001.fastq.gz Fastq/X4870NOSN/X4870NOSN_S1_L001_R1_001.fastq.gz
cp /home/CBFG/20210623_Nextseq/SW213_1_S1_R2_001.fastq.gz Fastq/X4870NOSN/X4870NOSN_S1_L001_R2_001.fastq.gz
cp /home/CBFG/20210623_Ne... |
80dff421c1a7e2b2a876c930db9f047a2215164ae696fc67f6c02f2871565ca7 | Shell | 5,716 | 115 | #!/bin/bash
# ------------------------------------------------------------------------
# clean.sh - wipe pwiz build artifacts.
#
# Linux/macOS counterpart of clean.bat, and the pwiz-sharp analogue of cpp
# pwiz's clean.sh two levels up. Same flags and same behaviour as clean.bat;
# keep the two in step when either cha... |
8c8d2d387a591d9b2e52767e3a576cc4ee2944e9aa94b665f9e2d5d239497491 | Shell | 5,766 | 166 | #!/usr/bin/env bash
set -euo pipefail
cd /raid/mbrown/simplemind
SMCORE_BIN="/raid/mbrown/.micromamba/envs/smcore/bin"
export PATH="$SMCORE_BIN:$PATH"
ARTIFACT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATASET_CSV="$ARTIFACT_DIR/kidney_ct_images_40.csv"
BB_ADDR="${BB_ADDR:-127.0.0.1:18082}"
PAYLOAD_HOST="${... |
14a75c695b78a6adee3c105b592fdf1f96b59cc505be4b442f752874c572f734 | Shell | 5,859 | 178 | #!/usr/bin/env bash
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# ---------------------------------------------------------------------------
# Configuration
# ---------------------------------------------------------------------------
baseP="/scratch/tlei/VOTCLOC"
codedir="$baseP/code"
script_dir="$(cd "$(di... |
20101ee8f83f521b4f348562e575998b0fcaa0447afb0ac87d44fe708e17a1e0 | Shell | 6,024 | 32 | wget -qO- ftp://ftp.ensemblgenomes.org/pub/protists/release-24/fasta/albugo_laibachii/dna/*.dna_sm.toplevel.fa.gz | gunzip -c | sed "s/>/>Protist:albugo_laibachii:/" >> Protists.fa
wget -qO- ftp://ftp.ensemblgenomes.org/pub/protists/release-24/fasta/bigelowiella_natans/dna/*.dna_sm.toplevel.fa.gz | gunzip -c | sed "s/>... |
29cff66deae260bf2c1751f91a11bf4d84d530e3c926e87949712ac636481aac | Shell | 6,026 | 188 | #!/bin/bash
# Find DICOM files with identical series/image date/time
# Usage: ./check_duplicate_acq_time.sh <dcm_folder> [--output <file>]
DCM_FOLDER=""
OUTPUT_FILE=""
# Parse arguments
while [[ $# -gt 0 ]]; do
case $1 in
--output)
OUTPUT_FILE="$2"
shift 2
;;
*... |
3fe84f777ba04e5f4d1eed3fba3614601130cc0fcc62004640ffd00f9d1c757b | Shell | 6,176 | 124 | #!/usr/bin/env bash
# ------------------------------------------------------------------------
# tcbuild.sh — single TeamCity entry point for pwiz-sharp on Linux
# (Core Linux x86_64, bt17). Analogue of tcbuild.bat.
#
# Sequence (mirrors tcbuild.bat, minus the Windows-only steps):
# 1. dotnet --version (logs which SD... |
a67d70f9c4f25ec9575d00d55ec2b4fe652c92f175e025f9870621ee12e52f00 | Shell | 6,220 | 168 | #!/usr/bin/env bash
# =============================================================================
# launch_glm_local.sh — Local launcher for run_glm.py
#
# Usage:
# bash launch_glm_local.sh -n <analysis_name> -s 01,10
# bash launch_glm_local.sh -n <analysis_name> -f subseslist.txt
# bash launch_glm_local.sh -... |
57ca83f52b6aaa13a070cdfe1d3963262dd0ae8924a707c580d5fa869e92b39b | Shell | 6,304 | 84 | wget -c http://ftp.sra.ebi.ac.uk/vol1/run/ERR267/ERR2676410/A1-1-1_BM.bam
wget -c http://ftp.sra.ebi.ac.uk/vol1/run/ERR267/ERR2676411/A1-1-1_tail.bam
wget -c http://ftp.sra.ebi.ac.uk/vol1/run/ERR267/ERR2676757/A1-2-1_BM.bam
wget -c http://ftp.sra.ebi.ac.uk/vol1/run/ERR267/ERR2676758/A1-2-1_tail.bam
wget -c http://ftp.s... |
a9fed423f1010c958d905213f833b707fae0262cd86ade4493386f71a3fdc277 | Shell | 6,315 | 186 | #!/usr/bin/env bash
# =============================================================================
# run_glm_slurm.sh — Slurm launcher for run_glm.py
#
# Usage:
# bash run_glm_slurm.sh -n <analysis_name> -s 01,10
# bash run_glm_slurm.sh -n <analysis_name> -f subseslist.txt
# =====================================... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.