sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9465c4f617df1729953915cf5a5128240c43250dc641f5742a477e75be45f5cd | Shell | 1,385 | 46 | #!/usr/bin/env bash
## Compare overlap similarity between segmentations:
## Simple CNN and Simplified CNN
## XCorrelation
TMPDIR=$(mktemp -d --tmpdir)
trap "rm -rf $TMPDIR" 0 1 2 15
set -ux
printf "id,xcorr,lhc,lcsf,rhc,rcsf\n" > $OUT_FILE
compare_cnns() {
local BASE_DIR="${HVR_VALIDATION_DIR:-$(git -C "$(dirname... |
0c0b78d699ce0d4710775909e06f203113d170404615bbc49a3b086e4b63a011 | Shell | 1,393 | 52 | #! /bin/bash
dirname="temp"
mkdir -p -- "$dirname"
task_name=""
config_num=""
moment=$(date +"%m%d_%T")
#log_file="train_log_$moment.txt"
log_file="train_log.txt"
function usage
{
echo "-t or --task for task_name; -i or --config for config_num; -l or --log for log_file"
}
while [ "$1" != "" ]
do
case "$1" in
... |
7590e184032ad2cdc77357a0376fd9af510c64f01a0066893ce87b9fc4018491 | Shell | 1,393 | 38 | #!/usr/bin/env bash
set -e
echo -e " START: T2w2T1Reg $0"
WD="$1"
T1wImage="$2"
T1wImageBrain="$3"
T2wImage="$4"
T2wImageBrain="$5"
OutputT1wImage="$6"
OutputT1wImageBrain="$7"
OutputT1wTransform="$8"
OutputT2wImage="$9"
OutputT2wTransform="${10}"
T1wImageBrainFile=`basename "$T1wImageBrain"`
if [ ! -d "$WD" ];... |
7abf0b227cfb240664ecbc264e23a4836e17e69431d6d3820f3bb8caaa5d8b4d | Shell | 1,439 | 39 | #!/bin/bash
#SBATCH --partition=gpu4_medium,gpu8_medium,gpu8_long,gpu4_long
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G
#SBATCH --gres=gpu:1
#SBATCH --job-name=TCGA_02
#SBATCH --output=log_TCGA_02_%A_%a.out
#SBATCH --error=log_TCGA_02_%A_%a.err
module load pathganplus/3.6
python3 ./run_represe... |
54b8a3d01839d0b9440006ea3de16d3ad805b3ab3c1b17edd72f602924fbb624 | Shell | 1,443 | 50 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=500G
#$ -l mem_free=20G
#$ -l h_vmem=20G
#$ -l h_rt=96:00:00
#$ -o ./logs
#---------------------------------------------------------------------
#The two paths below are the same, replace for the path to your kmer counts. -t above is the number of samples
path=$1
outdir=$1
ref... |
d269856cbb50c88eb6596fefa163d581ceef9c19429fe508db69ef8108724206 | Shell | 1,443 | 29 | #!/bin/bash
######################################################################################
###############clean the vcf file to get rid of the XY and MT snps ###################
######################################################################################
if [ -v $1 ]
then
echo 'this script should be ... |
fc45ab9191497f542ed9134164efc2a598ec9146bfa51c6bbbbaa173e18cc16a | Shell | 1,447 | 69 | #!/bin/bash
set -e
while getopts "sb:" opt; do
case $opt in
s) use_sra=1 ;;
b) branch="$OPTARG" ;;
*) echo "Usage: $0 [-s] [-b <branch_name>]" && exit 1
esac
done
shift $(($OPTIND - 1))
if [ "$branch" == "" ] ; then
branch="master"
fi
set -x
yum install -y git zip unzip pandoc
g... |
869e8e7b544a342e01cb3b6bbd6184b45eb63c72aae3fae83cfe39af28094052 | Shell | 1,456 | 38 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-init-pip
LIBCUML_WHEELHOUSE=$(rapids-download-from-github "$(rapids-artifact-name wheel_cpp libcuml cuml --cuda "$RAPIDS_CUDA_VERSION")")
CUML_WHEELHOUSE=$(rapids-d... |
2ff5e3b58546940ec58682563cfb4955b9cb88c63cb6d76d3c18f104bd681b22 | Shell | 1,461 | 51 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=500G
#$ -l mem_free=26G
#$ -l h_vmem=26G
#$ -l h_rt=96:00:00
#$ -o ./logs
#$ -pe local 4
#---------------------------------------------------------------------
fastq=$1
outdir=$2
mkdir -p $outdir
refpath=$3
#--------------------------------------------------------------------... |
cc11a745bcf35ab8a068cf7974f2ffafbce57b0cee66bbdaeb757216ce3e4ac0 | Shell | 1,462 | 89 | #!/bin/sh
#
# Builds an index from UMD Freeze 3.0 of the Bos Taurus (cow) genome.
#
BASE_CHRS="\
Chr1 \
Chr2 \
Chr3 \
Chr4 \
Chr5 \
Chr6 \
Chr7 \
Chr8 \
Chr9 \
Chr10 \
Chr11 \
Chr12 \
Chr13 \
Chr14 \
Chr15 \
Chr16 \
Chr17 \
Chr18 \
Chr19 \
Chr20 \
Chr21 \
Chr22 \
Chr23 \
Chr24 \
Chr25 \
Chr26 \
Chr27 \
Chr28 \
Chr29 ... |
39e5091469fd080ccbe74a41073104dacb876115f60e2ae11bc49e53a0974141 | Shell | 1,481 | 45 | #!/bin/sh
# Define input and output directories
int=~/Input
out=~/Output
# Define the path to ChromHMM.jar
chromhmm_jar="/net/bmc-lab5/data/kellis/users/zunpeng/04_Softwares/ChromHMM/n/ChromHMM/ChromHMM.jar"
# Define the list of brain tissues and corresponding sample IDs, defined from the Epimap data
brain_samples=(... |
97ce94194a5c260e0aae290a35edcab41d10b563b85f9b02e8595d3566781291 | Shell | 1,483 | 40 | #!/bin/bash
#SBATCH --job-name=process_row # Job name
#SBATCH --ntasks=1 # Number of tasks
#SBATCH --cpus-per-task=4 # Number of CPU cores per task
#SBATCH --time=120:00:00 # Maximum runtime
#SBATCH --mem=16G # Memory allocation
#SBATCH --array=1-1400%400
BIDSDIR=OASIS/raw_data # Input BIDS directory
DERIVSDIR=O... |
904d0bdda52566480c2967fdac0713f6c75726423756600c3bee4d99d6281115 | Shell | 1,490 | 46 | #!/bin/bash
# Description:
# Run FSL randomise for young vs. old baseline group comparisons for percent variance in BOLD explained by HRCO2, HR, and CO2 regressors.
# Load the FSL module for accessing FSL tools
module load FSL
# Define paths for mask, output directory, and input files
mask_path="data/masks/MNI152_T1... |
aa943494cdd78336ae3aa12f53605aa1436320ec459045dc8236490070758a5f | Shell | 1,501 | 62 | #!/bin/bash
# Training script for RCM Lesion Classification (ResNet34 + GRU)
# Usage:
# bash scripts/run_lesion_training.sh # Regular training
# bash scripts/run_lesion_training.sh --test # Test run with small dataset
# bash scripts/run_lesion_training.sh --fine_tune PATH # Fine-t... |
5a07a15c92c55bfd53c6fa18f568bf62a574d7af8be3b58664c6d78d020b8593 | Shell | 1,507 | 46 | #!/bin/bash
# Description:
# Run FSL randomise for young vs. old baseline group comparisons for percent variance in BOLD explained by HRCO2, HR, and CO2 regressors.
# Load the FSL module for accessing FSL tools
module load FSL
# Define paths for mask, output directory, and input files
mask_path="data/masks/MNI152_T1... |
7e4f2b94e8efa6a841f4e4eea8b9701e7deb7b11e3869e9190b47fe2f71f2802 | Shell | 1,509 | 27 | #!/bin/bash
################## GETTING CORRECT ALT/REF ###############################
##################################################################
# prepare the manifest file and extract the reference allele #
# from the reference genome fasta file #
###############################... |
c198160c5f57178cea5060b07444e2b0766714a0b4a216189e8ce5f99efc4221 | Shell | 1,509 | 47 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2022-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
# Support invoking test_cpp.sh outside the script directory
cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../
. /opt/conda/etc/profile.d/con... |
c4081ef388616115938af8e5735f30b875b74828f86073e74d595d8516a22c92 | Shell | 1,532 | 33 | #!/bin/bash
set -e
#quick script to regenerate inflated 59k surfaces to match original HCP 32k
#Example call:
# . SetUpHCPPipeline.sh
# StudyFolder=/data/Phase2_7T
# Subject=102311
# T1wFolder="$StudyFolder"/"$Subject"/T1w
# AtlasSpaceFolder="$StudyFolder"/"$Subject"/MNINonLinear
# LowResMeshes=59
# Example_1res_inf... |
df5dfdeed1b94ddf9e266724720e19814db1362305c036d8227e5c4ece5e7a01 | Shell | 1,537 | 36 | #!/bin/sh
# version.sh -- Script to build the htslib version string
#
# Author : James Bonfield <jkb@sanger.ac.uk>
#
# Copyright (C) 2017, 2019 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Softwa... |
9ab706a58e07c0185b020eb9e49a8f5132cc53f20a4a22e4f99cdb78e912d2f5 | Shell | 1,544 | 48 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2023-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
rapids-logger "Downloading artifacts from previous jobs"
CPP_CHANNEL=$(rapids-download-from-github "$(rapids-artifact-name conda_cpp libcuml cuml ... |
eed69f562558915bfd933457c7706afc0bdb09b1414556e2f04782818e891eee | Shell | 1,554 | 34 | OUTPUT_FOLDER=outputs/train/pancreas/pert_ode_model_$(date +%Y%m%d_%H%M%S)
python perturb.py --trainer_ckpt_path outputs/train/pancreas/ode_model/model-final.pt \
--model.dim 64 \
--model.input-dim 668 \
--pert-model-type trigger \
--pert.perturbation-num 8 \
--pert.trigger.replace-num-candidates 1... |
94cf3046a9a4b64a5b05f59e7605f3a0735c07324ddafadb26eaab0ea0a97c25 | Shell | 1,580 | 49 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2022-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-configure-sccache
source rapids-datetime-string
export CMAKE_GENERATOR=Ninja
rapids-print-env
rapids-generate-version > ./VERSIO... |
47d3f04bf2e34a4025ee0742c38b8e65ecee482b65bcd8d068f2b54a228b9d66 | Shell | 1,584 | 28 | #!/usr/bin/env bash
# Copyright (c) OpenMMLab. All rights reserved.
sed -i '$a\\n' ../demo/docs/*_demo.md
cat ../demo/docs/*_demo.md | sed "s/#/#&/" | sed "s/md###t/html#t/g" | sed '1i\# Demo' | sed 's/](\/docs\//](/g' | sed 's=](/=](https://github.com/open-mmlab/mmpose/tree/master/=g' >demo.md
# remove /docs/ for l... |
5e5872cc99adecec99ec9ef54a75a63f66fef1caa87198e697e2be9b37292d44 | Shell | 1,585 | 62 | #!/usr/bin/env bash
# Assign options
while getopts ":d:c:i:m:" opt; do
case $opt in
d)
main_dir=$OPTARG # main directory
;;
c)
cohort=$OPTARG # cohort
;;
i)
sessions=$OPTARG # ids
;;
m)
modality=$OPTARG # modality
;;
esac
done
raw_dir="$main_dir/ra... |
63228206044274ad727a77168fb5f6ca6df7c8b26617c8647808ca64dfc5ed32 | Shell | 1,587 | 39 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
# This script runs all scikit-learn examples with the cuml.accel plugin.
# Any arguments passed to this script are forwarded directly to pytest.
#
# Example usage:
# ./run-examples.sh ... |
d31af696dcd25e07abcb332a4e2a57c1c0bf05d89a7296789026bb4262263da3 | Shell | 1,602 | 61 | #!/bin/bash
## C. Vriend - Amsterdam UMC - Aug '24
# slurm settings
#SBATCH --job-name=MBA
#SBATCH --mem=4G
#SBATCH --partition=luna-cpu-long
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=24
#SBATCH --time=02-0:00:00
#SBATCH --nice=2000
#SBATCH --mail-type=END,FAIL
#SBATCH --output=MBA_%A.out
# running containerized... |
2421397ecc6b5dd110dcd6808ebcbd470ad69c30a8f8cbe834b04b3ee0073b43 | Shell | 1,606 | 52 | #!/usr/bin/env bash
# ============================================================
# CONTROL: dw2 (features.8+12, /16) + per-stream GATE only. NO wavelet.
# Isolates the gate's effect on the two backbone streams, so:
# (this) - dw2_plain = what the gate alone does
# dw2_wav_gate - (this) = the wavelet stre... |
4bf44a7b7895b666c9145c9a96c144d7172ca48268eced3c09410c4025175d88 | Shell | 1,624 | 63 | INSTANCE_TAG="testing round 2"
COMMAND='echo "Success" > /home/ubuntu/testing.log'
# AMI="ami-660ae31e"
INSTANCE_TYPE="p2.xlarge"
AMI="ami-6a01e812" #extract
# INSTANCE_TYPE="c3.2xlarge"
INSTANCE_COUNT=1
KEY_NAME="taskonomy"
SECURITY_GROUP="launch-wizard-1"
SPOT_PRICE=0.4
ZONE="us-west-2"
START_AT=1
EXIT_AFTER=1
# N... |
b72bd6e0cdfc79502633b000e3295f36dc802d410181b675f5d76b81fd4a80e7 | Shell | 1,628 | 57 | #!/bin/bash
set -e
# Spin up the PostgreSQL database container
podman run --name postgres-container \
-e POSTGRES_HOST_AUTH_METHOD=trust \
-p 5432:5432 \
-v data:/docker-entrypoint-initdb.d \
-d postgres:latest
# Allow some time for the container to initialize
sleep 5
# Set up database: Create onsid... |
15d97b004f48e5ab7f91a5f7e755a73d6630c212ea6f1fc4d7a6bb9b0c7f7731 | Shell | 1,630 | 72 | #!/bin/sh
#
# Downloads assembled sequence for M. musculus (mouse) from NCBI.
#
# From README_CURRENT_BUILD:
# Organism: Mus musculus (mouse)
# NCBI Build Number: 37
# Version: 1
# Release date: 05 July 2007
#
M_MUS_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/Assembled_chromosomes
M_MUS_MT_FTP=ftp://ftp.ncbi.ni... |
13b0df05a34677b43b662a7bcae39ccbdd629ab2e320312cea45c81c115fb49c | Shell | 1,634 | 52 | #!/usr/bin/env bash
# ============================================================
# MobileNetV2, leaner 2-layer depthwise (/8 + /16):
# -le features.4.conv.1 144ch /8 (== MATLAB block_3_depthwise, 28x28x144)
# -le features.8.conv.1 384ch /16 (== MATLAB block_7_depthwise, 14x14x384)
# 528 concat channels... |
0993325a3641b0d890e83f8e41549c544d6976153e06b5c5434eacbd802fd97c | Shell | 1,636 | 41 | #!/bin/bash
set -e
echo -e "\n START: run_topup"
workingdir=$1
configdir=${HCPPIPEDIR_Config}
#topup_config_file=${FSLDIR}/etc/flirtsch/b02b0.cnf
topup_config_file=${configdir}/b02b0.cnf
${FSLDIR}/bin/topup --imain=${workingdir}/Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --config=${topup_config_file} --out=${w... |
8e612edca54a281e1cbb7ca11297d583fc09a0e7ac25150b4fd1cd8dd3ab80b4 | Shell | 1,655 | 55 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-init-pip
package_name="libcuml"
package_dir="python/libcuml"
rapids-logger "Generating build requirements"
rapids-dependency-fil... |
b28b6375adaef22208a74029c07c7523b9ff7974b8e615411f28249daba3c960 | Shell | 1,656 | 51 | #!/usr/bin/env bash
# ============================================================
# STEP 2 experiment: MobileNetV2 backbone, all 15 MVTec classes.
# Identical to the 20-epoch WRN50 baseline EXCEPT:
# -b mobilenetv2 (was wideresnet50)
# -le features.6 -le features.13 (stride /8 and /... |
b405226f9320741b8c3f244a1b87d62696b1a3995ed8c03347bd06e7ec54fdac | Shell | 1,656 | 28 | #!/usr/bin/env bash
# Copyright (c) OpenMMLab. All rights reserved.
sed -i '$a\\n' ../demo/docs/*_demo.md
cat ../demo/docs/*_demo.md | sed "s/#/#&/" | sed "s/md###t/html#t/g" | sed '1i\# 示例' | sed 's/](\/docs\//](/g' | sed 's=](/=](https://github.com/open-mmlab/mmpose/tree/master/=g' >demo.md
# remove /docs_zh-CN/ f... |
b52288d2956051e840f75a5199a1480b504bb113f3222d93a374525a0dc7fefa | Shell | 1,657 | 43 | #!/bin/bash
################## Quality control for genotype data ###############################
if [ -v $1 ]
then
echo 'to run this script you need R with the following packages installed: argparse, ggplot2, ggrepel, RColorBrewer, doParallel'
echo 'this script should be run like this:'
echo './QualityControl_GT.sh... |
573c98a4e05bdc4fe80e751074c6688808b9ee752f23febd1278cf2070840140 | Shell | 1,659 | 64 | #!/bin/bash
set -e
# Spin up the database
podman run --name mysql-container -e MYSQL_ALLOW_EMPTY_PASSWORD=yes -p 3306:3306 -d mysql:latest
# Allow some time for the container to initialize
sleep 5
# Set up database
podman exec mysql-container mysql -e "
CREATE DATABASE IF NOT EXISTS onsides CHARACTER SET utf8mb4 CO... |
83898d7ff6f9a59df332b96f214fec6e54edccd7eaeb65452ed6af17061233aa | Shell | 1,660 | 45 | #!/bin/bash
input_dir="/SeaExp_1/MRI_PET/HABS/processed/Amyloid_nii"
output_dir="/SeaExp_1/MRI_PET/HABS/processed/coreg_avg"
# input_dir="/SeaExp_1/MRI_PET/HABS/processed/Amyloid_nii/test"
# output_dir="/SeaExp_1/MRI_PET/HABS/processed/Amyloid_nii/test/output"
mkdir -p "$output_dir"
for nifti_file in "$input_dir"/*... |
09ef12a63a09a9aa241b75cc7c7507c1492fe586ab5b785667acb112d027883b | Shell | 1,668 | 40 | DATETIME=$(date +%Y%m%d_%H%M%S)
OUTPUT_FOLDER=outputs/experiment/pert/mnist/pert_subset_$DATETIME
export WANDB_API_KEY=YOUR_WANDB_KEY
python perturb_mnist.py \
--pert.model-type subset_sampling \
--pert.perturbation-num 64 \
--pert.subset-sampling.no-use-scheduler \
--pert.subset-sampling.lr 1e-3 \
... |
735fcc9402b5c2ad184ee83d8d0428eb0b078b3274e14dc35420c4da394da176 | Shell | 1,711 | 37 | #!/usr/bin/env bash
# Multi-seed gating ablation on MVTec AD (answers Reviewer 1's stability challenge).
# Two configs at the 20-epoch schedule where the +0.006 gate gain was measured:
# (a) dw2 : MobileNetV2 features.8+12, NO gate
# (b) dw2 + gate : same, WITH gate
# Across SEEDS (default 3). Each (config... |
e8112390fa16c91ad2876bcf515edd738049f3a5913aa282455fe9bd32ed521e | Shell | 1,711 | 49 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request 4 CPUs
#$ -pe omp 4
#$ -m ea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=12:00:00
conda activate py3.11
# module load python3/3.10.12
# module load pytorch/1.13.1
arch="ViTAutoEnc"
ps=32
vs=128
bs=2
num_heads=6
dataset="NACC_raw"
# arch="... |
1028b5824bdb49c74961b1fe1e8738bc0991a9fc6cd23cdaea5436e7466fcafc | Shell | 1,714 | 28 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=00:30:00
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=16
module load hisat2
module load samtools
module load bedtools
# 14866306
# without qc
# bash align.sh -r SRR11998214,SRR11998215,SRR11998216 -d ../../operons/data_odb/txid169963 -l S -q N -f txid1699... |
785ebe5cd0b12d2022052e9785b56a46dc15d02261647c02627d339e9cd5673c | Shell | 1,716 | 77 | #!/bin/bash
Help()
{
# Display Help
echo "Syntax: scriptTemplate [-r|d|l|q|f]"
echo "options:"
echo "r RNA-seq access codes separated by ','."
echo "d Directory"
echo "l Layout, P for Paired or S for Single."
echo "q Quality Control, Y or N."
echo "f Fasta file name"
}
while... |
26a85ef73f3e001f5ea4ac8dc63cfd1a2e898c495c6438fce6c61079630d3ba2 | Shell | 1,728 | 47 | #!/bin/bash
# #SBATCH --partition=gpu4_medium,gpu8_medium,gpu8_long,gpu4_long
#SBATCH --partition=gpu4_dev
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G
#SBATCH --gres=gpu:1
#SBATCH --job-name=02_project
#SBATCH --output=rq_02_project_%A_%a.out
#SBATCH --error=rq_02_project_%A_%a.err
module load p... |
eae8c470d346e81df8d82f31dac5ddabedf8ba5e8056e2cc8767266b0dd06c85 | Shell | 1,742 | 59 | #!/usr/bin/env bash
# this copyfile script is different because A4 only provides us with niftis. Therefore the folder structure is different.
# Assign options
while getopts ":d:i:m:" opt; do
case $opt in
d)
main_dir=$OPTARG # main directory
;;
i)
sessions=$OPTARG # rids
;;
m)
... |
8c777c33d4412cdfebd1807e155b6b2e5dc6277cf4d2874373058bb73a1bf117 | Shell | 1,747 | 46 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
# Support invoking test script outside the script directory
cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../ || exit 1
# Common setup steps shared by Python t... |
8ecfa54b40eb56b7136016e5028d1fe14960a8dc5284b5ab53338a420708dacd | Shell | 1,751 | 36 | OUTPUT_FOLDER=outputs/eval/pancreas/pert_ode_model_$(date +%Y%m%d_%H%M%S)
python perturb_eval.py --trainer_ckpt_path outputs/train/pancreas/pert_ode_model_20231221_155249/model-final.pt \
--eval_data_folder datasets/pretrain/pancreas/trajs/sampled_traj_test.npz \
--model.dim 64 \
--model.input-dim 668 \
... |
fedfa3a50a43c181fce7b294fa8965f91972056b4ae33bfec8f29f5c20e53edf | Shell | 1,757 | 28 | #!/usr/bin/env bash
set -euo pipefail
# Reset JP download artifacts so Snakemake will re-scrape and re-download.
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
JP_DIR="${ROOT_DIR}/_onsides/jp"
find "${JP_DIR}" -type f -name "*.html" -path "*/med_index_page/*" -delete 2>/dev/null || true
find "${JP_DIR}" ... |
0f1d26086e125e43589ffe489d281b1b5cb981787b40f4f0ba248a5930de7686 | Shell | 1,765 | 55 | #!/usr/bin/env bash
# ============================================================
# dw2 (features.8+12, /16) + WAVELET high-freq stream + per-stream GATE.
# -le features.8.conv.1 384ch /16
# -le features.12.conv.1 576ch /16
# --wavelet 1 2-level Haar detail subbands (6ch), fine edge/texture cue
# --g... |
84faca8f552edb4730a77d21f6dc40301d93d96ce6fd9c55c2a08166fdc70946 | Shell | 1,772 | 56 | #!/usr/bin/env bash
# ============================================================
# GATED 3-layer: dw2 (features.8+12, /16) + features.6 (/8) + per-stream GATE.
# -le features.6.conv.1 192ch /8 (reference grid -> localization)
# -le features.8.conv.1 384ch /16
# -le features.12.conv.1 576ch /16
# Rat... |
4296c0ed3319a64c8e4d76f12665dea6a36f4266a69c219239c7ba19d3c4b91e | Shell | 1,774 | 74 | #!/bin/bash
# Evaluation script for RCM Layer Classification
# Usage: bash scripts/run_layer_evaluation.sh --checkpoint PATH_TO_MODEL
# Default values
CONFIG_FILE="configs/layer_evaluation_config.yaml"
CHECKPOINT=""
OUTPUT_DIR="outputs/layer_evaluation"
DEVICE="auto"
# Parse arguments
while [[ $# -gt 0 ]]; do
ca... |
2c918fb33b4f68d88e2520ca7235caa077e00f8835917c2632d21f68e53dbe69 | Shell | 1,785 | 49 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2022-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
. /opt/conda/etc/profile.d/conda.sh
rapids-logger "Configuring conda strict channel priority"
conda config --set channel_priority strict
rapids-logger "Downloading artifacts fro... |
066a6bf09406f21d1ce77d7e65a5cef592e77d678353e8a1c90a1bcb2163b482 | Shell | 1,791 | 75 | #!/bin/bash
# Evaluation script for RCM Layer Classification
# Usage: bash scripts/run_layer_evaluation.sh --checkpoint PATH_TO_MODEL
# Default values
CONFIG_FILE="configs/layer_evaluation_config.yaml"
CHECKPOINT=""
OUTPUT_DIR="outputs/layer_evaluation"
DEVICE="auto"
# Parse arguments
while [[ $# -gt 0 ]]; do
ca... |
a31d25b97a6f14af0357ef9c3c56c0f09146705b1f5e60238687aa412406e255 | Shell | 1,806 | 81 | #! /bin/bash
## Run SNIPE ADNI subjects from list
# Directories
BASE_DIR="${HVR_VALIDATION_DIR:-$(git -C "$(dirname "$0")" rev-parse --show-toplevel)}"
LIB_DIR=${BASE_DIR}/libraries/snipe_adni
TMP_DIR=${BASE_DIR}/tmp/nlpb_hcvc
QC_DIR=${BASE_DIR}/plots/qc_adni-bl/nlpb/all
OUT_DIR=${BASE_DIR}/data/derivatives/adni-bl_n... |
20a2114d14c3054498ab095e8bfcaad5d0d266fde09018ae3ecc3de82569b0c2 | Shell | 1,824 | 57 | #!/usr/bin/env bash
### Parse HCVC segmentations (detailed + AMY)
## Extract voxel num for each label and calculate complete HC/CSF
## Labels:
## 111 - L_HC_Tail
## 112 - L_HC_Body
## 113 - L_HC_Head
## 121 - L_CSF_Tail
## 122 - L_CSF_Body
## 123 - L_CSF_Head
## 130 - L_AG
## 211 - R_HC_Tail
## 212 - R_HC_Body
## 213 ... |
e794d62db88111d0b2605dc29e416d9e697673bc558d2cc35ec94958874d534f | Shell | 1,837 | 31 | #!/usr/bin/env bash
# Copyright (c) OpenMMLab. All rights reserved.
sed -i '$a\\n' ../../demo/docs/en/*_demo.md
cat ../../demo/docs/en/*_demo.md | sed "s/^## 2D\(.*\)Demo/##\1Estimation/" | sed "s/md###t/html#t/g" | sed '1i\# Demos\n' | sed 's=](/docs/en/=](/=g' | sed 's=](/=](https://github.com/open-mmlab/mmpose/tree... |
385f6446dc82ad3217109cbf4b08a2171c35a85d0dcb378f21b284417d4a1f28 | Shell | 1,842 | 64 | #!/bin/bash
################## Filter SNPs and annotate vcf with LRR and BAF ###############################
if [ -v $1 ]
then
echo 'to run this script you need vcftools and bcftools installed globally'
echo 'this script should be run like this:'
echo './Preproc_CNV.sh <path folder>'
else
path=$1
cd $path
echo... |
ce7e9f6b494d00cc7728d66a2dc8d462169ba4299ca9211306daaa8aa8914006 | Shell | 1,848 | 61 | #!/bin/bash
corrected_args=()
docker_args=()
mounts=0
FS_LICENSE="${FS_LICENSE:=$HOME/freesurfer_license.txt}"
if [ -f "${FS_LICENSE}" ]; then
>&2 echo "Using freesurfer license from ${FS_LICENSE}"
else
>&2 echo "Freesurfer license not found at ${FS_LICENSE}. You can either set FS_LICENSE to the path of the ... |
e7794123d89b1bf38848696a948bbb653137e22ad4314eba9ed0bbcd776dfe98 | Shell | 1,856 | 55 | #!/usr/bin/env bash
# ============================================================
# MobileNetV2, THREE depthwise layers: rich features + finer localization.
# -le features.6.conv.1 -> 192ch @ /8 (reference grid, 36x36 -> localization)
# -le features.8.conv.1 -> 384ch @ /16 (== block7_depthwise)
# -le fe... |
1a3ba2762927ba22e82191f59e8bd9e5bff08637e26c4332c52e5fc0b259b950 | Shell | 1,876 | 31 | #!/usr/bin/env bash
# Copyright (c) OpenMMLab. All rights reserved.
sed -i '$a\\n' ../../demo/docs/zh_cn/*_demo.md
cat ../../demo/docs/zh_cn/*_demo.md | sed "s/^## 2D\(.*\)Demo/##\1Estimation/" | sed "s/md###t/html#t/g" | sed '1i\# Demos\n' | sed 's=](/docs/en/=](/=g' | sed 's=](/=](https://github.com/open-mmlab/mmpos... |
efc2c90042c80b48bdeb16f3f679567b0d721e96aa3974910ae53339d14e777e | Shell | 1,876 | 89 | #!/usr/bin/env bash
# SPDX-FileCopyrightText: Copyright (c) 2020-2025, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
# Reports relevant environment information useful for diagnosing and
# debugging cuML issues.
# Usage:
# "./print_env.sh" - prints to stdout
# "./print_env.sh > env.txt" - prints to file "env... |
ec8b643e317c4c24026ebe4b66d41c0ec087f707cbc5972aeb9a6da604837ff6 | Shell | 1,883 | 71 | #!/usr/bin/env bash
## Shell script to generate a single LaTeX file compiling all figures
## CONSTANTS
HERE="${HVR_VALIDATION_DIR:-$(git -C "$(dirname "$0")" rev-parse --show-toplevel)}"
FIGSDIR=${HERE}/plots
METADATA=${FIGSDIR}/metadata.json
OUTPUT=${FIGSDIR}/figures.tex
## Create the master file with the preamble
... |
758f31de4cec46136de9e01e522222b7d651b70c3fb7b07a30811e549cf5ee99 | Shell | 1,890 | 70 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2023-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
package_name=$1
package_dir=$2
shift 2
# Parse optional flags
stable_abi=false
while [[ $# -gt 0 ]]; do
case "$1" in
--stable)
stabl... |
606b3c9d511621c5c36b75bd0dcb5a90d24cf798abdf4b575967ab6f81462759 | Shell | 1,897 | 74 | #!/bin/sh
#
# Downloads sequence for the galGal3 version of G. gallus (chicken)
# from UCSC.
#
BASE_CHRS=chr1
# Add autosomes 2-28
i=2
while [ $i -lt 29 ] ; do
BASE_CHRS="$BASE_CHRS chr$i"
i=`expr $i + 1`
done
# Add autosome 32
BASE_CHRS="$BASE_CHRS chr32"
# Add sex chromosomes
BASE_CHRS="$BASE_CHRS chrW chrZ"
# Ad... |
2a4e1adf789927b73b8b4ee9785ae47a4249f52ab2837baf947a88afbb638397 | Shell | 1,903 | 103 | #!/bin/sh
#
# Downloads sequence for the mm8 version of M. musculus (mouse) from
# UCSC.
#
# Note that UCSC's mm8 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script builds and index for ju... |
b8f2819c87ba65bb46b01d0b24e3c948e24bbe3a8c82f5a2631481ef3a7144ad | Shell | 1,912 | 74 | #!/bin/bash
# Evaluation script for RCM Lesion Classification (with ablation study)
# Usage: bash scripts/run_lesion_evaluation.sh --checkpoint PATH_TO_MODEL
# Default values
CONFIG_FILE="configs/lesion_evaluation_config.yaml"
CHECKPOINT=""
OUTPUT_DIR="outputs/lesion_evaluation"
DEVICE="auto"
# Parse arguments
while... |
415cead79f37b302128ee07cad5ab01044d0255f08cb2f5f979f0d8c8f711ca0 | Shell | 1,913 | 104 | #!/bin/sh
#
# Downloads sequence for the mm9 version of M. musculus (mouse) from
# UCSC.
#
# Note that UCSC's mm9 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script builds and index for ju... |
4da2df188ff34109e2482bafc463e82a4fc4c74fd12a80d5fc94f6808e2ec654 | Shell | 1,916 | 61 | #!/usr/bin/env bash
# ============================================================
# 3-layer MobileNetV2 (depthwise) + PCA-residual stream.
# Backbone layers (unchanged from dw3):
# -le features.6.conv.1 192ch /8 (reference grid)
# -le features.8.conv.1 384ch /16
# -le features.12.conv.1 576ch /16
# ... |
efb3bb4409167b189a6956a409bf08f8e62525f1a40af9b50bc2a9c571061ef2 | Shell | 1,961 | 64 | #!/bin/bash
#
# Runs jackhmmer search with bitscore thresholds
#
#SBATCH --cluster=<clustername>
#SBATCH --partition=<partitionname>
#SBATCH --account=<accountname>
#SBATCH --job-name=jackhmmer
#SBATCH --output=jackhmmer.out
#SBATCH --gres=gpu:0 # Number of GPU(s) per node.
#SBATCH --cpus-per-task=4 ... |
b580a6f479ee8740e9f3fb49d8f8d40569f5ef9a6fe0dd434a14790d7cf02497 | Shell | 1,972 | 31 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=16
# module load gcc
# module load gnuplot
# module load hisat2
# module load sra-toolkit
# module load trimmomatic
# module load fastqc
module load fastp
# bash qc.sh -r SRR15049591,SRR15049592,SRR15049593 -d ../../operons/data... |
519534edb418652baf2c136c1b928c82d174489c165e0e69c5d25c3a4af0345c | Shell | 1,983 | 51 | #!/usr/bin/env bash
# #ADNI
# DATA_DIR="/SeaExp_1-ayan/MRI_PET/ADNI/processed/T1_nii"
# CSV_FILE="/SeaExp_1-ayan/MRI_PET/ADNI/processed/T1_nii/ADNI_T1.csv"
# #Output directory for FastSurfer
# OUTPUT_DIR="/SeaExp_1-ayan/MRI_PET/ADNI/processed/fastsurfer"
# A4
# DATA_DIR="/SeaExp_1-ayan/MRI_PET/A4/processed/T1_nii" # f... |
fc28177c8723953b3ce5b73b569dc0379338691e7a1b9d3a898b1f88c453e8cd | Shell | 2,002 | 80 | #!/usr/bin/env bash
set -e
echo -e "\nRunning $0"
get_batch_options() {
local arguments=("$@")
unset command_line_specified_t1
unset command_line_specified_mask
unset command_line_specified_outpath
unset command_line_specified_EnvironmentScript
local index=0
local numArgs=${#arguments[@]... |
c4d29a4e2b18a99e1f9d58cbe878ef8ba74c579a89648b247187e5d0d6aa1e38 | Shell | 2,026 | 56 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2023-2026, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-init-pip
package_name="cuml"
package_dir="python/cuml"
RAPIDS_PY_CUDA_SUFFIX="$(rapids-wheel-ctk-name-gen "${RAPIDS_CUDA_VERSION}... |
28669602e3b5dc173f32bde7f9bf08ee1e6d3e08fb11bd28da28b76d076a4109 | Shell | 2,027 | 58 | #!/usr/bin/env bash
# ============================================================
# MobileNetV2 with EXPANDED DEPTHWISE features (replicates the
# MATLAB SimpleNet setup that worked well):
# -le features.8.conv.1 -> 384ch @ /16 (== block7_depthwise)
# -le features.12.conv.1 -> 576ch @ /16 (== block11_dept... |
6e086a61988ae41ad65043d59f429e022c54875c0ff35a05f6ca526cac94ca0f | Shell | 2,035 | 97 | #!/bin/sh
#
# Downloads sequence for the rn4 version of R. norvegicus (rat) from
# UCSC.
#
# Note that UCSC's rn4 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script builds and index for ju... |
e33918bdf8061ff599c862cd507efcb377a2f20268a8bfac634d8cc32d954d67 | Shell | 2,045 | 86 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-a577d6dd" #extract
#INSTANCE_TYPE="p2.xlarge"
INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="c3.2xlarge"
... |
b48c169bbeb6f1d799574b01ae2e812118dc1cf5aea106d4182f3e08180bdec6 | Shell | 2,046 | 65 | #!/bin/bash
#SBATCH --job-name=Pope_KRR
#SBATCH --account=
#SBATCH --time=30
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=6G
#SBATCH --cpus-per-task=6
#SBATCH --mail-user=
#SBATCH --mail-type=FAIL
#SBATCH --output=slurmout/job-%j.out
# NOTE: Above settings may need to be adjusted, especially if running the null models
# ... |
e6c64ac5eec57becf04f4770508da7bdc11790d675dc95c2a12fec089fd06b74 | Shell | 2,046 | 54 | #!/bin/bash -l
# run this script from adrd_tool/
conda activate /projectnb/vkolagrp/skowshik/conda_envs/adrd
/projectnb/vkolagrp/skowshik/conda_envs/adrd/bin/pip install .
# install the package
# cd adrd_tool
# pip install -e .
# define the variables
prefix="."
train_path="${prefix}/pseudodata/synthetic_train.csv"
... |
8b427f37d770308a76d6a9c89c22a309e2bd70219d0b48c82db2197278bff306 | Shell | 2,092 | 70 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l h_fsize=100G
#$ -l mem_free=4.5G
#$ -l h_vmem=4.5G
#$ -l h_rt=96:00:00
#$ -pe local 8
#$ -t 1-41
## the following line is needed for sambamba
PATH="/users/scristia/.linuxbrew/bin:$PATH"
module load samtools
CORES=8
umask g+w
# Inputs
fqdir="../fastq"
bamdir="../bam"
beddir="../bed"
... |
d9c1c6af177877cefa882e58e05d88ebaec8dd4c3bb29b96ab75df18d80295ee | Shell | 2,097 | 37 | #!/bin/bash -e
#SBATCH HPC/SLURM commands here
#SBATCH --mem=500G
module add bbmap/37.28
module add SPAdes/3.15.5
module add python/anaconda/2020.11/3.8
cd /path/to/folder
line=$(sed "${SLURM_ARRAY_TASK_ID}q;d" /path/to/folder/repair_trimmed_md.txt) # list of spades.log files to identify broken sequences
sample_id=$(e... |
4b13531ca24616bc4c3f4c9a25d5ae4658dac15b3050e91cbee43aafec893705 | Shell | 2,108 | 65 | #!/bin/sh -e
# test/with-shlib.sh -- make shared libhts available via $LD_LIBRARY_PATH etc.
#
# Copyright (C) 2020 University of Glasgow.
#
# Author: John Marshall <John.W.Marshall@glasgow.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated doc... |
11b9d66812361a8b7f5627d896979940495fb27e593a2e1bee7af4149f9546ba | Shell | 2,166 | 104 | #!/bin/sh
#
# Downloads sequence for H. sapiens (human) from NCBI. This script was
# used to build the Bowtie index for H. sapiens 37.
#
# From README_CURRENT_BUILD:
# Organism: Homo sapiens (human)
# NCBI Build Number: 37
# Version: 1
# Release date: 04 August 2009
#
BASE_CHRS="\
chr1 \
chr2 \
chr3 \
chr4 \
chr... |
eeecb2d2e2240e4be01229191684e3315cc47d042017b50097893c57ce801527 | Shell | 2,168 | 56 | #!/usr/bin/env bash
# Assign options
# conda activate synthseg_38
while getopts ":i:o:" opt; do
case $opt in
i)
inpath=$OPTARG # CSV file with paths to images to process
;;
o)
outpath=$OPTARG # Output directory
;;
esac
done
# ./run-synthseg.sh -i /projectnb/vkolagrp/varuna/A4/proc... |
f760346d9ce2e23f69858f7a00270a5db9e3fed03948def5eea642e676d3a3e3 | Shell | 2,174 | 54 | #!/bin/bash
mkdir -p 4D_data
mkdir -p 4D_data_only_ligand
mkdir -p 4D_data_only_ligand_tracking
mkdir -p 4D_data_only_protein
mkdir -p no_MD
mkdir -p MD_DA/complex
mkdir -p MD_DA/only_ligand
mkdir -p MD_DA/only_protein
mkdir -p reduced
mkdir -p fep
wget https://zenodo.org/record/10390550/files/4D_complex_test_set.zip... |
295497c9727ba45377ce3391a1a8c0872587af8ae17560775b1ed7b6d80c6118 | Shell | 2,217 | 59 | #!/bin/sh
# version.sh -- Script to build the htslib version string
#
# Author : James Bonfield <jkb@sanger.ac.uk>
#
# Copyright (C) 2017-2018 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Softwar... |
84a97a18cd1d730482c6f0515080bb9ba1076ab063fddbf3b9963431c149a09f | Shell | 2,232 | 121 | #!/bin/sh
#
# Downloads sequence for the hg18 version of H. sapiens (human) from
# UCSC.
#
# Note that UCSC's hg18 build has three categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
# 3. The alternative-haplotype files, named chr?... |
892816b735609c30b7f86dbfbd3f2fc5c9c42618906ee53fbb79f45582cdc8e6 | Shell | 2,235 | 78 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# AMI="ami-660ae31e"
INSTANCE_TYPE="p2.xlarge"
AMI="ami-7edd3606" #extract
INSTANCE_COUNT=1
KEY_NAME="taskonomy"
SECURITY_GROUP="launch-wizard-1"
SPOT_PRICE=0.4... |
d9e9a147850e08fba12e5575c0d7e60a466a3c6a4cd21728395a563858a40e27 | Shell | 2,284 | 77 | while getopts ":d:c:i:m:" opt; do
case $opt in
d)
main_dir=$OPTARG # main processed directory directory
;;
c)
cohort=$OPTARG # cohort
;;
i)
id_hash=$OPTARG # id csv file
;;
cp)
copyfiles=$OPTARG # whether to run copyfiles
;;
reo)
reorient=$OP... |
859571d3e6a5da594a51f4ed37e875cc3662a51d8350359e0e2ca8eaf55f570c | Shell | 2,292 | 66 | #!/bin/bash
# Assign options
while getopts ":d:i:m:c:" opt; do
case $opt in
d)
inpath=$OPTARG # Raw directory
;;
i)
sessions=$OPTARG # specific adni ids
;;
m)
modality=$OPTARG #modality
;;
c)
cohort=$OPTARG # cohort
;;
esac
done
ml dcm2niix
if [ -n ... |
9c46d5885640aded9e43d6bd0e8ea9ecad1da8eecdc8b0a0064c9a7b894f2fca | Shell | 2,301 | 76 | #!/bin/bash
source /home/ubuntu/.bashrc
dirname="temp"
mkdir -p -- "$dirname"
task_name=""
config_num=""
moment=$(date +"%m%d_%T")
#log_file="train_log_$moment.txt"
log_file="train_log.txt"
resume=""
function usage
{
echo "-t or --task for task_name; -i or --config for config_num; -l or --log for log_file"
}
whi... |
d086951dd02d217b0fec3f01195590394ff4f6c3d553c6ab881ee3ef37b06a88 | Shell | 2,307 | 75 | #!/usr/bin/env bash
## This script will copy all nifti files from the raw folder to the processed folder
# Assign options
while getopts ":d:m:t:" opt; do
case $opt in
d)
main_dir=$OPTARG # main GAAIN Tracer directory
;;
m)
modality=$OPTARG modality Amyloid or T1
;;
t)
tra... |
1e44431f6dc45ce1a1094457da4c20149ffd388b3f3b0c011806a20c0c37029c | Shell | 2,320 | 46 | #!/bin/bash
echo "This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here"
# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR setting for your setup
#expor... |
6b4873e537ec75be0c19c57f691ff7ac59c5e46eb417cc82fa516bdccb7e74d8 | Shell | 2,366 | 97 | #!/usr/bin/env bash
## Compare overlap similarity between segmentations:
## { MALF, NLPB, CNN } — manual labels
## XCorrelation
## FUNCTIONS
# Recode labels to L-HC: 1 & R-HC: 2 & L-VC: 3 & R-VC: 4
# Reshape to Dorothee's labels
recode() {
local input="$1"
local reference="$2"
local output="$3"
itk_resample \
"... |
ec1fbff27a2ea6008bd7c415e75b9f26cf5e16b872453cd6a222d281ad89e1fa | Shell | 2,385 | 69 | #!/bin/bash
resume=""
function usage
{
echo "--resume, -r for resuming action"
}
while [ "$1" != "" ]
do
case "$1" in
-r | --resume) shift
resume=1
;;
-h | --help ) usage
exit
... |
ee3e46fc130af8be54327fa15b368cbdadc703dce3c8d83b4e625fe32cd123b8 | Shell | 2,454 | 80 | #!/bin/sh
#
# Downloads sequence for H. sapiens (human) from NCBI. This script was
# used to build the Bowtie index for H. sapiens.
#
# From README_CURRENT_BUILD:
# Organism: Homo sapiens (human)
# NCBI Build Number: 36
# Version: 3
# Release date: 24 March 2008
#
GENOMES_MIRROR=ftp://ftp.ncbi.nih.gov/genomes
FI... |
db036c46ce04f4db4512bf48277f08a332d3470110528c1eb3e9a25a7457e0f2 | Shell | 2,501 | 34 | #!/bin/bash
#SBATCH --account=def-lpenacas
#SBATCH --time=10:00:00
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=16
module load hisat2
module load samtools
module load bedtools
# 14866306
# without qc
# bash align.sh -r SRR11998214,SRR11998215,SRR11998216 -d ../../operons/data_odb/txid169963 -l S -q N -f txid1699... |
0dea679792f9e3939e6d71287cf616da1d079ba82d34d9c8a490ee0b7c9cb93c | Shell | 2,544 | 93 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # Compile_MATLAB_code.sh
#
# Compile the MATLAB code necessary for running the PostFix Pipeline
#
# ## Copyright Notice
#
# Copyright (C) 2017 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ##... |
5fd63dbc9108ac6f4491aa3368de4920a6aa525e9f61cba9e7393f2e4f8111ba | Shell | 2,565 | 96 | #!/usr/bin/env bash
## Shell script to generate a single LaTeX file compiling all tables
## CONSTANTS
HERE="${HVR_VALIDATION_DIR:-$(git -C "$(dirname "$0")" rev-parse --show-toplevel)}"
TABLESDIR=${HERE}/tables
METADATA=${TABLESDIR}/metadata.json
OUTPUT=${TABLESDIR}/tables.tex
## Create the master file with the prea... |
523741be3c0c253b49932289c11febfa5488b5da566d9ad44484ac5b5cee1e17 | Shell | 2,594 | 95 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-d0a16fa8" #extract
#INSTANCE_TYPE="p2.xlarge"
INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="c3.2xlarge"
... |
8bc4320ca871b25993c0205a2f47050fda4f460db9411ff2b2be40c49dc5bf98 | Shell | 2,613 | 85 | #!/bin/bash
# SPDX-FileCopyrightText: Copyright (c) 2025-2026, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0
set -euo pipefail
source rapids-init-pip
LIBCUML_WHEELHOUSE=$(rapids-download-from-github "$(rapids-artifact-name wheel_cpp libcuml cuml --cuda "$RAPIDS_CUDA_VERSION")")
CUML_WHEELHOUSE=$(rapids-d... |
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