sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
44b0d6801c27a5aee834c7c64fc9cb26aab1b1ec5963fff9260f5cab25b35ffb | Shell | 1,604 | 36 | #!/bin/sh
datadir="/media/sf_Projects"
datadir="/media/sf_MRI-Data/Projects"
project=${1}
vnum=${2}
hum_num=${3}
datadir=${datadir}/${project}/${vnum}/${hum_num}
bids=${vnum}_${hum_num}
echo ${datadir}
echo --------------------------------------------------------------------------------------------------------------... |
faa074bd07b0617ce1ec4fa876a61ba276e1982eae807c24c5ab421948aa6d3d | Shell | 1,619 | 52 | #!/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 -g <GMToAffineTmpList> -o <outDir... |
66da70d351bb9258154ed565daa76c050ba63ace840cfed61da8af47bef686e5 | Shell | 1,624 | 45 | #!/bin/bash
export MODEL_PATH=/gluster/zhihan/backup/dna/690/6
for model in $(ls $MODEL_PATH)
do
export MODEL="$model"
export CHECKPOINT=$(ls $MODEL_PATH/$MODEL | head -1)
if [ ! -d "/gluster/zhihan/DNABERT/examples/data/ori_results/$MODEL" ]
then
python run_finetune.py \
--model_typ... |
414a253d48b776efa53213466e2026e564ab8cec809855dab5683104b6e503cf | Shell | 1,632 | 59 | #!/usr/bin/env bash
# This installs a minimal environment, just enough to build the documentation.
# It then builds the documentation
ENV_FLAG=-n
ENV_NAME=bpreveal-docbuild
CONDA_BIN=conda
######################
# DON'T CHANGE BELOW #
######################
SCRIPT_NAME=$(readlink -f -- "$0" )
DOC_DIR_NAME=$(dirnam... |
8fba34d67d17f8cea240deb5bda52c9af333071640439d111aa6a54abc4fc647 | Shell | 1,635 | 48 | #!/bin/bash
#SBATCH --job-name=genome_design_pipeline
#SBATCH --output=/path/to/phage_filter_%j.log
#SBATCH --error=/path/to/phage_filter_%j.err
#SBATCH --time=48:00:00
#SBATCH --signal=B:USR1@300
#SBATCH --open-mode=append
#SBATCH --requeue
#SBATCH --partition=cpu_batch
#SBATCH --nodes=1
#SBATCH --cpus-per-task=96
#SB... |
9f3aacbd0e30b90200835a730f21ace9a9b15a467ff774445c9e74303143fc76 | Shell | 1,641 | 61 | #!/bin/bash
#SBATCH --job-name=rbp_cnn_tf
#SBATCH --output=/lustre/grp/gglab/liut/logs/rbp_cnn_tf_%A_%a.log
#SBATCH --error=/lustre/grp/gglab/liut/logs/rbp_cnn_tf_%A_%a.err
#SBATCH --gres=gpu:1
#SBATCH --mem=16G
#SBATCH --time=02:00:00
# array index 由 submit_rbp_cnn_tf.sh 传入 --array=0-N
CODE_BASE=/lustre/grp/gglab/liu... |
256ba5f09a5b285a886d159cd777c164034f27e7cd3586f77d17541610fa7493 | Shell | 1,647 | 39 | #!/usr/bin/env bash
# Build miniforge installers for Linux
# on various architectures (aarch64, x86_64, ppc64le, riscv64)
# Notes:
# It uses the qemu emulator (see [1] or [2]) to enable
# the use of containers images with different architectures than the host
# [1]: https://github.com/multiarch/qemu-user-static/
# [2]:... |
80b468092a76e439a3426f2ebbb15c76932e1601ea9d9cd677c69700deaf8463 | Shell | 1,649 | 52 | #!/bin/bash
# Base directories
base_ckpt_dir="checkpoints"
base_logs_dir="logs"
# Experiment 1: Run training with 10 different seeds. Shuffle is false.
# for seed in {0..9}
# do
# ckpt_dir="${base_ckpt_dir}_seed_${seed}"
# logs_dir="${base_logs_dir}_seed_${seed}"
# shuffle=false
# subsample=1
# echo "Run... |
db9df04869144f63af50be867fc88bd4825d663e36f7fabbe1c5cc615076a169 | Shell | 1,650 | 43 | #!/bin/bash
CONDA_PATH=$(which conda)
# Activate the fastsam Conda environment
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate fastsam
# Enable nullglob so *.tiff expands to nothing if no match
shopt -s nullglob
# Define project root
proj_dir="/home/matt/HDD_exp/C2.1 gloid live imaging"
# # Defi... |
b2fb898ff6a67280bcd7fe8add40ec80349290231666d776267e63eeb2e36ac9 | Shell | 1,664 | 55 | set -xe
device_id=7 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=demo
split=simulation
result_dir=./results
seed=1
epochs=1
batch_size=2
accumulation_steps=1
test_batch_... |
bb3a9c91ed55fa8cf18e69c06de36e61386f3301c45638175e13ae2afab9b39e | Shell | 1,665 | 56 | #!/bin/bash
if [ $# != 2 ] ; then
echo "Usage :" $(basename $0)" <smooth x(mm)> <smooth y(mm)>"
echo "Hardcoded to work with SPAIN resting state data"
echo "Needs FSL and AFNI modules loaded"
exit 1
fi
# Paths
dir="/root/dir"
code_dir="/${dir}/code"
echo "Starting..."
declare -a sub=("sub-SPAIN01" "sub-SPAIN02... |
acaee2b53eeb9dab5075dc440c793fe27143b4d868e878b8a57f2602d7955905 | Shell | 1,667 | 53 | #!/bin/sh
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=8
#SBATCH --array=1,2,4,5,7,8
#SBATCH --mem=48G
#SBATCH --qos=nopreemption
#SBATCH -p cpu
QUERY_PATH="query_list.txt"
query_name=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $QUERY_PATH)
echo "processing ${query_name}"
DATASET="/scratch/ssd004/datasets/cellxgene/scb_st... |
691a7f9c0de5e0344b328113a7b74d642beb2f58e2b28ec9b1f71fdf08bf6564 | Shell | 1,670 | 57 | #!/bin/bash
# Florian Bénitière 11/05/2026
# Download and prepare all reference resources required for variant annotation
# Supports GRCh37 and GRCh38 genome versions
set -e
set -o pipefail
# ============================
# Check argument
# ============================
if [ $# -ne 1 ]; then
echo "Usage: $0 <genome... |
0096b64e73b323d6ecded15535b4ba639fd343c9cc41aee42b8d346e78ad52b3 | Shell | 1,674 | 49 | #!/usr/bin/env bash
# Run all microcircuit training jobs for this experiment folder.
#
# Usage:
# bash run.sh [NUM_SEEDS, default: 5]
#
# Steps:
# 1. Regenerate parameter files via change_params.py
# 2. Launch all simulations as a background process
# 3. Wait for all processes to finish
#
# SLURM compatibility:... |
baad4a1cc1317d56681af157389fe8772a0123ecd226c709125f2d4b3ad9cd30 | Shell | 1,674 | 49 | #!/usr/bin/env bash
# Run all microcircuit training jobs for this experiment folder.
#
# Usage:
# bash run.sh [NUM_SEEDS, default: 5]
#
# Steps:
# 1. Regenerate parameter files via change_params.py
# 2. Launch all simulations as a background process
# 3. Wait for all processes to finish
#
# SLURM compatibility:... |
cf784a9a67c7580c3b847f9fae8a3cd97b58d34795d214892b4b8f96c75ee6de | Shell | 1,675 | 49 | #!/usr/bin/env bash
# Run all microcircuit training jobs for this experiment folder.
#
# Usage:
# bash run.sh [NUM_SEEDS, default: 5]
#
# Steps:
# 1. Regenerate parameter files via change_params.py
# 2. Launch all simulations as a background process
# 3. Wait for all processes to finish
#
# SLURM compatibility:... |
4994a39bba0cc892da17560a1dc0b0460e03a57ae6fd0e4dc33746114277cdbd | Shell | 1,681 | 38 | # Path of the folder containing all data
dir="/root/dir"
sct_dir="/sct/dir/7.0"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPA... |
61165750e592d1449b0d1e22b3d719b03477f30f9e66e0bdf5d57ab08e85df6d | Shell | 1,685 | 49 | #!/usr/bin/env bash
#
# copyright (c) 2017-present, facebook, inc.
# all rights reserved.
#
# this source code is licensed under the MIT license found in the
# license file in the root directory of this source tree.
#
# script for FB15k
DIR=data/FB15k/
FASTTEXTDIR=../../
# compile
pushd $FASTTEXTDIR
make opt
popd
ft=$... |
d8912757939d2632776c27284a15d95f88376d8b305ed11516fcf7e140cbfbc8 | Shell | 1,685 | 40 | #! /bin/sh
# Last successfully run on Mar 7th, 2021 with git repository version v0.17.1-Schaefer2018_LocalGlobal
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FRE... |
283894414a693d6d0167690ad4e2e53fa3adac20b30d681c62862d38d73973bf | Shell | 1,687 | 68 | #! /bin/bash
ORIG_DIR=$1
SMOOTH_DIR=${ORIG_DIR}_smooth
mkdir ${SMOOTH_DIR}
AXPY_FILE=`find ${ORIG_DIR} -name "*.dat" | grep axpy`
for FILE in ${AXPY_FILE}
do
echo $FILE
BASE=${FILE##*/}
./smooth ${ORIG_DIR}/${BASE} 4 ${SMOOTH_DIR}/${BASE}_tmp
./regularize ${SMOOTH_DIR}/${BASE}_tmp 2500 15000 ${SMOOTH_D... |
9aaa50a253a0fcf8250ae858ffe17e0ef78ea44645b5c23852b94535ef7ffc07 | Shell | 1,689 | 46 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
SPM_ENCODE=flores/scripts/spm_encode.py
DATA=data_tmp
SPM_MODEL=criss_checkpoints/sentence.bpe.model
DICT=criss... |
64487201e7c61271fbc885e3e0b606cd9cd0a950d76f4232928bcf312c1196b8 | Shell | 1,699 | 54 | #!/bin/bash
WHAT=$1
DIR=$2
cat ../gnuplot_common_settings.hh > ${WHAT}.gnuplot
echo "set title " `grep ${WHAT} ../action_settings.txt | head -n 1 | cut -d ";" -f 2` >> $WHAT.gnuplot
echo "set xlabel " `grep ${WHAT} ../action_settings.txt | head -n 1 | cut -d ";" -f 3` "0.000000,0.000000" >> $WHAT.gnuplot
echo "set xr... |
fbf57e6d6c8950f4c07461b2a0738321bd7902132dbae06a79399a1931b68b07 | Shell | 1,710 | 54 | set -xe
device_id=0 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse133344_k562gi_oe_pert227_84986_19264_withtotalcount
split=simulation
result_dir=./results
seed=1
epoc... |
ef9f602c39772242ad0ccdabac2a78518f1b2348f195214fd88e868669f426be | Shell | 1,711 | 35 | #!/bin/sh
datadir="/media/sf_MRI-Data/Projects"
project=${1}
vnum=${2}
hum_num=${3}
datadir=${datadir}/${project}/${vnum}/${hum_num}
bids=${vnum}_${hum_num}
echo ${datadir}
if [ -f ${datadir}/seg/${bids}-tfl.nii.gz ];then
echo "seg/tfl file found"
fi
if [ -f ${datadir}/seg/*${bids}-tse.nii.gz ];then
echo "seg/tse... |
f4eda5fa407ec0931d5771f1387bb9869593b63fd28ce3d1dde6a35b5aa96463 | Shell | 1,712 | 62 | #!/bin/bash
workdir=/Volumes/public/Backup/horiDir/qst/TauLNM/analysis_PSP_VBM/
#for hcp_subj in 100307 100408 101309 101915 103111 103414 103818 105014 105115 106016;do
for hcp_subj in 100307 ;do
for LRRL in LR RL;do
indir=/Volumes/public/Backup/horiDir/qst/HCP/${hcp_subj}/MNINonLinear/Results/rfMRI_REST1_${LRR... |
dc0103af1b53f3ec7d974baf1ff4fd10c3fc5205c9edb63d1cce6606ecae4e9b | Shell | 1,713 | 54 | set -xe
device_id=0 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=demo
split=simulation
result_dir=./results
seed=1
epochs=1
batch_size=2
accumulation_steps=1
test_batch_... |
7772b941d78b4b91b59360647e9927d293906c52959f427f0f60305ac28f0d70 | Shell | 1,737 | 57 | #!/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 -g <GMToNonlinTmpList> -o <outDir... |
2615226a02a24c34ab4f4a80aafb5b58dd90fdebd46364ee01786488a79c01fa | Shell | 1,739 | 18 | #!/bin/bash
#SBATCH --job-name=CCVAE
#SBATCH --output=emnist_output.txt
#SBATCH --error=emnist_error.txt
#SBATCH --ntasks=1
#SBATCH --gres=gpu:1
#SBATCH --mem=32GB
#SBATCH --time=01:00:00
source $HOME/test/bin/activate
module load libffi
# python $HOME/ambiguous-dataset/ambiguous/train/train_MNIST_final_ccvae.py --da... |
67f7c7fd24bb9c32018078dd719fbf2919150bb11613a3ec5216c994eb03fe9e | Shell | 1,739 | 63 | #!/bin/bash
# ================================================
# Script: get_assembly_cache.sh
# Author: Florian Bénitière
# Date: 11/05/2026
#
# Description:
# Download the indexed VEP cache files for the specified genome assembly.
# Supports GRCh37 (hg19) and GRCh38 (hg38).
#
# Usage:
# ./get_assembly_cache.sh ... |
c453bc85ee3a38206a692172aaf6d20870366e3c34f0dc5ddeb7d4637d0e1c1a | Shell | 1,739 | 47 | #!/usr/bin/env bash
# Run all SSN training jobs for this experiment folder.
#
# Usage:
# bash run.sh [NUM_SEEDS, default: 5]
#
# Steps:
# 1. Regenerate per-sweep parameter files via change_params.py
# 2. Launch every (sweep_id, seed_id) combination as a background process
# 3. Wait for all processes to finish
#... |
a6d2f916e0a17e57271673a3ec7af73c27ab98bebc0f5301482d29d295c6b46c | Shell | 1,740 | 64 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
SPM_ENCODE=flores/scripts/spm_encode.py
DATA=data_tmp
SPM_MODEL=criss_checkpoints/sentence.bpe.model
DICT=criss... |
7d9d256b822e2c6ac46d24949f7a1ef9014c31debe652c07212d6ce8372210e8 | Shell | 1,742 | 54 | #!/bin/bash
WHAT=$1
DIR=$2
cat ../gnuplot_common_settings.hh > ${WHAT}.gnuplot
echo "set title " `grep ${WHAT} ../action_settings.txt | head -n 1 | cut -d ";" -f 2` >> $WHAT.gnuplot
echo "set xlabel " `grep ${WHAT} ../action_settings.txt | head -n 1 | cut -d ";" -f 3` " offset 0,0" >> $WHAT.gnuplot
echo "set xrange [... |
d8a79dc77e6c7d623ed73723599e2963d5aa4546899c41a5ceb9a054d818f13b | Shell | 1,745 | 58 | #!/bin/sh
# CBIG_IndCBM_create_MSHBM_list.sh <surf_list_dir1> <surf_list_dir2> ... <output_dir>
# This function generate file list for the MSHBM model in replication. The folder structure is the same as MSHBM model.
# Input:
# surf_list_dir?: Surface file list of subject ?.
# output_dir: Path of output folder.... |
77ab29af1b18dfa48b6eca64e82031d03a9e50d6c169829114c5155a9390a706 | Shell | 1,747 | 49 | #!/bin/bash
dir="/root/dir"
# read subject, session, and z coordinate variables from a csv file
while IFS="," read -r data chop_z; do
echo "Data: ${data}"
echo "Chop z coordinate: ${chop_z}"
# Extract subject, session, and run values from data
sub=$(echo "$data" | cut -d'_' -f1)
ses=$(echo "$data... |
c3c243f035f9d5502efd3d4429a1dedeb61473fa0828b562dbee714be91225b5 | Shell | 1,752 | 56 | set -xe
device_id=0 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse90063_k562_ko_tf20_37160_19264
split=simulation
result_dir=./results
seed=1
epochs=15
batch_size=6
ac... |
88126708d79695b1af1378d90bbbcaedba59967dbbeaee92245e8b04eb0650ac | Shell | 1,754 | 56 | set -xe
device_id=0 # which device to run the program, for multi-gpus, set params like device_id=0,2,5,7. [Note that] the device index in python refers to 0,1,2,3 respectively.
# params
data_dir=./data/
data_name=gse90546_k562_63587_19264_10k_log1p
split=simulation
result_dir=./results
seed=1
epochs=15
batch_size=6
... |
b5953f558d47ec18891046d07c2f91d6f69238a3edf84d705d4b9808fda38fb5 | Shell | 1,754 | 40 | #! /bin/sh
# Last successfully run on Mar 25th, 2020 with git repository version v0.17.0-Fix_Absolute_Path
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
... |
82ea03dcc3e7348c1e609a1c4e41bf7ac36d819b0e67821c1679a389d6bfe3ce | Shell | 1,757 | 46 | #!/bin/bash
set -e
sizes="large xlarge"
declare -A ckpt_urls
ckpt_urls[large]="https://dl.fbaipublicfiles.com/hubert/hubert_large_ll60k_finetune_ls960.pt"
ckpt_urls[xlarge]="https://dl.fbaipublicfiles.com/hubert/hubert_xtralarge_ll60k_finetune_ls960.pt"
test_dir=$(pwd)/examples/hubert/tests
split=sample
echo -e "$... |
2cb04e064000513a75d63386ef69e3719ac3964b918fba459cbbc93af0708e4c | Shell | 1,758 | 52 | # Path of the folder containing all data
dir="/root/dir"
# Define conditions and mask types
declare -A analyses=(
["standard"]="randomise_first_trial_censored"
["paramod"]="randomise_first_trial_censored_paramod"
)
declare -A avgs=(
["run-1-avg"]="run-13-avg"
["run-2-avg"]="run-24-avg"
["ses-A-avg"... |
d001a25d8d892669f9d1b4252e90ab720a44bc298f475be7e4deb984bab3466a | Shell | 1,762 | 59 | #!/bin/bash
# submit_rbp_cnn_tf.sh
# 提交 cnn_transformer × 172 RBP × seed=666 的 Slurm array job
#
# 使用方式（在集群 luminary 上，于脚本所在目录执行）：
# cd /lustre/grp/gglab/liut/Kattention_aten_test/scripts/RBP
# bash submit_rbp_cnn_tf.sh
#
# 前置要求：
# 1. conda activate pytorch（或含 torch/h5py/einops/sklearn 的环境）
# 2. 若缺依赖：pip instal... |
4946b3db85c51ecd2ab75a5fa0556440a4574bfdbc236e8414003c8d09363c27 | Shell | 1,770 | 49 | #!/bin/bash
# This function submit the job for generation of premultiplied matrix.
#
# Input arguments:
# 1) out_dir: output directory to which the output matrices would be saved.
# 2) job_name: name of the job to be submitted to the cluster.
# 3) lh_fmri_fullpath_txt: left hemisphere subject fullpath input.
# 4) rh_fm... |
b61bf75a150e22dc12efae5cca5bf385f8733ee58d516fcfcfa8100f5a718200 | Shell | 1,786 | 50 | #!/bin/bash
# Job name:
#SBATCH --job-name=mixer
#
# Project:
#SBATCH --account=nn9114k
#
# Wall clock limit:
#SBATCH --time=1-00:00:00
#
#SBATCH --cpus-per-task=20
# Max memory usage:
#SBATCH --mem-per-cpu=4600M
# Job array specification
#SBATCH --array=1-20
## Set up job environment:
source /cluster/bin/jobsetup
... |
a75e9044ec799c6ad0c3aecbb21f5f7eee0f2f02ceb7726f08826a49196bcfd8 | Shell | 1,787 | 33 | #!/bin/sh
#PEER standalone usage example
#For complete documentation please see
#https://github.com/PMBio/peer/wiki/
# Simple PEER application
echo "Simple PEER application. All default prior values are set explicitly as demonstration. Output in peer_out_simple/"
./peertool -f data/expression.csv -n 20 -i 100 --a_pa... |
b70d4d06e19e28cb99d3bb94b248c01907bae6cab4789ff98d696b5779b95f4e | Shell | 1,798 | 68 | #!/bin/bash
# Experiment A extra seeds: run seed=1 and seed=2 for all hyperparameter configs
# RC tasks: KNET_rc (abs-ran_fix2); Markov: KNET (markov_1_0_50000)
# 2 jobs in parallel; runs from: Kattn-sim-dev/src/simulation/
PYTHON=/rd1/liut/miniconda3/envs/kattn-sim/bin/python
source env_setup.sh
KERNEL_SIZES=(6 8 10... |
1549d05f3819997dbb7ff95a537a1774ecb12323a500e4bd23485a9c8daa3821 | Shell | 1,803 | 89 | #! /bin/sh
set -e
build_dir=$2
branch="master"
if [ "$1" != "master" -a "$1" != "refs/heads/master" ]; then
branch="develop"
fi
echo "BUILD_DIR: $build_dir"
echo "BRANCH: $branch"
git clone -b $branch --depth 1 https://github.com/boostorg/boost.git boost-root
cd boost-root
# Use a reasonably large depth to p... |
aabf7232dc0e56f471d084f59a29e7c91d0b20a45d2aa3157ddadfdbcacbd388 | Shell | 1,803 | 51 | #!/bin/bash
subj='S07'
root_dir='/ifs/loni/groups/loft/FanhuaGuo/Experiment/ASL_Mesoscopic2025'
output_dir=$root_dir/SUMA/$subj/CBF
cd $output_dir
#####===================== whole brain
prefix=T1warp_whole
fixed=HCP_template.nii
# moving=cutrT1.nii
moving=T1_al_ns.nii
base_mask=none
in_mask=none
base_mask_SyN=none
i... |
9a8d969233dba1519b41ce37ccaf8f5d3a50a75789af2e5c51cfa132e3aa3e0a | Shell | 1,805 | 43 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_5.out
source activate mlfold
folder_with_pdbs="../PDB_complexes/pdbs/"
output_dir="../PDB_complexes/example_5_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_chains=$out... |
0c89b1a4e3beb6ab946903d1cc52dda9d390ea1bb58d6fbe45a6682b80c11765 | Shell | 1,816 | 59 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
source_lang=kk_KZ
target_lang=en_XX
MODEL=criss_checkpoints/criss.3rd.pt
SPM=criss_checkpoints/sentence.bpe.mo... |
dcbb642caee94917b4a4ca3ad25f59e9aaef666cc01673276b39b2c2e6ab3341 | Shell | 1,830 | 53 | #!/bin/bash
# Job name:
#SBATCH --job-name=mixer
#
# Project:
#SBATCH --account=p33_norment
#
# Wall clock limit:
#SBATCH --time=16:00:00
#
#SBATCH --cpus-per-task=8
# Max memory usage:
#SBATCH --mem-per-cpu=7600M
# Job array specification
#SBATCH --array=1-20
## Set up job environment:
source /cluster/bin/jobsetup... |
50bc7572ef0aab42bdecc4743e6a53f553e80a8b469c3023edd335114319cbdf | Shell | 1,836 | 49 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
SRC=en
TGT=is
MODEL_NAME=wmt21.dense-24-wide.En-X
PATH_TO_FAIRSEQ_PY=.
TMP_DIR=generation_tmp
mkdir -p $TMP_DIR... |
6e9bc05b82d398ba29ffbd85a587e947fa57eddc749511937176254e192c1c1d | Shell | 1,837 | 73 | #!/usr/bin/env bash
set -euo pipefail
BASE_DIR="ismb26/models"
ESM_PATH="/cta/share/users/esm/ESM-1b"
TRAIN_FILE="data/GeneOntology/nrPDB-GO_train.txt"
VAL_FILE="data/GeneOntology/nrPDB-GO_valid.txt"
TEST_FILE="data/GeneOntology/nrPDB-GO_test.txt"
OUT_ROOT="ismb26/segments"
# Round-robin GPUs
GPUS=(0 1 2)
gpu_i=0
... |
fc9e0448ba4d95a219396321dc7b730ef1d2f81ec7b5e74f0fef65ddfd5d98a9 | Shell | 1,838 | 68 | RESULT_PATH=./asset/ckpt/broadband
PARAM=./asset/config/param_camPitch1.85_RGB_pitch395nm_864_semiBroad.py
DEVICE=cuda:1
BRIGHTNESS_CLAMP=1
BRIGHTNESS_REGULARIZER_COEFF=1.0
SHARPNESS_REGULARIZER_COEFF=1
CONTRAST_CLAMP=1
PSF_LOSS_WEIGHT=1.0
MASKED_LOSS_WEIGHT=1
L1_LOSS_WEIGHT=1
DA_LOSS_WEIGHT=1
SSIM_LOSS_WEIGHT=1
PERCE... |
065167b8440493931c3cfb6174376e022efe0739d56241f5ce10cb01e7eef208 | Shell | 1,846 | 47 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Environment Resources Script
# ==================... |
035e06c232622b7c4d4d2eb2c29bec280a6c48d353cbe1c86d28877876f4ef3f | Shell | 1,850 | 68 | #! /bin/bash
WHAT=$1
DIR=$2
echo $WHAT script generation
cat $WHAT.hh > $WHAT.gnuplot
DATA_FILE=`find $DIR -name "*.dat" | grep $WHAT`
echo plot \\ >> $WHAT.gnuplot
for FILE in $DATA_FILE
do
LAST=$FILE
done
echo LAST=$LAST
for FILE in $DATA_FILE
do
if [ $FILE != $LAST ]
then
BASE=${FILE##*/} ; BASE=... |
0ea7db7828b769b5dffd8e1cb49edcae52dfcd630c6318a6b4cb16cd9e305a3e | Shell | 1,853 | 51 | #!/bin/bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# 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, mo... |
ba41ca80313e4ae58c9db9d5788df7c256870c25c4cf375d9f460fd19860e476 | Shell | 1,859 | 49 | #!/bin/bash
if [ $# -ne 3 ] ; then
echo 'Usage: '`basename $0`' <input file to be smoothed> <x FWHM size (mm)> <y FWHM size (mm)>';
echo "Needs FSL and afni modules loaded"
exit 1;
fi
# path to AFNI's nifti_tool
#NTPATH=$(dirname $(which nifti_tool))
#if [ "$NTPATH" = "" ] || [ "$FSLDIR" = "" ] ; then
# echo "Nee... |
64a17ebfbb541d80e73b0e32b62b7ab735ab56aafa9042359d00a03e3e92c414 | Shell | 1,862 | 56 | #!/bin/bash
# This script creates a list that contains the full paths to unit test subjects's surf data.
# Each line is one subject with different runs.
# Written by Xiaoxuan and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# set paths
data_dir=$CBIG_TESTDATA_DIR/stable_proje... |
a9964b47fb0bf04d69e1221bfeffaf37d9fb6c02442fd270757d2ff6d663120c | Shell | 1,883 | 46 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environment variabl... |
02dcec4beecb8a74afcc7c706f050c1a6751f803049cb600aaac6c3459b7b185 | Shell | 1,890 | 47 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
PY_BIN_ROOT=
# PyPI dependency
${PY_BIN_ROOT}pip install sentencepiece sacremoses
# Get data
if [ ! -d "data" ]; then
mkdir d... |
7df6a6481da2126c1fa1b5b1f33fe369198b847c3bf0bf09641d3c50c32542a1 | Shell | 1,903 | 58 | #!/bin/bash
#SBATCH --job-name=rc-tasks
#SBATCH --gres=gpu:1
#SBATCH --mem=48G
#SBATCH --time=12:00:00
#SBATCH --cpus-per-task=4
# NOTE: --output, --time, --mem can be overridden by submit_rc_tasks.sh via sbatch CLI
set -euo pipefail
# Positional args: MODEL TEST_CONFIG SAMPLE_SIZE SEED LR BATCH
MODEL=${1:?Usage: $0 ... |
afbb58df684d30f95842bd631180fe2b64054b47f264a5208074c0bb7e7a3350 | Shell | 1,917 | 43 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# 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, c... |
7347f3034b4bb0f762fe6647d24d3c4393b6fb12e11f6c6bfa4b256c7e74055a | Shell | 1,929 | 66 | #!/bin/bash
# submit_crispr_cnn_tf.sh — CRISPR CNN-TF Slurm 提交脚本
# 11 datasets × 2 models (cnn_transformer, cnn_transformer_pm) × 5 folds = 110 runs
# LR: 1e-3（见 job_crispr_cnn_tf.sh）
#
# Usage (on luminary, from Kattn-sim-dev/src/crispr/):
# bash submit_crispr_cnn_tf.sh [--dry-run]
DRY_RUN=0
[[ "$1" == "--dry-run" ... |
f854c6d0d758c9c7ba60bf0152ef2321d297356d3f856e779a222781657afe52 | Shell | 1,931 | 58 | #!/bin/bash
#SBATCH --job-name=markov-tasks
#SBATCH --gres=gpu:1
#SBATCH --mem=48G
#SBATCH --time=12:00:00
#SBATCH --cpus-per-task=4
# NOTE: --output, --time, --mem can be overridden by submit_markov_tasks.sh via sbatch CLI
set -euo pipefail
# Positional args: MODEL TEST_CONFIG SAMPLE_SIZE SEED LR BATCH
MODEL=${1:?Us... |
09170f63dcd1f2e274e80cdaa23fc956106b744571e3a3044b6d8225cfef4be6 | Shell | 1,941 | 28 | ## get embedding
# CUDA_VISIBLE_DEVICES=1 python run_embedding_sc.py --ckpt_path ../0.1B-trans-pGAU-shuffle5-autobin100-mask0.3-bts1024-0226-bin100-k8s-lr1e-4-resume/models/model_step=35999.ckpt --ckpt_name 50M-0.1B-res --data_path ./data/split_norm/Target_expr_resp_19264.{durg}.csv
# CUDA_VISIBLE_DEVICES=1 python run... |
1d5c848cb74f5bca71ebc32004833e1dd6c5ec04c5d07765cc67abdf7aa33300 | Shell | 1,943 | 72 | #!/bin/bash
# Experiment A: Hyperparameter scan (kernel_size × num_kernels) for KNET
# RC tasks use KNET_rc (plain); Markov uses KNET (diagonal mask)
# Runs 2 jobs in parallel (GPU: ~19GB / 24.5GB)
# Run from: Kattn-sim-dev/src/simulation/
source env_setup.sh
KERNEL_SIZES=(6 8 10 12 15)
NUM_KERNELS=(16 32 64 128)
MAX... |
6bf31e95d44a245f81ec555033331aa379a17c9d52d9f3243d4030c7b4dd6d69 | Shell | 1,949 | 68 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Environment Resources Script
# ==================... |
5225c87cdd04620edb1704aebf2b1b7ae175645e877efbe1ba57e2db2ac56ae8 | Shell | 1,956 | 73 | #!/bin/bash
dir=/Volumes/public/Backup/horiDir/qst/TauLNM/PET_SUVR/PSP_GMandWM/
cd ${dir}
arg=""
#for subj in smwGMWM_SI_LE_16-036-AP09_20170906_MPRAGE_sag smwGMWM_SI_LE_17-034-C005_20190307_MPRAGE_sag smwGMWM_SI_LE_17-034-C010_20210330_MPRAGE_sag smwGMWM_SI_LE_17-034-MC005_20190306_MPRAGE_sag smwGMWM_SI_LE_17-034-... |
c7d0cc332d5c93eea952df6e139dd46706498bc9fbde71b0fd813b3c6847be79 | Shell | 1,960 | 35 | #!/usr/bin/env bash
##
# @file test_blackbox.bash
# @author Simon Yu
# @date 10/03/2025
# @brief Script for testing blackbox models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
./test_blackbox.py -r "42.awa2.blackbox.resnet34.2024.12.14.8.11.PowerEdge-R720"... |
0c5aa51e7a20bf59f8e323230b80d0bf9faa83fca70c3a413791b3c048ec1507 | Shell | 1,966 | 46 | #! /bin/bash
# Written by Tianchu Zeng and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
echo "Executing this script will install a new environment called CBIG_py3_aws and install package aws-cli."
read -p "Are you sure? (y/n) " answer
if echo "$answer" | grep -iq "^y"; then
... |
a023ee37482c8a5b71b7af34fd91cb5ca2a224159eff0255697eb0648b4a140b | Shell | 1,966 | 45 | #! /bin/sh
# Last successfully run on Oct 30th, 2020 with git repository version v0.17.1-Schaefer2018_LocalGlobal
# Written by XUE Aihuiping and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$... |
2ed8615ffc83a7a4a59a96e26a659d75a574209a3bb5e001d0549e5a6e2ac12e | Shell | 1,970 | 44 | #! /bin/sh
# Last successfully run on Dec 7, 2019 with git repository version v0.15.4-Update_KRR
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREES... |
367afee335524cc05212a9ffc301eb12df7b0e286993ff3133bc7f7c707838bc | Shell | 1,974 | 60 | #!/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 -g <GMList> -o <outDir> [-q <queu... |
83929ef10ff4d35faed81df87b7980ef802e5e38d50e349f54e566c1cf26b6d2 | Shell | 1,989 | 75 | #!/bin/bash
# ================================================
# Script: get_alphamissense_resources.sh
# Author: Florian Bénitière
# Date: 11/05/2026
#
# Description:
# Downloads and indexes AlphaMissense annotation files for VEP.
# Supports genome versions GRCh37 (hg19) and GRCh38 (hg38).
# Indexes files with t... |
bc1bd722a271e084266c7214f05be9156191a739e882617146acdc956bd939e3 | Shell | 1,991 | 56 | #!/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 -d <docs> -k <noTopics> -r <noIni... |
97e29cda884337fc10bc892cabc34f58adee429b43ccd93f0a24c4158ce37233 | Shell | 1,994 | 49 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outDir=$1
# reference directory
workspace=${CBIG_TESTDATA_DIR}/stable_projects/\
disorder_subtypes/Sun2019_ADJointFactors/step1_SPM_VBM
refDir=${workspace}/results/VBM_create_new_template
imgList... |
9ee6e9622ed91fc7f50ba9488d3f62688cac45607833576086d16facb2c7dff2 | Shell | 1,995 | 44 | #!/bin/sh
# Last successfully run on Oct 16th, 2019 with git repository version v0.15.3-Update_proj_refs_and_add_KRR_LITE
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER... |
999a69863f2f5934e2e9cad918e7ce97b58af76d60fe9c740eb3ca3404c48f0a | Shell | 1,996 | 54 | #!/bin/bash
# This script will generate the subject fullpaths for the given subject list
# It checks through all possible runs of each subject if the corresponding fMRI data exists
# A fullpath is then generated and tabulated into a csv file
#
# Input arguments:
# 1) subject_list_path: a text file, each line being a su... |
a7cbcf19dc61172da7d47a747da525cf4c783bef5b3dd7629978bdf1c887b305 | Shell | 2,003 | 62 | #!/bin/bash
dir=/Volumes/public/Backup/horiDir/qst/TauLNM/PET_SUVR/PSP_tau/
cd ${dir}
arg=""
#for subj in s8SUVRwRM_F200_mcPMPBB3_FL_LE_16_036_AP009_1_1 s8SUVRwRM_F200_mcPMPBB3_FL_LE_17_034_C005_1_1 s8SUVRwRM_F200_mcPMPBB3_FL_LE_17_034_C010_1_1 s8SUVRwRM_F200_mcPMPBB3_FL_LE_17_034_MC005_1_1 s8SUVRwRM_F200_mcPMPBB3_... |
2a4097edb1f7ca29f5b605f88d5b06e6a2cf44e50475166fbf71d77a8cd1e2fc | Shell | 2,010 | 46 | #! /bin/sh
# Last successfully run on May 31st, 2021 with git repository version v0.20.0-Kong2022_ArealMSHBM
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; th... |
68ff40506ae5e5a4b4b1b5e5e1c575cce58c3d48529b2a6b6d32b20be3f9a8f2 | Shell | 2,020 | 57 | #!/bin/bash
workdir=/home/yukihori/Desktop/horiDir/qst/TauLNM/analysis_PSP_Tau/
PETdir=/home/yukihori/Desktop/horiDir/qst/TauLNM/PET_SUVR/PSP_tau/
GSPdir=/home/yukihori/Desktop/horiDir/qst/GSP1000/
cd ${workdir}
for gsp_subj in `seq -f '%04g' 1 21`;do
for run in 1 2;do
indir=${GSPdir}/sub-${gsp_subj}/func/
for ... |
19c1b90d3bc04ba603ff62cc1c800a1a60c4c7f513289cbbbbaeb90eb231f7dc | Shell | 2,021 | 61 | #!/bin/bash
ARGS=`getopt -o "t:d:e:m:o:b:g:s:w:a:f:" -l "task_name:,data_cat:,epoch:,mean_output:,optimizer:,per_device_batch_size:,gradient_accumulation_steps:,eval_step:,warmup_ratio:,eval_batchsize:,frozen_bert:,model:,do_train:,learning_rate:,seed:,output_file:" -n "test.sh" -- "$@"`
eval set -- "$ARGS"
while tr... |
1e5e036c834a3b430b7f7f11d9f778e893f87458e9491e2a2a7b55bb3974ecae | Shell | 2,024 | 45 | #!/bin/sh
# Last successfully run on Apr 2nd, 2023 with git repository version v0.27.2-update_reorder_func
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
... |
65043898f8b7efa71778c81ff7939d27300f149e3dfe14ef05bf37236bfa9b13 | Shell | 2,028 | 60 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
doc_dir=$1
out_dir=$2
unit_test_path=${CBIG_REPDATA_DIR}/stable_projects/disorder_subtypes/Sun2019_ADJointFactors
if [ -z "$1" ]; then
doc_dir=${unit_test_path}/step2_MMLDA/results/BrainBehav... |
2813d74b232dad1030966ef2338141ed1d8ecf7f107739a4e217a817b9689475 | Shell | 2,036 | 78 | #!/usr/bin/env bash
train_common () {
fairseq-train "$DATA" \
--combine-val \
--train-subset train \
--num-workers 2 \
--validate-interval-updates 1000 \
--save-interval-updates 1000 \
--no-epoch-checkpoints \
--ddp-backend fully_sharded \
--memory-efficient-fp16 \
... |
3e5bfdaa12c90cca5bcc95e41525cdde235dcd703d8517bef4912d92b8808c87 | Shell | 2,043 | 57 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
4f2d8ef8b9585c2c3ffee17ba1a08bdc948cea5deed37607c59512059031a96e | Shell | 2,051 | 50 | #!/bin/bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# 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, mo... |
33557449f629c1d7e5a60920f747fd10be02cd150f345e01ba3db37658b1666b | Shell | 2,070 | 59 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# data should be downloaded and processed with reprocess_RACE.py
if [[ $# -ne 2 ]]; then
echo "Run as following:"
echo "./exa... |
89b0bad1259e8b27c0eb53e7744e107f9f321448ea4053757fbb6fef80418eb5 | Shell | 2,078 | 67 | #!/bin/bash
export PATH="${PATH}:${HOME}/tools/annovar"
# Building the annovar database for Orfanage
gtfToGenePred -genePredExt nextflow_results/V47/orfanage/orfanage.gtf data/annovar_orfanage_db/hg38_refGene.txt
retrieve_seq_from_fasta.pl \
--format refGene \
--seqfile /project/s/shreejoy/Genomic_references/GE... |
6a835acaa3ce270ae7557776d7e97c7362083b856df203cc3a007c59a8f5b990 | Shell | 2,091 | 78 | # MIT License
#
# Copyright 2018 Broad Institute
#
# 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, merge, ... |
cb574ecc3a680de54020d47ff5a2e28d20cf8b2281e2ffb2b41cf307c92bdaf9 | Shell | 2,091 | 42 | #!/bin/bash
# Download and prepare all reference resources and dockers required for variant annotation
set -e # Exit immediately if a command exits with a non-zero status
set -o pipefail # Properly propagate errors through pipelines
# ============================
# Environment Resources Script
# ===================... |
eaa8e5bef821e17642364f12ee41d867c5527cc271c108770a7c827b4d2b5c75 | Shell | 2,092 | 77 | #!/bin/bash
# Florian Bénitière 11/05/2026
# Download, bgzip-compress, and index GRCh38 reference genome for VEP pipelines
# Usage: ./ref_genome.sh <genome_version>
# Example: ./ref_genome.sh GRCh37
set -e
set -o pipefail
# ============================
# Check argument
# ============================
if [ $# -ne 1 ]; ... |
10d801fc57cbc57c19a3272eb85f48970b93541005b82c500a5ef795f3a367d7 | Shell | 2,108 | 63 | #!/usr/bin/env bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey)
# 2014 Guoguo Chen
# Apache 2.0
[ -f ./path.sh ] && . ./path.sh
# begin configuration section.
cmd=run.pl
stage=0
decode_mbr=true
word_ins_penalty=0.0,0.5,1.0
min_lmwt=7
max_lmwt=17
iter=final
#end configuration section.
... |
faa7f5b47831214bd2cbca05bc33253c56b7d3150f213633a7915bf5567b09cf | Shell | 2,119 | 66 | #!/bin/bash
##########################################################################################################
## This program computes connectomic outputs using seed region based on standard connectomes ##
## script by Andreas Horn, August, 2016. ... |
b6e4fa04f624e3192b077fb4f229368d277ae95ef1295e6e19c025041fc0517c | Shell | 2,120 | 66 | #!/usr/bin/env bash
#
# labgascore_prov_protect_reflogs.sh
#
# Disables git reflog expiry on every repository cloned under a given root.
#
# The reflog records which commit each clone actually had checked out at
# any past moment, and is the only way to reconstruct the dependency
# versions behind an analysis that was ... |
693a3d92bc0427a6cf2fe6aeeadbb6509b737d387deebc734def8311ffc25d61 | Shell | 2,126 | 61 | #!/bin/bash
# Example usage of simulate-for-posterior.py for different models
# Example 1: YRI_CEU model
# Parameters: N_A, N_YRI, N_CEU_initial, N_CEU_final, M, Tp, T
echo "Simulating YRI_CEU model..."
python simulate-for-posterior.py \
--model YRI_CEU \
--params 1e4 2e4 5e3 3e4 1e-4 1e4 2e4 \
--output-di... |
5124ed3f1262eea8aa0c84bdb224c47d4cdd5adf380a8f3773c8a2fb88708e87 | Shell | 2,136 | 54 | #!/bin/bash
# Job name:
#SBATCH --job-name=mixer
#
# Project:
#SBATCH --account=nn9114k
#
# Wall clock limit:
#SBATCH --time=1-00:00:00
#
#SBATCH --cpus-per-task=20
# Max memory usage:
#SBATCH --mem-per-cpu=4600M
# Job array specification
#SBATCH --array=1-20
## Set up job environment:
source /cluster/bin/jobsetup
... |
6b6ba0085c20e2c32b2b733455d412e40c94a2218915a62627b00caf48f7fe0c | Shell | 2,141 | 51 | # Pancreas
PANCREAS_FLAT_FILES="https://smi-public.objects.liquidweb.services/cosmx-wtx/Pancreas-CosMx-WTx-FlatFiles.zip"
PANCREAS_OUTPUT_ZIP="cosmx/pancreas/Pancreas-CosMx-WTx-FlatFiles.zip"
mkdir -p cosmx/pancreas
if [ -f $PANCREAS_OUTPUT_ZIP ]; then
echo "File $PANCREAS_OUTPUT_ZIP already exists."
else
ech... |
699f0fc671e8e692263130aaedf8243bc26c1cb8813c14f0e65e6b78dd66ddf7 | Shell | 2,154 | 74 | #!/bin/bash
# Labeled datasets to test on "C4_database_hull_labelled.h5"
LABELED_DATASETS=(
"C4_database_lisberger_harmonized_labelled.h5"
)
#"C4_database_hausser.h5"
# All available datasets for pretraining
ALL_PRETRAIN_DATASETS=(
"C4_database_hull_unlabelled.h5"
"C4_database_hull_labelled.h5"
"C4_dat... |
ecfb14cb9197708d1a6b3eedca6c947e9f7aac6769f2b9548131ca8dd043ecfe | Shell | 2,168 | 51 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outDir=$1
# reference direcotry
workspace=${CBIG_TESTDATA_DIR}/stable_projects/\
disorder_subtypes/Sun2019_ADJointFactors/step1_SPM_VBM
refDir=${workspace}/results/VBM_use_given_template
imgList=... |
7e5de5ecd4c65bc29f5d03667479858c91f6da08fa5f6564eaf96618692dc6c7 | Shell | 2,169 | 56 | #!/bin/bash
# Job name:
#SBATCH --job-name=mixer
#
# Project:
#SBATCH --account=p33_norment
#
# Wall clock limit:
#SBATCH --time=16:00:00
#
#SBATCH --cpus-per-task=8
# Max memory usage:
#SBATCH --mem-per-cpu=7600M
# Job array specification
#SBATCH --array=1-20
## Set up job environment:
source /cluster/bin/jobsetup... |
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