sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
07bb97d4b738eb64ace22323920504724b91e0f4cfa3f5c016f1570e2fda2cae | Shell | 1,435 | 18 | #!/bin/bash
#Assign variables to be built into the inputs json
PROJ="<project_name>"
FLOC="<path/to/general/project/folder/${PROJ}"
OUT="${PROJ}_<suffix>" # Suffix should match the one from fill_MPRAmatch.json
ACC="${FLOC}/setup/<path/to/replicate_index>"
ID=`awk '{print $2}' ${ACC} | uniq | awk '{aggr=aggr",\""$1"\"... |
41185efbd06f25e62263942e39a0f4f90a977e3c2bcf2620bd8bbe1397f301ae | Shell | 1,435 | 32 | export CARLA_ROOT=${1:-/home/kchitta/Documents/CARLA_0.9.10.1}
export WORK_DIR=${2:-/home/kchitta/Documents/transfuser}
export CARLA_SERVER=${CARLA_ROOT}/CarlaUE4.sh
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI/carla
export PYTHONPATH=$PYTHONPATH:$CARLA_RO... |
32c763439b32dc423110e7591cff37e68851ca8cf87f852c2f84198b00965936 | Shell | 1,437 | 30 | #!/bin/bash
#
# Gokberk Alagoz
#
# This script will extract and order required columns from dyslexia and rhythm
# impairment summary statictics. Then will rename field names accordingly.
#-----
# PATHS
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
# Dyslexia
awk 'NR>1 {print $19, $16, $17, $25,... |
d3d6d596a470f85bfd87b33c30a39c3eaebdb31a60858c7b81c053f908953f73 | Shell | 1,441 | 51 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_h_hybrid_pt_1200e'
DATA_PATH='YOUR_PATH/data/hybrid_train.csv'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for 2 node, etc.
GPUS=${GPUS:-64}
GPUS_PER_NODE=${GPUS_P... |
eb74e4bcba6b95578a36f0b4603f886a3b66519c84a21e99ed2eb4f16ef64656 | Shell | 1,441 | 30 | #!/bin/bash
#
# Gokberk Alagoz
#
# This script will extract and order required columns from dyslexia and rhythm
# impairment summary statictics. Then will rename field names accordingly.
#-----
# PATHS
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/"
# Dyslexia
#awk 'NR>1 {print $19, $16, $17, $25... |
220fd204555f1d78898fbdde7eed21d68ed893b96a12eb724c0b6681dc49ab24 | Shell | 1,449 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
280aa752079788ed5914692c7e1b6a0fdb6f4dbec3a712be36d63a17114f22f6 | Shell | 1,451 | 36 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
5d5fbc089e11e578c2a04575db01de182350aa0acd99bd3a25ecd0d362c43941 | Shell | 1,451 | 20 | #region.1Mb.bed is human locus; region.1Mb.mouse.bed is mouse locus
BASEFILE="region.1Mb.intervals.100ntStep" #for Mouse locus use "region.1Mb.intervals.100ntStep.mouse"
#generate 100nt step with 10.5Kb window size
bedtools makewindows -b region.1Mb.bed -w 10500 -s 100 | perl -ne '@a=split/\t/; print $_ if $a[2]-$a[1... |
7f7866668fa39d18291d22040e27a8afc7aeb00796c91fad4d332686db983622 | Shell | 1,451 | 62 | #!/bin/bash
set -ex
# This function installs protobuf 2.6
install_protobuf_26() {
pb_dir="/usr/temp_pb_install_dir"
mkdir -p $pb_dir
# On the nvidia/cuda:9-cudnn7-devel-centos7 image we need this symlink or
# else it will fail with
# g++: error: ./../lib64/crti.o: No such file or directory
ln -s /usr/l... |
84234554e253900e28424c146e61e9dfb8ff2a86044b6ed5d026219ebf58b701 | Shell | 1,453 | 51 | #!/bin/bash
#=========================================================================
# create plink filesets for each chromosome in 1000 genomes phase 3 data,
# then merge into one plink fileset
#=========================================================================
# create file to list fileset prefixes to merg... |
f729fcb76e46e9ab899da25a0d51ab30da4afc8f87127eb5e320fce9de201a6d | Shell | 1,457 | 60 | #MOLGENIS walltime=05:59:00 mem=10gb ppn=6
#string Project
#list Sample_ID
#list SentrixBarcode_A
#list SentrixPosition_A
#string resultDir
#string callrateDir
#string gapVersion
#string logsDir
#string intermediateDir
#string diagnosticOutputFolder
set -e
set -u
set -o pipefail
#Function to check if array contains ... |
30c72143d13cce3320c426b6b85527a6630078a2f9fa0b73ffdfb1fbed3f945b | Shell | 1,459 | 44 | # command interpreter to be used
#$ -S /bin/bash
#
# name
#$ -N class_rln
#
# merge stdout and stderr stream of job
#$ -j y
#
# output file
#$ -o ../../../../data/tutorials/synth_sumb/rln/medium_1/out_run4.log
#
# use current working directory
#$ -cwd
#
# define mail notification events
#$ -m n
#
# request the given re... |
d580349d6e0bd132ad838f036695e5cc06290069a91e917de3483eb080ae86bb | Shell | 1,459 | 23 | #!/usr/bin/env bash
# Phase 0 spike — iteration #2: raw-BAM-byte identity under IDENTICAL invocation.
# Runs Bismark twice with byte-identical command lines (relative input, -o ., --temp_dir tmp)
# so the @PG CL strings match, then compares the raw BAM bytes (BGZF-framing determinism).
set -u
export PATH="$HOME/microma... |
a1883c29aa9827b53072c366cfc8158e5963b2cd96d8086ac200f786fbb4a073 | Shell | 1,462 | 21 | echo "Running case 1, curv dep = -20"
python3 main.py --ntasks 1 --submit-tscc mito --mesh-file /root/scratch/meshes/mito_mesh.h5 --curv-file /root/scratch/meshes/mito_curv.xdmf --outdir /root/scratch/curvdepneg20 --curv-dep=-20
sleep 10 # avoid opening mesh file at the same time in other cases
echo "Running case 2, ... |
0a956924ae3cb17251f1265accf87247e3cf2d6cbefbd214a0c5846b892e5f51 | Shell | 1,467 | 44 | #!/bin/bash
#SBATCH --time=30:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=51250M # memory per CPU core
#SBATCH -J "NSDprep" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= pp... |
d826447f9b62bdf2fec232f5ec28eeaf2d30569fee03e37e1c904072440334f6 | Shell | 1,467 | 44 | #!/bin/bash
#SBATCH --time=40:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=51250M # memory per CPU core
#SBATCH -J "NSDprep" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= pp... |
a2bbbd8fbcf84ebfeab1dc85820fe442afef5c6315c09c657150958118789b81 | Shell | 1,468 | 52 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_g_hybrid_pt_1200e'
DATA_PATH='YOUR_PATH/data/hybrid_train.csv'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for 2 node, etc.
GPUS=${GPUS:-64}
GPUS_PER_NODE=${GPUS_P... |
5fc8250b4d351da8b7099f92ffa7556cdd9d1054c0cc3bf0bb851a2ea2d277d5 | Shell | 1,470 | 39 |
#!/bin/bash
## 1. receive arguments from submit_jobs.sh
env_var=$1
# BatchNum=0
script=/home/siyuan/jobs/suzukii_WGS/EAA/downstream/GSEA/random_SNP/scripts/output_gene_list/all_trimmed_outliers/scripts/GO_SNP_parallel_genomic_permutation_modifiedsuz_$env_var.pl
in_outlier_prefix=/home/siyuan/jobs/suzukii_WGS/EAA/baye... |
7ccbaec2ea721a2d3164d7b8469b656bb596102a171298af183bc9b11ee03f8d | Shell | 1,471 | 69 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
d271d72bda7bd13b5da88b191b4aaad4e01e4141fd683cde397bada9f85fa9e4 | Shell | 1,473 | 46 | ##################################################################################
# This script builds all the executables for the rolling-circle analysis pipeline
#!/bin/bash
BASE_DIR=$(pwd)
# These two paths need to be modified for your local installation:
CMAKE_PREFIX_PATH="/mnt/home/software/libraries/seqan/seqa... |
c7d3a62c7213ef9f0129eebb6c6aa77de50643757444c5e28799daf9e7493849 | Shell | 1,475 | 30 | #!/bin/bash
################################################################################
# Simulate CSDP on target pattern database
################################################################################
GPU_ID=$1 ## GPU identifier (0 should be used if only one GPU exists)
## demo model sizing/setup/data... |
e41dc63ee80ae8d6180207ab3f6251e3ff870477840f938c5a3576ef26884c38 | Shell | 1,475 | 43 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
win_len=$3
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/window_diversity/results/winlen_$win_len\_mincov_$mincov\_mincount_$min_count
sd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/window_diversity/scripts
script=$sd/win_div_by_filtered_sites.py
calc_script=$... |
9887f230b3818064d6aa65312fb395b4f1661344bdad4e52589de6fc685d0770 | Shell | 1,480 | 61 | #!/bin/bash
# ----- #
# Job name
#SBATCH --job-name=EEG_filter_bank_decoding
# ----- #
# Jobs to run; each element corresponds to a subject.
# Only run n at a time with (%n) at the end of the command!
# Counting the python way!
# Now using dataset: MUNICHMI.
#SBATCH --array=0-9%5
# ----- #
# Computational resource... |
3302530d8c083775d1454d8d094c65da2dcb9ca010bfa1588c4c79b053527ba9 | Shell | 1,487 | 62 | #!/bin/bash
# ----- #
# Job name
#SBATCH --job-name=Burst_detection
# ----- #
# Jobs to run; each element corresponds to a subject.
# Only run n at a time with (%n) at the end of the command!
# Counting the python way!
# Now using dataset: DREYER 2023.
# SBATCH --array=0-85%7
#SBATCH --array=0,2,12
# ----- #
# Com... |
ddf74285161d9f3c086aeeaad10469f9a4f6f6f0bd3dd5c8809c8a58bd600bff | Shell | 1,488 | 47 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f6134c92d141c52c54e3640b9e02e37242f45bb6c682fcbe860a1615b31ac8dd | Shell | 1,488 | 54 | phenos=$(cat data/mega/mega_np.pheno | \
awk 'NR==1{for (i=3; i<NF; i++) printf $i "\n"; print $NF}')
for pheno in $phenos
do
Rscript --vanilla code/magma/02_subset_pheno.R \
-p data/mega/mega_np.pheno \
-o tmp/"$pheno".tmp \
-r data/mega/related_rm/"$pheno".remove \
--phenotype "$p... |
02133f43db1f1b97a0ea6f8773d7920198bba6e0abd7799caab0bcd48524da8c | Shell | 1,489 | 47 | # create file to list fileset prefixes to merge
echo > ./tmp/mc_caa_plink_fileset_prefixes.tmp
# create plink fileset for each chromosome.
# using --snps-only because some indels have multiple versions
# and plink can't account for this very well.
# have to write duplicate variant ids to file because some still presen... |
30c71de88e8c68ca7fb76b0f680bd75b39a98da8d1b718d23b17f09e5d06ea74 | Shell | 1,489 | 61 | #!/bin/bash
# ----- #
# Job name
#SBATCH --job-name=Kernel_convolution_decoding
# ----- #
# Jobs to run; each element corresponds to a subject.
# Only run n at a time with (%n) at the end of the command!
# Counting the python way!
# Now using dataset: CHO2017.
#SBATCH --array=0-48%7
# ----- #
# Computational resou... |
78eada0285fc67f690f99b8975e9d2187d4c155ebcfe92889ab4787132652d14 | Shell | 1,490 | 17 | #!/bin/sh
#python train_multilabel.py --image-size "${1} ${2}" --augment 0 --seed 1 --n_classes 3
#python train_multilabel.py --image-size "${1} ${2}" --augment 1 --seed 1 --n_classes 3
python eval_multilabel.py --results-dir "/mnt/ds3lab-scratch/webermau/rey-figure/spaceml-results/data_78x100-seed_1/final-3_scores/r... |
9968cf40a642b20ef0d2ed01c80883ec634872175e841af1057e6ba517881658 | Shell | 1,493 | 49 | #!/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: $0 -g <GMToStdTmpList> -o <outDir>
... |
011ca1b5ab33e911eef0441b52a14814b7578d22c20988d781ef1bdbb9a81262 | Shell | 1,494 | 49 | #!/usr/bin/env bash
# Configure below, then run: ./scripts/run_tumor_tracking.sh (paths are relative to your cwd)
SEG_DIR="tumor_volume"
OUTPUT_CSV="./tumor_volumes.csv"
PATIENT_ID=""
FILENAME_PATTERN='(?P<date>\d{4}[-_]\d{2})\.nii\.gz$'
CONNECTIVITY=26 # 6, 18, or 26
MIN_VOLUME_MM3=20 ... |
419c69117b3fbfb05ecc955d4f3f4ced0086555b5abbcc419c550b6dd7beeb21 | Shell | 1,497 | 45 | #!/bin/bash
#Purpose: Project tSNR maps to fsaverage6 surface.
#Inputs: tSNR maps from Step1, freesurfer native output
#Outputs: .shape.gii (HCP WB compatible) surface SNR maps
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/... |
fb318f9c81947f90e8464e40abb6272f4ea8ffd98415d587a1c39427eed07d70 | Shell | 1,497 | 37 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Fst/syn_Fst/results/syn_SNP_data
dir_snp=/home/siyuan/jobs/suzukii_WGS/call_snp/amb/updated_poolsnp/paratest/test_maxcov/call_snp_maxcov_99/mincov_$mincov\_mincount_$min_count
dir_mpileup=/home/siyuan/jobs/suzukii... |
956cb45c1727c946d28e0e4ea49e1f630e546865853dffd8720a56c11d6a4b93 | Shell | 1,499 | 43 | #!/bin/sh
# test OB with CML
# $1 is inputfile root
# $2 is inputfile suffix
# $3 is inputfile type
# e.g. cycleformats.sh foo mol mdl
# Make sure we know the absolute path of the programs we're trying to
# call, in case the test is called from somewhere eles
if `env | grep ^builddir > /dev/null 2>&1`; then
BABEL=... |
0c9c4d6a0bdc9f3ea686b014d222fe4d5f001a9f81cf856e280c9216c36e26d8 | Shell | 1,500 | 45 | # command interpreter to be used
#$ -S /bin/bash
#
# name
#$ -N ref2_5gjv_rln
#
# merge stdout and stderr stream of job
#$ -j y
#
# output file
#$ -o ../../../../data/tutorials/synth_sumb/rln/5gjv/out_run1.log
#
# use current working directory
#$ -cwd
#
# define mail notification events
#$ -m n
#
# request the given re... |
07f5caa6e91d7833068cbcbe7dbbc91d728516a1b122c4a36c6ff0fbca5d464a | Shell | 1,502 | 37 | #!/bin/bash
#
# This script will run LAVA for all relevant annotations.
#
# Gokberk Alagoz, 29 June 2022 - last updated Feb 2023
inputDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/LAVA/input/"
refpanel_1kgp3="/data/workspaces/lag/shared_spaces/Resource_DB/1KG_phase3/GRCh37/plink/1KG_phase3_GRCh37_EUR... |
ee3fafcd24c122fe994f2d7072a72dabf8a17f0171c23ad7865c97e65d80b5b1 | Shell | 1,502 | 42 | # command interpreter to be used
#$ -S /bin/bash
#
# name
#$ -N mb_align_all
#
# merge stdout and stderr stream of job
#$ -j y
#
# output file
#$ -o ../../../../data/tutorials/synth_sumb/rec/nali/out_run1.log
#
# use current working directory
#$ -cwd
#
# define mail notification events
#$ -m n
#
# request the given res... |
2adb3f49bfdbbb418f34efeb841be128064429e27e9a91655c8569c4f1a11c01 | Shell | 1,504 | 42 | # Check for interactive environment
set -e
if [[ $- == *i* ]]
then
echo 'Interactive mode detected.'
else
echo 'Not in interactive mode! Please run with `bash -i`'
exit
fi
echo ">>> update base conda"
conda update -n base conda
# Assure mamba is installed
if hash mamba 2>/dev/null; then
echo ">>> Found mamba inst... |
bd2618784dde666bd901fc4f9adf73bb01a3ee14d4cc95aca8cf3077601cde8e | Shell | 1,505 | 76 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
3894582c5121617ee0b83204ecb5086f475c7573e59ecb28d6790e3d0d516815 | Shell | 1,520 | 53 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_b_hybrid_pt_800e_k400_ft'
DATA_PATH='YOUR_PATH/data/k400'
MODEL_PATH='YOUR_PATH/model_zoo/vit_b_hybrid_pt_800e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for... |
3c5a9e6f251f2f9affd6a74b979a884363ab90ff0526cf5108bd94257344f28e | Shell | 1,521 | 58 | #!/bin/bash
# author : sjn
# date : Dec.2022
set -euox pipefail
if [[ $# != 3 ]]; then
printf "Require a reference's cpg locations, fiberseq-smk's all table output, and an output file name\n"
printf "Some references are available at /mmfs1/gscratch/stergachislab/sjn/data/cpg/\n"
exit -1
fi
ref_cpg=$1
exp_cpg=$... |
cbd6d6f25131647ab1e7029b3e2c8eee481ddbd78e3f0be7e850cb588ff0e2be | Shell | 1,522 | 21 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
mkdir -p outputs_from_test
echo -e "Running: ./strc -in::pdb=./test_inputs/5edw.pdb -select::aa -out::pdb > outputs_from_test/aa.pdb"
./strc -in::pdb=./test_inputs/5edw.pdb -select::aa -out::pdb > outputs_from_test/aa.pdb
echo -e "Running: ./strc -in::pdb=./tes... |
f068176c54e52fc8d3de66b67f6f434709c56afc9adabaca954f51b705043f79 | Shell | 1,523 | 53 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/it_l_hybrid_pt_1200e_k400_ft'
DATA_PATH='YOUR_PATH/data/k400'
MODEL_PATH='YOUR_PATH/model_zoo/vit_l_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 fo... |
6a00762f8923627dfe1a5d54fea4f95ba64388b36928958ceb6350c4c2b43253 | Shell | 1,530 | 58 | #!/bin/bash
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
a1a4bd4b15bdc706d506466042ab05643dae0a81d57cd9e8229c713cf9efd00c | Shell | 1,533 | 48 | #!/bin/bash
subj_ids=$1
acomp_list=$2 # tsv file, no header, col1 = sub IDs w/ sub- prefix and col2 acompcor exclusion "1" non-exclusion "0"
ses=baselineYear1Arm1 #2YearFollowUpYArm1 #baselineYear1Arm1
out_dir=/scratch.global/${USER}/analyses_reliability
analysis_type=MULTIVERSE #single #MULTIVERSE # if running single... |
6b11d05ebbcbecbfee2a03cff5dbc989f4a76a6112cb21694948aadfb50a226e | Shell | 1,534 | 43 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f363a94f2f025a95b05bb7226a393ad6f56c60c026727bfffa9aff549488f8b0 | Shell | 1,543 | 50 | #!/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... |
6cb878dc2e4faeaa6047c550a8cab6faa36928255ec0275ed878047a14dda351 | Shell | 1,544 | 66 | #!/bin/bash
set -ex
# This function installs protobuf 2.6
install_protobuf_26() {
pb_dir="/usr/temp_pb_install_dir"
mkdir -p $pb_dir
# On the nvidia/cuda:9-cudnn7-devel-centos7 image we need this symlink or
# else it will fail with
# g++: error: ./../lib64/crti.o: No such file or directory
ln -s /usr/l... |
2988123b2bd8457ec1981c494b6955e0ee1f573fa7494feb8535e417c80f7661 | Shell | 1,546 | 48 | #!/bin/bash
# Function to display help
function show_help {
echo "Usage: $0 [options] <output_directory> <observations>"
echo "example: ./run_pipeline.sh ../Data 10"
echo "Options:"
echo " -h, --help Show this help message and exit"
echo ""
echo "Arguments:"
echo " output_... |
236b85e533269c3160dd580b4a191717d9404cf7bf9af9a4b69d94eddcf103e3 | Shell | 1,549 | 35 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
9ef6c2dff8a12238d8318c028824d8c73580466a7cda3a47cd8436346e13024f | Shell | 1,553 | 43 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
0ce42a12cd4ee270a2ef862a289b4f11fa641ea4cefd4583902b5d98360a6b5c | Shell | 1,554 | 63 | #!/bin/bash
#no final slash !!
targetFold=$PWD/../../../soft/cgal/4.7
if [ -d "$targetFold" ]; then
echo "removing $targetFold before installing !!"
rm -r $targetFold/*
fi
mkdir $targetFold
# Copy already downloaded package
cp ./sources/CGAL-4.7.tar.gz $targetFold
cd $targetFold
gunzip CGAL-4.7.tar.gz
tar xvf C... |
ac4953df872d36767cd899976e9ec81ec718c9640db825e5a97a866f8d6e0181 | Shell | 1,554 | 43 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a9c71a65ae8da91d2f2027ab94251fc61cdac1490b8ed2582c645759eea784cc | Shell | 1,555 | 40 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure3/Results/"
#file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro/HCP/* | cut -f... |
ba4632e94dc4cdfd0d086f628f28c1f1098f2b34e2cc013b791bbe920ba47b9f | Shell | 1,555 | 40 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure3/Results/"
#file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro/HCP/* | cut -f... |
e4523fc534ab5fe58343797ee31083f6ec50c96892c82c1d7f02e591a2ab3bc3 | Shell | 1,558 | 44 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
wd=/home/siyuan/jobs/suzukii_WGS/reannotate/syn_diversity/mincov_$mincov\_mincount_$min_count
dir_snp=/home/siyuan/jobs/suzukii_WGS/call_snp/amb/updated_poolsnp/paratest/test_maxcov/call_snp_maxcov_99/mincov_$mincov\_mincount_$min_count
dir_mpileup=/home/siyu... |
a37b26876666d402f3f89e338af991b132305473ccd2d76973e363200c49a6c6 | Shell | 1,559 | 53 | #!/bin/bash
#Purpose: submit jobs to generate individual full-surface FC matrices
#Set paths and vars
HOME=/fslgroup/fslg_spec_networks/compute
CODE_DIR=${HOME}/code/HCP_analysis/FC_matrices/ALL
HOME_D=/fslgroup/fslg_autism_networks/compute
PREP_DIR=${HOME_D}/HCP_analysis/CBIG2016_preproc_FS6_ALL
#Submit a job for e... |
a0f1145d194aa8a84f9ef2a0209acd2b89d95d66200a57c8fb51671eba01c716 | Shell | 1,564 | 54 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_l_hybrid_pt_1200e_ssv2_ft'
DATA_PATH='YOUR_PATH/data/sthv2'
MODEL_PATH='YOUR_PATH/model_zoo/model_zoo/vit_l_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1... |
c2a35559a0abc26ab1defd80d28c37bf2a5c97f849f6b41576c0dfe83ac032a7 | Shell | 1,566 | 52 | #!/bin/bash
sample=abcd # abcd, ahrb or mls
ses=baselineYear1Arm1 # baselineYear1Arm1 or 2YearFollowUpArm1 for ABCD
mask_label=None # None, wilson-sub, wilson-supra
type=session # run or session
subj_ids=${1} # sub-IDs, move to temp to differentiate low/high motion mods
n=240
# if using runs, inp should be firstlvl; ... |
5364296c1f856b994bbb2eb716db2dda00d5aca27053139127f570261cfc09d2 | Shell | 1,567 | 71 | #!/bin/bash
# Script to run the neural matching algorithm on random and real-world networks.
alpha=("0.001")
beta=("1.0")
exe=./neural_matching.py # version to run.
#========================================================
#
#========================================================
echo "runnin... |
700c0fb44f63333fb29570e7e74dc393c83ba2e7c7047d8c754d12542c860034 | Shell | 1,567 | 37 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f656ae4c0adbccafaa0002907b5bd3104c15f0e065466758bf55ccf8500f044d | Shell | 1,567 | 54 | #!/bin/bash
set -o errexit
export ANTSPATH=<your ANTS path>
export SUPPORTPATH=<your path to the supporting tools>
if (( $# != 3)) ; then
echo "args = $#"
exit
fi
T1=$1
T2=$2
PREDICTION=$3
TEMPDIR=TMP-$$
mkdir -p ${TEMPDIR}
fslmaths ${T2} -mul ${T2} -mul ${T2} -mul ${T2} ${TEMPDIR}/t2t2t2t2.nii.gz
... |
858e6134ebdf08e2b10ec8171fc157120ed6ca66fb39f29e6180ff04a2ad0e5d | Shell | 1,570 | 47 | #!/bin/bash
#Purpose: Project tSNR maps to fsaverage6 surface.
#Inputs: tSNR maps from Step1, freesurfer native output
#Outputs: .shape.gii (HCP WB compatible) surface SNR maps
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/... |
89929d318cb8959d2a7835c732ecded3373ca6c255f0bb43cafcb6da7061dbfb | Shell | 1,573 | 39 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
9e615d69c754c163ef82ef5230218450c4060310454476eef5dcf81b8d4a4e70 | Shell | 1,574 | 28 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
028953360a58db91b07ee424c3817539823ffac16287bb6e087e46964df5de00 | Shell | 1,576 | 38 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
7d590fa8aac561e843c3dbb59ad67c4981b1cee90d06e9a698b6f638b9d09094 | Shell | 1,578 | 38 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id_list=$1
pipeline=$2
if [ -z "${id_list}" ];then
id_list=$CBIG_REPDATA_DIR/stable_projects/predict_phenotypes/ChenTam2020_TRBPC/lists/release2_subjects_with_rs_and_t1_pass_recon_all.txt... |
c14d2c42ba9adc9dacd76375a1139a64f2375e3f36889f3a83fbeffa52e73d17 | Shell | 1,578 | 59 | #!/bin/bash
plink \
--bfile /data_global/ROSMAP/rosmap_topmed_20210303/ROSMAP_NHW_imputed_final \
--fam /data_global/ROSMAP/rosmap_topmed_20210303/ROSMAP_NHW_imputed_final_converted.fam \
--keep data/rosmap/np_ids.txt \
--make-bed \
--out tmp/rosmap_qc0
cat tmp/rosmap_qc0.fam | awk '{print 1, $2, $3, $4, $5... |
f93a9ae4e784f62ca06517bf6d277ada1ab4750639bb18a811a81612c8a6b84c | Shell | 1,582 | 40 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id_list=$1
pipeline=$2
if [ -z "${id_list}" ];then
id_list=$CBIG_REPDATA_DIR/stable_projects/predict_phenotypes/ChenTam2020_TRBPC/lists/release2_subjects_pass_rs.txt
fi
if [ -z "${pipelin... |
2e2791c14abf27cf06013b9184c0e8074f5249dcda5e08594210109ac6ca2ac7 | Shell | 1,583 | 40 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
4fc560ec7b2935d2f328f8c4a2e1ed39e5132cdbd860f375e789138d9ea7532a | Shell | 1,583 | 60 | #!/bin/sh
# Example: ./preprocess_and_predict.sh /data /out_img $(VENV)/bin ${GPUID}
# TODO: generalise to types of MRI format (NIFTY or DICOM)
# TODO: generalise to types of image format (png or jpg)
MODELTYPE="resnet152"
MODELRUN="19112020"
#MODELDIR="./saved_models/resnet152/19112020/"
MODEL="10push0.8167.pth"
h... |
5ef68cca11d7ab438a655f0b576f94644b1cb47f6913ca6cab72b3bed2a2bed4 | Shell | 1,584 | 56 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_b_hybrid_pt_800e_ssv2_ft'
DATA_PATH='YOUR_PATH/data/sthv2'
MODEL_PATH='YOUR_PATH/model_zoo/vit_b_hybrid_pt_800e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 fo... |
4df825feebaf691552f8d0c027ef6d458c211705fe17371546825abc7e5c0fa4 | Shell | 1,586 | 65 | #!/bin/bash
# Default values
deltemp=""
mi_option=""
# Function to print usage
usage() {
echo "Usage: run_ucdwmhkit.sh <Raw 3DT1> <3DT1 stripped Mask> <Raw FLAIR> [--delete-temporary] [--mi]"
exit 1
}
# Check minimum number of arguments
if [ $# -lt 3 ]; then
usage
fi
# Parse required arguments
t1=$(read... |
054186531904ec941f447d4d18459561da6ecf30b2f40557b5db5447a38cec7f | Shell | 1,589 | 63 | CUDA_VISIBLE_DEVICES=7 python -m torch.distributed.launch \
--nproc_per_node=1 \
--master_port=$((RANDOM + 10000)) \
start.py \
--dataset PGPS9K \
--use_MLM_pretrain \
--evaluate_only \
--eval_method completion \
--resume_model log/*/best_model.pth
CUDA_VISIBLE_DEVICES=7 python -m torch.distributed.launch \
--nproc_pe... |
445382c9659a01e7cf4290bb69bdb3704c12d842af041ac12f5a0fdab363258e | Shell | 1,590 | 37 | #!/bin/bash
# A universal helper to enable NeuroDebian repository for a travis
# environment.
#
# Its purpose to remove all repetative actions from various .travis.yml spread
# across projects and gain control in the future to point to an alternative,
# more appropriate for travis deployments, mirror.
# for the prot... |
fcbfb873ce36be57e9d8e76ecf4246909d05f84ad83b586783608ee59cee6c31 | Shell | 1,597 | 38 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
98ea0d408f937b90e2bb2ac8f64376f789fb368457d222127cabace96385d08a | Shell | 1,600 | 73 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
fa62713174d828a14c88517113f99f3dd61adb9f24c384884776c956b523c2c2 | Shell | 1,600 | 56 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_h_hybrid_pt_1200e_ssv2_ft'
DATA_PATH='YOUR_PATH/data/sthv2'
MODEL_PATH='YOUR_PATH/model_zoo/vit_h_hybrid_pt_1200e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 ... |
855f5a683f4e8508afbecf3454d3419c492726e27570ef6aaf27d5f7e90fc1db | Shell | 1,601 | 37 | #! /bin/sh
# Last successfully run on Jan 22nd, 2018
# 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
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE C... |
5ca57aa61169efdd4c400259ef973a5f385d08d7ce78a0d56eaa34a1b743c2f2 | Shell | 1,607 | 39 | #!/bin/sh
# This file is part of AD-EV-characterisation.
# Copyright (C) 2022-2024 Emir Turkes, Stephanie Fowler, UK DRI at
# UCL, Columbia University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... |
699231da69d0d3fda64172c05c47fd01f35367113da88d0bd557e78f0a7f1e78 | Shell | 1,609 | 49 | #!/bin/bash
if [ $# -ne 4 ]
then
echo "Please, give 4 input files:"
echo "1) sorted bam file (map with star)"
echo "2) intron bed file"
echo "3) exon bed file"
echo "4) output root files"
exit
fi
p2b=/hpc/hub_oudenaarden/aalemany/bin/bedtools2/bin
p2s=/hpc/hub_oudenaarden/bdebarbanson/bin/samt... |
b332c23fd58cb789a5941d937fa55bf1b5ba35229badd4a7a0c12c11b6937200 | Shell | 1,610 | 37 | #!/bin/bash
#Purpose: Rename surface-projected preproc output as consecutive sessionsand copy to new location so as to align with 12 consecutive runs selected for FC Matrices
#Inputs: CBIG2016 preproc output
#Outputs: Consecutively named sessions.
#PATHS
PREP_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/CBIG2016_... |
5a60fe1d234606fe92784183f262572ae52ad6abfe938c585359adc9db4438ef | Shell | 1,612 | 61 | #!/bin/sh
# Example: ./preprocess_and_predict.sh /data /out_img $(VENV)/bin ${GPUID}
# TODO: generalise to types of MRI format (NIFTY or DICOM)
# TODO: generalise to types of image format (png or jpg)
MODELTYPE="resnet152"
MODELRUN="19112020"
#MODELDIR="./saved_models/resnet152/19112020/"
MODEL="10push0.8167.pth"
h... |
9994c86a8eabf594db5080d487f50e82c90a61b7d23eba07cfc148b9380aba04 | Shell | 1,614 | 48 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
b5d9beeb159a1c8361176960e3287390c18ece96a7871a99baca690d974fc7dd | Shell | 1,615 | 17 | # Download meshes at https://zenodo.org/records/10480304
# python3 main.py dendritic-spine-preprocess --input-mesh-file /root/shared/gitrepos/smart-comp-sci/meshes/1spine_PM10_PSD11_ERM12_cyto1_ER2_coarser.xml --output-mesh-file meshes-dendritic-spine-new/1spine_mesh_coarser.h5 --num-refinements 0
# python3 main.py den... |
e5a1f51a3e8a4f2869f09b66f27b464b092e4c8722243d95e7e9fce9c3bbcede | Shell | 1,616 | 23 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --mem-per-cpu 1G
#SBATCH --cpus-per-task 16
#SBATCH --time 24:00:00
#SBATCH --output=logs/%j.%x.out
cd /scratch/n.tan/extended-event-modeling/ || echo "cd failed.."
source activate sem-viz-jupyter
export PYTHONPATH=${PYTHONPATH}:/scratch/n.tan/SEM2
srun --output=logs/%j... |
1e4005a576c7550c922f074318ed3b0ffe50ccf77a722a9e466a91b4cc474d6f | Shell | 1,617 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
6e40ebf3082318f7f456fc0b8e73bb792ef050267af2bb7f4b3fc6b1e67a1f60 | Shell | 1,617 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
9b21556624e18cbe0d1d8b658ba4487f77ba35b17402205ed9762a858f31807b | Shell | 1,617 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
4253a7d3a375707428f55992c29f730632041bc7c2324d1453e1b100f0978fa9 | Shell | 1,618 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
5b6c4895c6299a5b06a516431a8ada90d9da8d136584362226bc28023ff490fc | Shell | 1,618 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
b44e6610ed97b45861994d1eef5ec874f7377ffc109e7796945290f489c768c2 | Shell | 1,618 | 48 | #!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J script.sh
# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1
# Number of desired cpus (all in same node):
#SBATCH --cpus-per-tas... |
5d4e66e0e9668cb42e535e10e114c98685a55da2550ee12c954f19100e43ee98 | Shell | 1,621 | 73 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
903fa8213296ea11afe1e46910c85bb82caea63a98a590e894a05e2c5a15834b | Shell | 1,622 | 62 | #!/bin/sh
#
# Vivado(TM)
# ISEWrap.sh: Vivado Runs Script for UNIX
# Copyright 1986-1999, 2001-2013 Xilinx, Inc. All Rights Reserved.
#
HD_LOG=$1
shift
# CHECK for a STOP FILE
if [ -f .stop.rst ]
then
echo "" >> $HD_LOG
echo "*** Halting run - EA reset detected ***" >> $HD_... |
0bf83cf568e634b1169199babf8f4448e6785bd60b756aaea33d74e249b38bb5 | Shell | 1,625 | 72 | #!/bin/bash
#AWS_ACCESS_KEY_ID=''
#AWS_SECRET_ACCESS_KEY=''
#AWS_SSH_PRIVATE_KEY_FILE=''
echo $AWS_SSH_PRIVATE_KEY_FILE
set -e
if [ -z ${AWS_ACCESS_KEY_ID} ]
then
echo "ERROR: You must set AWS_ACCESS_KEY_ID in the environment."
exit 1
fi
if [ -z ${AWS_SECRET_ACCESS_KEY} ]
then
echo "ERROR: You must set A... |
c91cf0af2062140c144296557651dfbac726377bfddcbb2396f94d39d8f7acd3 | Shell | 1,625 | 35 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
922bd9c4aceda48414f76e85a6c92d46d272bd3fd06beaea66ba023fdf07d6ad | Shell | 1,630 | 41 | #!/bin/bash
set -ex
if [ -n "$CLANG_VERSION" ]; then
if [[ $CLANG_VERSION == 7 && $UBUNTU_VERSION == 16.04 ]]; then
wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-7 main"
elif [[ $CLANG_VERSION == 9 ... |
de0531b75359aed990e35076f89a96763d13cbf6047b713e4591e7c4f3fb7e45 | Shell | 1,631 | 59 | #!/bin/bash
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
44efb17d9af0b25c48f928342e3ddb3621886eb60c85dd2db7521d9516e0bda9 | Shell | 1,634 | 57 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_b_hybrid_pt_800e_k710_ft'
DATA_PATH='YOUR_PATH/data/k710'
MODEL_PATH='YOUR_PATH/model_zoo/vit_b_hybrid_pt_800e.pth'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for... |
3f00bde97a1880c5f5c177af48fb3695197cdb496dc24796bf0f64bf321e761f | Shell | 1,637 | 37 | #! /bin/sh
# Last successfully run on Jul 7th, 2019
# Written by Minh Nguyen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh ... |
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