sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0ed2b56651884f14a3e18858168436bcb87678c50820cfb78fffea7ce18ea3aa | Shell | 1,365 | 35 | #!/bin/bash
export MRTRIX_NTHREADS=$1
#Generate fixel-fixel connectivity matrix
/cbica/projects/pnc_fixel_cs/bin/fixelconnectivity \
/cbica/projects/pnc_fixel_cs/data/MRtrix_recon/template/fixel_mask_10_new/ \
/cbica/projects/pnc_fixel_cs/data/MRtrix_recon/template/tracks_2million_sift.tck \
/... |
6b2cd48dc702a89ebe5e4069f20691d457b81fd854082f31eb922d8d013ec814 | Shell | 1,365 | 49 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
mkdir -p ${TASKCLUSTER_TMP_DIR}/ckpt || true
download_dependency_file "checkpoint.tar.xz"
cd ${TASKCLUSTER_TMP_DIR... |
62ac95461dab13993d7ab3536ca085236ff564864f452d2a658f59aba5bb2cce | Shell | 1,366 | 44 | #!/bin/bash
#SBATCH --job-name=v0J1_m1
#SBATCH --time=48:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
# >>> conda initialize >>>
# !! Content... |
dddc4b9510161cc14ea85d4479503b3cb884edf290146c44108faabe9089b7ef | Shell | 1,373 | 44 | #!/bin/bash
# Usage: bash download_pdb_mmcif.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt in... |
b6bfc7c1546f06ebd47696a66f013359ce90e99dd44d5e82b272b81db16f4bd8 | Shell | 1,378 | 38 | #this script should be run on the data transfer (dt) node on wynton
#!/bin/bash
# Create the reference_sources folder for the source files
source="/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/analysis_hapoe_chr/parameters/reference_sources"
mkdir -p "$s... |
c7f940381f81ce4636fc71c18a25e47b04502907630be2f1b05703792cd73f92 | Shell | 1,387 | 72 | #!/bin/bash
BDIR="$(pwd )"
echo "-------------------------------------------------"
echo "Installing and building bisweb in $BDIR"
echo "-------------------------------------------------"
sleep 1
cd ${BDIR}
git clone https://github.com/bioimagesuiteweb/bisweb src
cd ${BDIR}/src
git branch -l
git checkout devel
git p... |
2a1db88b9e3fd94e0e0dcf8fd88a03bb55e4c497f65363d8fe5ce185ad91b26b | Shell | 1,394 | 41 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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 applica... |
6906b28d1706d3f801151308e6d5816af24f1db92bb496815650c5ddf556ab43 | Shell | 1,396 | 41 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
b2eebc1c42d26a0fc92833fae516634735d9f294b9e75d0aa1f39359391700f7 | Shell | 1,402 | 21 | FILE=$1
if [[ $FILE != "ae_photos" && $FILE != "apple2orange" && $FILE != "summer2winter_yosemite" && $FILE != "horse2zebra" && $FILE != "monet2photo" && $FILE != "cezanne2photo" && $FILE != "ukiyoe2photo" && $FILE != "vangogh2photo" && $FILE != "maps" && $FILE != "cityscapes" && $FILE != "facades" && $FILE != "iphon... |
7013f2c3393842b06c955e6c0e68e9df4820f6079c40b0a594f22ebd4212c28c | Shell | 1,403 | 38 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pool1
#SBATCH --time 3-00:00:00
#SBATCH --job-name=combine
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10G
#SBATCH --error=logs/combine_grnboost_%A_%a.txt
#SBATCH --output=logs/combine_grnboost_%A_%a.txt
#SBATCH --array=1-12
###################
## 1)... |
eda712db712e8662552f4552deb4c08aa7ff1525f2cdab74aff53a4ac6a91ef4 | Shell | 1,407 | 41 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
2dd0534102ad6172123c1f24d30f21f9edca3acf9584c7b2da805dc9e30836f1 | Shell | 1,410 | 62 | #!/bin/bash
#SBATCH --mail-user=alanxu@usc.edu
#SBATCH --mail-type=ALL
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=24:00:00
#SBATCH --mem=24GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=oneweek
# Author: Alan Xu
# This script uses fastqc/0.11.9 to quality check the filtered re... |
b2033e368f1d03956fcfc286473d82aad0e7ca74f6d16fe68be7837ad91c9bd0 | Shell | 1,422 | 46 | #!/bin/bash
#SBATCH --job-name=ini_cond
#SBATCH --time=12:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
# >>> conda initialize >>>
# !! Conten... |
c35cb3c88b6f4f4b07cccd360c1501451ba161d19d2e78d0f898e8579a28bfa7 | Shell | 1,436 | 66 | #!/bin/bash
#SBATCH --qos=batch
#SBATCH --partition=compute
#SBATCH --job-name=cells_seg_well
#SBATCH -o cells_seg_well.out
#SBATCH -e cells_seg_well.err
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=10G
#SBATCH --time=00:30:00
usage="$(basename "$0") [-h] [-r row -c column -f configfile] -- \
Segment cel... |
79367784725185802baba71d81c00c5617287431df38b111fbd8e2943fa45474 | Shell | 1,440 | 43 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
91ef476076b0b60e631933c68a4e54c0be3e827f1ef4e2b19e68fa9b69f110b6 | Shell | 1,441 | 66 | #!/bin/bash
#SBATCH --qos=batch
#SBATCH --partition=compute
#SBATCH --job-name=stitch_well
#SBATCH -o stitch_well.out
#SBATCH -e stitch_well.err
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=160G
#SBATCH --time=03:00:00
usage="$(basename "$0") [-h] [-r row -c column -f configfile] -- \
Stitch all fields i... |
c244fe4881870250237e25487703e6bef53c5c799678a5a89a3210263f28d79f | Shell | 1,441 | 42 | #!/usr/bin/env bash
set -ex
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2
echo "COREBINARYDIRECTORY: ${COREBINARYDIRECTORY}"
which python
python --version
PYTHON_VERSION=$(python -c 'import sys;print ("{0}{1}".format(sys.version_info[0], sys.version_info[1]))')
python -m pip install numpy --progress-bar off
read ... |
8b4993f716af8b86d6fba794e6b47c8ba09a4ca2ff07596478a4bbae6f4cb299 | Shell | 1,444 | 43 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1
#SBATCH --exclude=compute-1-11,compute-1-12,compute-1-35
##SBATCH --time 3-00:00:00
#SBATCH --job-name=grnboost
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=46G
#SBATCH --error=logs/pyscenic_grnboost_%A_%a.txt
#SBATCH --output=logs/pyscenic_grnbo... |
83e0de48160f45d01e2f846e13bcc8ae025ccd0e4629233d7286292f09f9084a | Shell | 1,452 | 68 | #!/bin/bash
# this tries to install all the necessary dependencies...
# first argument is directory where stuff is to be installed
DEFAULT_INSTALL_DIR=~/split_seq_reqs
install_dir=$DEFAULT_INSTALL_DIR
if [ -z "$1" ]
then
echo "Default install dir: $install_dir"
else
install_dir=$1
fi
echo "Installing depende... |
f03d0ad01c0387e3f639f02b505d13b85fc30c6d37198af22cc935b3d6c6f98e | Shell | 1,461 | 15 | export BIOHOME=/home/bb/valejose/valejose
export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/coding_noncoding/"
input_prefix="${BIOHOME}/bioseq2seq/data/mammalian_200-1200_train_RNA_balanced"
rna="${input_prefix}.fa"
prot="${BIOHOME}/bioseq2seq/data/mammalian_200-1200_tr... |
8253cd3e0de5db7e14f45583b731b7ee0388730435970cd9deefe5e25c86c639 | Shell | 1,464 | 39 | #!/bin/bash
#$ -cwd
#$ -N magma_steps1-3_PD
#$ -o ./logs/magma-gsa_steps1-3_PD_MNT06Jun2022.o
#$ -e ./logs/magma-gsa_steps1-3_PD_MNT06Jun2022.e
#$ -l bluejay,mem_free=16G,h_vmem=20G
echo "**** Job starts ****"
date
## Load MAGMA
module load magma/1.10
## Set some variables/paths
model="snp-wise"
ANNO=/dcs04/lieber/... |
c09881d9a3c7abc63a9d73b30d54e480534b88f392ae435008f4394f3177961d | Shell | 1,467 | 56 | #!/bin/bash
set -xe
package_option=$1
source $(dirname "$0")/tc-tests-utils.sh
source $(dirname "$0")/tf_tc-vars.sh
BAZEL_TARGETS="
//native_client:libdeepspeech.so
//native_client:generate_scorer_package
"
if [ "${package_option}" = "--cuda" ]; then
BAZEL_ENV_FLAGS="TF_NEED_CUDA=1 ${TF_CUDA_FLAGS}"
BAZEL... |
5778e62b7dfc1f6c2b1f2636ca100d594f9a2fc30c8f3fbc9bef41486efc06d8 | Shell | 1,472 | 40 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen_bigmem
#SBATCH --time 3-00:00:00
#SBATCH --job-name=combine
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --dependency=afterok:3315363
#SBATCH --mem=48G
#SBATCH --error=logs/combine_all_%A.txt
#SBATCH --output=logs/combine_all_%A.txt
###################... |
6184bc0ec8b8cc47ee090aea03cdd35680288e10f9be38c52239508b70f5297b | Shell | 1,473 | 32 | #!/bin/bash
PYTHON_BIN="/usr/bin/python3" # changes to your python
ENV_BIN="/root/miniconda3/bin" # change to your env
DATA_DIR="./data"
CUDA_VISIBLE_DEVICES=0 "$PYTHON_BIN" inference.py \
--jackhmmer_binary_path "$ENV_BIN/jackhmmer" \
--hhblits_binary_path "$ENV_BIN/hhblits" \
--hhsearch_binary_path "$ENV_BIN... |
f9c7d3d2dd5c266cebc4509297b08be7a05162f10177e285a5b3e35ad5f09a3e | Shell | 1,475 | 29 | #!/bin/sh
## Load Connectome Workbench module
module load connectome-workbench/1.3.2-fasrc01
## Define input data
cifti_in=/ncf/hcp/data/analyses/myelin/Adversity_Project/data/myelin_maps/HCD1320_Winter2022/HCD1320_Winter2022.All.MyelinMap_IndPseudoCorr_MSMAll.32k_fs_LR.dscalar.nii
# cifti_in=/ncf/hcp/data/analyses/... |
5c90cc7769357425bfdf4e3c3d0a3ddf17ea6d83338709b0aca6b861d4ecfbca | Shell | 1,481 | 39 | #!/bin/bash
#$ -cwd
#$ -N magma_steps1-3-gsa_ADHD
#$ -o ./logs/magma-gsa_steps1-3_ADHD_MNT06Jun2022.o
#$ -e ./logs/magma-gsa_steps1-3_ADHD_MNT06Jun2022.e
#$ -l bluejay,mem_free=16G,h_vmem=20G
echo "**** Job starts ****"
date
## Load MAGMA
module load magma/1.10
## Set some variables/paths
model="snp-wise"
ANNO=/dcs... |
40f7cde54a2f6431dcca4a9af2c48c132c6a7fead3bf0990c28d052f5f88d8fb | Shell | 1,485 | 40 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1
#SBATCH --time 3-00:00:00
#SBATCH --job-name=download
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=25G
#SBATCH --error=logs/download_mkfastq_%A_%a.txt
#SBATCH --output=logs/download_mkfastq_%A_%a.txt
#SBATCH --array=7%1
PROJDIR=/projects/pfenni... |
114188246a232e31dced0fbc00338810c2949bc48b9319e75a90a5c67d8fdac5 | Shell | 1,487 | 61 | #!/bin/bash
#$ -cwd
#$ -pe local 8
#$ -l mem_free=8G,h_vmem=10G,h_fsize=300G
# qsub code/spaceranger/filename.sh
############################
# Script to run Space Ranger
############################
# Round 1 LC samples: NextSeqMiSeq
# load spaceranger module (if required)
# module use /jhpce/shared/jhpce/module... |
3f619fa9f1b1f8fff21704db3ceb4a75c799072a860c6de4c14befc9cb86cf68 | Shell | 1,490 | 47 | #!/usr/bin/env bash
known_te=($1)
echo 'get classification info and convert #unknown to #DNA/Helitron'
for j in *mod.EDTA.TElib.novel.fa; do
for i in `cat $j.real`; do
grep $i $j;
done| \
perl -nle 's/#unknown/#DNA\/Helitron/; print $_' > $j.real.ori &
done
wait
echo 'aggregate novel TE libr... |
4f693fdc2845c7a932d30ccdc359df959f4c4a02bd7976b1d54afdd15b135078 | Shell | 1,490 | 36 | #!/bin/sh
# version.sh
#
# Author : Petr Danecek <pd3@sanger.ac.uk>
#
# Copyright (C) 2018-2021 Genome Research Ltd.
#
# 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 restric... |
d8600695db8a0e53fd0220f776c413db6f9fc7ac85985c714177544be3a00693 | Shell | 1,491 | 39 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# for STEPS label fusion on foler of images with registration already done
# usage: ./labfusion_batch.sh atlas $1 $2 $3 $4
# $1: folder include all the images for label fusion
# $2: atlas (in_vivo ex_vivo)
# $3: STEPS parameter k (kernel size in... |
0fd91b131851ad4043e396214d0c5807e816db5bf1343ab1c7cdfdbc375c39f7 | Shell | 1,493 | 34 | #! /bin/bash
export FREESURFER_HOME=/Applications/freesurfer/7.2.0
export SUBJECTS_DIR=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/sub-3
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cd SUBJECTS_DIR
recon-all -base sub-3_base -tp sub-3_ses-1_T1w \
-tp sub-3_ses-2_T1w \
... |
55083cb3c825283ff844448d56176721bf89dd19dd87fef4243a6d2fddc4a8a6 | Shell | 1,496 | 57 | #!/usr/bin/env sh
# Create the imagenet lmdb inputs
# N.B. set the path to the imagenet train + val data dirs
EXAMPLE=examples/imagenet
DATA=data/ilsvrc12
TOOLS=build/tools
TRAIN_DATA_ROOT=/path/to/imagenet/train/
VAL_DATA_ROOT=/path/to/imagenet/val/
# Set RESIZE=true to resize the images to 256x256. Leave as false ... |
04edcd5c8dd1011d8bab9de7775af00b4f9ba971dfd4acc5252fb774a9f733df | Shell | 1,497 | 41 | #!/usr/bin/env bash
BRANCH=$(basename $1)
GIT_REPO=$2
COMMIT_SHA=$3
PR_NUMBER=$4
EFS=/mnt/efs
mkdir -p ~/.mxnet/datasets
for f in $EFS/.mxnet/datasets/*; do
if [ -d "$f" ]; then
# Will not run if no directories are available
ln -s $f ~/.mxnet/datasets/$(basename "$f")
fi
done
python3 -m pip ... |
b50b07123fb14151aacccd32bdf8963448434703505dc314d9c1579fdabff1a7 | Shell | 1,497 | 55 | #!/usr/bin/env bash
# Run all tests for the ethoscope node package
# This script runs unit tests, integration tests, functional tests, and generates coverage reports
set -e # Exit on any error
echo "Running Ethoscope Node Package Tests"
echo "===================================="
# Change to the node package direc... |
9e8310bbe99cf0cc0809be3f8d29d94002d9d694b16b31cf1097c2a61924ff95 | Shell | 1,510 | 43 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
c5a3fa3e16981bb1f687a5a25474e7c5b3cf6c052380adf32fd8ac4ba71d6e07 | Shell | 1,515 | 52 | #!/bin/bash -ve
## Error: ./__test_runMe.singleFQ.sh: line 44: ../../util/RSEM_util/summarize_RSEM_fpkm.pl: No such file or directory
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
../../Trinity.p... |
a10d92186f1ebbd1e7ff28e81ac85942e94ddf196413a75ce276c8e76539a692 | Shell | 1,517 | 46 | #!/bin/bash
#SBATCH --job-name=mc_surfs
#SBATCH --time=48:00:00
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
# >>> conda initialize >>>
# !! Conte... |
028f17dfb928382b936af3dcbe01761adfb1d384123ea90bc02f19027ba7c45e | Shell | 1,523 | 43 | #!/bin/bash
#
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 appli... |
b30cd463d84dd7af17032e91dba3e721124383eb47d0828cfdf973facdad556c | Shell | 1,523 | 46 | #!/usr/bin/env bash
set -ex
export PATH=/usr/bin:${PATH}
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2
echo "COREBINARYDIRECTORY: ${COREBINARYDIRECTORY}"
which python
python --version
PYTHON_VERSION=$(python -c 'import sys;print ("{0}{1}".format(sys.version_info[0], sys.version_info[1]))')
python -m pip install n... |
d84dc2aff8cc0c7732e6c7d0bb8e0ed52e0a1e1ab5db66cc7d5c2e8bdfdeaee1 | Shell | 1,525 | 57 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -pe local 4
#$ -N snRNA-seq_LC_CR6.1
#$ -o logs/snRNA-seq_LC_CR6.1-includeIntrons.$TASK_ID.txt
#$ -e logs/snRNA-seq_LC_CR6.1-includeIntrons.$TASK_ID.txt
#$ -m e
#$ -t 1-3
#$ -tc 3
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: $... |
5ac7b292c92a07428890c39e6d951d471143128cfc077cac92b57db8e3c195b0 | Shell | 1,530 | 40 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.09.12
# usage: ./leave_one_out_STAPLE.sh atlas (in_vivo ex_vivo)
# $1: atlas (in_vivo ex_vivo)
ROOT_DIR=$(pwd)
echo "Bash version ${BASH_VERSION}..."
ATLAS=$(basename $1)
export QSUB_CMD="qsub -l h_rt=1:00:00 -l h_vmem=9.9G -l... |
50b5cd247415b165a1b095b5677115f70ad2c2c2f9584f59fdd949331a008954 | Shell | 1,534 | 43 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# usage: ./leave_one_out_dice.sh $1 $2 $3
# $1: atlas (in_vivo ex_vivo)
# $2: STEPS parameter k (kernel size in terms of voxel number)
# $3: STEPS parameter n (number of top ranked local atlas to select for label fusion)... |
60e192c9b389353fcbc3d8b5ea15050523f6a57ef7e3f8171b0b99f8544d52c3 | Shell | 1,538 | 23 | #!/bin/sh
models="ResNet50word ResNet50speaker ResNet50music ResNet50audioset"
randnetw="False"
#layers="input_after_preproc relu0 maxpool0 relu1 maxpool1 relu2 relu3 relu4 avgpool relufc final"
layers="input_after_preproc conv1_relu1 maxpool1 layer1 layer2 layer3 layer4 avgpool final" # for resnet50music, it is relu1 ... |
83d279c9b8c3d253eacc28dcf36f18c40f1f049131c9fbeb3ac9b9b0915221ac | Shell | 1,542 | 50 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_uncertainty_mve
train_path=../data/uncertainty/train.csv
val_path=../data/uncertainty/val.csv
test_path=../data/uncertainty/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimizatio... |
9057eaa7d77a6a9f0e1af411bf73065316ac88bb304b0a305119ebdf10fc8b3b | Shell | 1,542 | 72 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
electronver=$2
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
if [ -z "${electronver}" ]; then
echo "No electron version given, aborting."
exit 1
fi;
bitrate=$3
set_ldc_sample_filename "${bitra... |
0522568cf3e75b995d3ae94125f938cdadb8ec635913ad23bc8bec8108ccd8fa | Shell | 1,544 | 49 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_uncertainty_ensemble
train_path=../data/uncertainty/train.csv
val_path=../data/uncertainty/val.csv
test_path=../data/uncertainty/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimi... |
2b70a67db22ebbd353686e0e152471db5835512d1acb4449489d16c0050ee3e6 | Shell | 1,544 | 41 |
# initialized parameters
set proj_mesh = fsaverage6
set down_mesh = fsaverage5
set sm = 6
# volume to surface
set regfile = ${subject}_bld${runfolder}${reg_stem}.dat
set output = $surffolder/$hemi.${BOLD}_$proj_short.nii.gz
mri_vol2surf --mov ${BOLD}.nii.gz --reg $regfile --hemi $hemi \
--projfrac 0.5 --trgsubject ... |
5e493a598b69bc0f3f7bc24009524f2883aca5b188fa93b695647d27f00553fe | Shell | 1,544 | 41 | #!/bin/bash
#$ -cwd
#$ -N magma_step3-gsa_AD
#$ -o ./logs/magma-gsa_step3_AD_MNT29May2022.o
#$ -e ./logs/magma-gsa_step3_AD_MNT29May2022.e
#$ -l bluejay,mem_free=16G,h_vmem=20G
echo "**** Job starts ****"
date
## Load MAGMA
module load magma/1.10
## Set some variables/paths
model="snp-wise"
ANNO=/dcs04/lieber/lcoll... |
0fd867bfdc7a3657ca30ca3ad0cb2e26f26affbf2b4a0baa21a74cd941d819a1 | Shell | 1,547 | 65 | #! /usr/bin/bash
#SBATCH -o /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/out/%A_%a_%x.out
#SBATCH -e /cellar/users/dlaub/projects/ML4GLand/EUGENe_paper/scripts/err/%A_%a_%x.err
#SBATCH -p carter-compute
#SBATCH -J profile_mem
#SBATCH -a 24,17
#SBATCH -c 2
#SBATCH --mem 64G
echo Starting
date
wdir=/cel... |
eb359b3c284c9befaf7b046389f54b15e60b1a310ec8c4b8fe31e2c49d48a9f0 | Shell | 1,549 | 26 | ln -s /data/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq/data/raw_data/fastq_merged \
/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq/data/raw_data/fastq
PROJDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
## calculate MD5 Sum
find /data/pfenninggroup/singleCell/Logan_BU_Stri... |
5b73aa717e2bdfba42b5641b6f9a1081f2ef58461bf0df9cfad97b4f06c065b0 | Shell | 1,553 | 49 | #!/usr/bin/env bash
#
# Wrapper script for initializing the runtime environment before running
# a GenePattern module on a compute node.
#
# Usage: run-with-env.sh \
# [-c <env-custom-site.sh>] \
# [-e GP_ENV_CUSTOM=<env-custom-site.sh>] \
# -u <dotkit-id.0> -u <dotkit-id.1> ... -u <dotkit-id.N> \
# -e... |
643870a2707d57f2ea75e68411ee39edb000ebf7631064043e00a0cf2dd018eb | Shell | 1,555 | 41 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen_bigmem
#SBATCH --time 6:00:00
##SBATCH -w compute-1-40
#SBATCH --job-name=ctx
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=125G
#SBATCH --dependency=afterok:3315375
#SBATCH --error=logs/pyscenic_cistarget_%A.txt
#SBATCH --output=logs/pyscenic_cist... |
e0be21621dcbe2cad4887c6c89f392dc7d346218dbb76f36da669f961a284940 | Shell | 1,558 | 62 | NPROC=$(grep -c processor /proc/cpuinfo)
export MAKEFLAGS="-j ${NPROC}"
OPENSSL_ROOT=openssl-1.0.2q
# Hash from https://www.openssl.org/source/openssl-1.0.2q.tar.gz.sha256
OPENSSL_HASH=5744cfcbcec2b1b48629f7354203bc1e5e9b5466998bbccc5b5fcde3b18eb684
CMAKE_ROOT=cmake-3.11.4
function check_var {
if [ -z "$1" ]; t... |
2c9f5c596307c84d89872b30c56b2f0f73ad45e4d7c80b1ae016c59391368145 | Shell | 1,562 | 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... |
cb3359d4b07a0fc45072c287e78381faa2930f07dc95ff9f43438b7f4e394098 | Shell | 1,573 | 35 | #!/bin/bash
#SBATCH --job-name=behavior_plot
#SBATCH --output=output/behavior_plot%j.out
#SBATCH --error=output/behavior_plot%j.err
#SBATCH --mem=16000
#SBATCH --cpus-per-task=4
#SBATCH --time=01:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-20
#SBATCH --constraint=11GB
#SBATCH --partition=normal
# List of the networks... |
8ce5ad1a9a7e3d58c6db12f97e00499335085b55345bd55fc952fb61ed5739ec | Shell | 1,587 | 58 | #!/bin/bash
echo ""
echo ""
echo "Checking for bad stuff in cpp code"
echo ""
echo " ------------------------------------------------"
echo " Looking for new"
echo ""
grep new cpp/*.h cpp/*.cpp cpp/*.txx | grep -v shared | grep -v uniq
echo " ------------------------------------------------"
echo " Looki... |
af6dae60cdf621f13561b94a82a8536f29a2dd91b29a00882012b94475651914 | Shell | 1,587 | 65 | #!/bin/bash
pip uninstall -y numpy
pip uninstall -y pandas
pytest \
--cov-append \
--cov-report=xml \
--cov=rpy2.rinterface_lib \
--cov=rpy2.rinterface \
--cov=rpy2.rlike \
--cov=rpy2.ipython \
--cov=rpy2.robjects \
rpy2-rinterface/src/rpy2/rinterface/tests \
rpy2-robjects/src/rpy2... |
253c7f0e1ce7441725b5ed4d119d1ec6f01c2619426bd7a171dd2fda94f11993 | Shell | 1,590 | 34 | #!/bin/bash
#SBATCH --job-name=null_hmax
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=24:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0,10,20,30,40,50,60,70,80,90
#SBATCH --exclude=node093,node040,node097,node098,node094,node037... |
60b0aafcb35e81c17d6e730d17f72d1bfd63db00b3d5ef60ada27d2da61559fb | Shell | 1,593 | 70 | #!/bin/bash
# Script to pull storage from remote server
REMOVE=false
ONLY_STATS=false
BASE_DIRECTORY="\$SCRATCH"
ARGS=""
while [ $# -gt 0 ]
do
while getopts i:b:ds flag
do
case "${flag}" in
i) ID="${OPTARG}";;
b) BASE_DIRECTORY="${OPTARG}";;
d) REMOVE=true;;
s) ONLY_STATS=true;;
... |
c44dad5d529baae9a63bdaf0071eb2aa88de0ad7eba9cf7449040c0343454ad3 | Shell | 1,595 | 17 | source src/lib/CHEX.bash
## 1. Run the SCAP-T general pipeline per 12 samples in paralell
parallel --progress -j 1 --pipe -N1 launcher_parallel.sh - 12 < data/E.chex/info/config.csv
## 2. Run CHEX-seq pipeline per 12 samples in paralell
sed 1d data/SampleInfo.csv | parallel --progress --colsep ',' -j 12 "doNewPipe --... |
b7c04bc0e615018771d1ebf233533dbc00bf9be3a78b95c80ffccd0b74cf5eb3 | Shell | 1,597 | 50 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_uncertainty_evidential
train_path=../data/uncertainty/train.csv
val_path=../data/uncertainty/val.csv
test_path=../data/uncertainty/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_opti... |
63e876100daeba190940699fa1f01c9817a2a50345892bfe3c3580e42b137465 | Shell | 1,605 | 80 | #!/bin/bash
sam2wig(){
chrlen=$1
chr=$2
infi=$3
nosingle=$4
minins=$5
maxins=$6
threads=$7
outfi="$infi.$chr.wig"
tmp="$infi.$chr.sam"
samtools view -@ $threads $infi $chr | \
./genwig2.py $chrlen $chr - $outfi $nosingle $minins $maxins
echo "completed: $chr"
}
exp... |
ffa45b403225b93d91a44ba0ebbdd115cc9ed8830e261ec73abb498b6d7c3930 | Shell | 1,618 | 45 | #!/bin/bash
mkdir -p 'data/raw/'
####################################
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Download TCGA PanCanAtlas Data
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
####################################
####################################
# RNAseq data
####################################
# Normalized RN... |
ef70d053c5b5b530f20a7b3411c930ff95d971f4c8495920f0357fe7abef3203 | Shell | 1,620 | 68 | #!/usr/bin/env bash
set -euo pipefail
if [[ $# -ne 1 ]]; then
echo "Usage: $0 <output.dll>" >&2
exit 2
fi
output="$1"
zig="${ZIG:-zig}"
export ZIG_LOCAL_CACHE_DIR="${ZIG_LOCAL_CACHE_DIR:-$PWD/.zig-local-cache}"
export ZIG_GLOBAL_CACHE_DIR="${ZIG_GLOBAL_CACHE_DIR:-$PWD/.zig-global-cache}"
mkdir -p "$ZIG_LOCAL_CA... |
525ef4e38781ddc0b8c51f73c25e6cdc130114af532ea284321369f5c0a40836 | Shell | 1,623 | 53 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
626ff5e71eb230ac7b1bde9bc78fe90fbb1e2cafbf271c7916b61980b26041df | Shell | 1,626 | 50 | #!/bin/bash
set -e
dir=$(cd -P -- "$(dirname -- "$0")" && pwd -P)
usage="$(basename "$0") [-h] [-f <final_annotated.gtf>] [-g <reference_genome.fasta>] [-i <gene_name>]
This program will obtain and align all transcripts coming from a given gene, in order to obtain a consensus.
Arguments:
-h show this help text
... |
180b0632436b4c632bd7b5ba382804e2c4cf0bce27673f13234efa96858b938c | Shell | 1,628 | 1 | phyloFit --tree "((((((((((((((Sheep,goat),Cet_Chiru),Cattle),((RedDeer,WhiteLippedDeer),Daviddeer)),(Okapi,Giraffe)),(((((KillerWhale,(Dolphin,Cet_Bottlenose-dolphin)),(Cet_River-dolphin,Cet_Beluga_whale)),SpermWhale),(Cet_Grey_whale,(MinkeWhale,Cet_Minke-whale))),Cet_Hippopotamus)),Pig),(Camel,Cet_Alpaca)),(((Per_Prz... |
23e50594e123cbdc88971b225fc955fdf2895c238e973553734110aa7bb98422 | Shell | 1,631 | 44 | #!/bin/bash
# Copyright (C) 2022 Giansalvo Gusinu
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge... |
8fbc9d636916fe76da9c166bf46b46f7ef2e05b160165d642cf4e23742d64ec5 | Shell | 1,638 | 46 | #!/bin/bash
# Usage parse_log.sh caffe.log
# It creates the following two text files, each containing a table:
# caffe.log.test (columns: '#Iters Seconds TestAccuracy TestLoss')
# caffe.log.train (columns: '#Iters Seconds TrainingLoss LearningRate')
# get the dirname of the script
DIR="$( cd "$(dirname "$0")"... |
8627847af0177643dcc7ca978f58973992aed52a8cfb8b55a6eb875d615c3b2c | Shell | 1,641 | 56 | #!/bin/bash
# Compile code
make clean
./bootstrap.sh && make -j 8
sleep 2
# Benchmark parameters
SIMTIME=100
STATRUNS="1 2 3 4 5"
HOSTNAME=`hostname`
DATE=`date +"%Y-%m-%d"`
# REVISION=`git log --pretty=oneline -1 | cut -d " " -f 1`
REVISION=`git describe`
TMPDIR=`mktemp -d`
echo "temp dir= $TMPDIR"
trap "{ rm -rf $T... |
9869fd077c97435c52a2879fc3d3d7aea461bed9c86dba364f66e5d08f2f80ed | Shell | 1,642 | 43 | # this script will run FastSMC on a simulated data as described in the paper (in FILES/FASTSMC_EXAMPLE/)
# parameters can be changed if desired
# This example will run multiple jobs in different threads on the same machine. If you are running FastSMC on a cluster
# then it may be more appropriate to instead use the jo... |
6329a0977e81ddce549dd12e4230a62bda7c77b1e02ce293b5ebc44e66f6b49c | Shell | 1,645 | 58 | #!/usr/bin/env bash
############################################################
# run-rjava-with-env.sh
# Run an 'Rjava' module using gp-common.sh library
# Alternative to run-rjava.sh
#
# Usage:
# run-rjava-with-env.sh \
# -c env-custom \
# -u java/1.8 -u r/2.15 -- \
# [java-flags] \
# -cp class... |
e33e33bf78a5ada0a64da0aab17170896402695492b608906b6f930ab7709353 | Shell | 1,649 | 57 | #!/bin/bash -ve
KMER_SIZE=29
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
... |
40cdae86efb560a8e335f44d4450febb6be960f712754a332e8892589a62c7d5 | Shell | 1,654 | 40 | #!/bin/bash
#$ -cwd
#$ -pe smp 2
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=02:00:00
#$ -j yes
data_dir=/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/
script_dir=/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-... |
773e3b37e14d961ce01c3fe8d3e8aad738a1b87e7b1821ad7a4646624431c814 | Shell | 1,654 | 46 | #!/usr/bin/env bash
##############################################################################
#
# wrapper script for starting the GenePattern Server as a background process
# Usage:
# ./start-genepattern.sh
#
# # optionally set server customization environment
# ./start-genepattern.sh -c server-env-cu... |
a5636be895df00691d70339e6e2a59703ee20a5e814efa5664908d9f4340d0fd | Shell | 1,657 | 74 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
electronver=$2
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
if [ -z "${electronver}" ]; then
echo "No electron version given, aborting."
exit 1
fi;
bitrate=$3
set_ldc_sample_filename "${bitra... |
298bcd83f5256d325fec2cfb8e7c6d3cd168d8acf5a313ee00138f4764c78bd0 | Shell | 1,658 | 46 | #!/bin/zsh
# This script will creat folder 'generate_profiles_and_ini_params',
# from which Step1_2 will generate the group.mat which will be used in the next step
##########################
# Specify output directory
out_dir='/Users/wang/Desktop/Research_projects/BBSC/Functional/Parcellation'
cd $out_dir
######... |
c7383977c65c2c1af79b63dc6f8b8103bf0dbf247e58392f34ce0839b97b0712 | Shell | 1,667 | 53 | #!/bin/sh
#
#
#___INFO__MARK_BEGIN__
##########################################################################
#
# The Contents of this file are made available subject to the terms of
# the Sun Industry Standards Source License Version 1.2
#
# Sun Microsystems Inc., March, 2001
#
#
# Sun Industry Standards Source ... |
40037b2c6cea4cd8ee8c2e03c2a290a12067833b0d23d179304ac47232640ace | Shell | 1,717 | 38 | #!/usr/bin/env bash
# Build the FA4 CI container on the runner and convert it to a SIF — no registry involved.
#
# tools/ci/docker/build_local_sif.sh [OUTPUT_DIR] # default OUTPUT_DIR = $CI_WORK_DIR
#
# Output: OUTPUT_DIR/local-sif/flash-attn-4-cu13.0-<date>-<sha>.sif — publish that path as the repo
# variable F... |
a0f60f208f920176266ae5712659a8c029d447e18cb31775ccc19561b4a0d888 | Shell | 1,717 | 39 | #!/usr/bin/env bash
#
# Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# 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
#
# Unle... |
efd7d11137d837c50323947050dfa69052edcce4328a3df70bc19ff5bb26f72e | Shell | 1,717 | 43 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# usage: ./dice_batch.sh $1 $2 $3 $4 $5
# $1: destination atlas folder to be tested (only use label subfolder)
# $2: source atlas folder containing multiple manual labels
# $3: folder containing the parcellated structure... |
8612d078c873031f6bc7415a208cdefc8b6175f47b9488395dfcff8787743b45 | Shell | 1,721 | 41 | #!/usr/bin/env bash
# hacky helper script to draft a new release
# ------------------------------------------
#
# requires (and checks) that local repo is in branch 'main' and in the same state as 'origin/main'
# performs some sanity checks, before drafting a new release on github
# after release is manually published... |
eae90f814c538ba253affac6b220c25c44d9aa485450869d6cb0dd2133c4c0f2 | Shell | 1,722 | 53 | #!/bin/bash
#
# Copyright 2022 Deepfold Team
#
# 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 law or agre... |
414a8e1fd0996706369bda84b01315c104f825c6280e6a4f3dc6d9f07feefaa2 | Shell | 1,727 | 52 | #!/bin/bash
#
# Copyright 2022 Deepfold Team
#
# 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 law or agree... |
465ec681675a69be7a54e89bb5dfc2f9e88135eb9b936f1d53ee085870872976 | Shell | 1,730 | 48 | wget ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/gp2protein/gp2protein.unigene.gz
gunzip gp2protein.unigene.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/text/pdb_chain_pfam.lst
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz
gunzip idmapping.dat.gz
wget h... |
55d1e5735a586cac1b4f660db94e7f2d91dd78800432cb33898e20c72326f04a | Shell | 1,742 | 60 | #!/bin/bash
# Usage: bash download_all_data.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt install a... |
c343551100d5382b685b229c61667f1bedba014eea1263eabe55f5dc539f7b13 | Shell | 1,758 | 54 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_bde_charges
train_path=../data/bde_charges/train.csv
val_path=../data/bde_charges/val.csv
test_path=../data/bde_charges/test.csv
train_constraints_path=../data/bde_charges/train_constraints.csv
val_constraints_... |
0a70bd39ca847b4ec406dfbe417383dcccf01b20079d33e4860c86879f20897c | Shell | 1,761 | 36 | #!/bin/bash
set -u -e
# Build the install package for MacOS.
# This script must be run from the root of the repository after running build_installer_macos.sh
PACKAGE_NAME=alphamap
# BUILD_NAME is taken from environment variables, e.g. alphamap-1.2.3-macos-darwin-arm64 or alphamap-1.2.3-macos-darwin-x64
rm -rf ${BUILD... |
3a2b821d040cf73db0dc7653bfd4d25f79b67532fdfc63be2097ed244a6e0243 | Shell | 1,779 | 54 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_atom_bond_137k
train_path=../data/atom_bond_137k/train.csv
val_path=../data/atom_bond_137k/val.csv
test_path=../data/atom_bond_137k/test.csv
train_constraints_path=../data/atom_bond_137k/train_constraints.csv
v... |
e6ad512cc60d2430205bf90232e0ef3630024a2cc7f3fd86edeec6ba83a7aed0 | Shell | 1,795 | 52 | #!/bin/bash
## assume script is launched from vsearch/man/
## assume any internal link is relative to the md file itself (important)
## usage:
## bash scripts/generate_manpages.sh
## (re)generate every manual page in ./manpages/
## bash scripts/generate_manpages.sh <markdown_source> <manual_page>
## c... |
bd695be6559074b9c92e586f747530de12556eb69bcf533bcc2eedc952c7ef87 | Shell | 1,800 | 61 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
cc8b2bbb3d1e1e3e080a6f70bcf8357f2186c88f23fe18fbc83e6a3025fb2aba | Shell | 1,802 | 59 | #!/usr/bin/env bash
#
# compute-version.sh — Derive a version string from Git state.
#
# Output format:
# Tag build (release): v1.2.3
# Dev build (clean): v1.2.3.dev4+gabc1234
# Dev build (dirty): v1.2.3.dev4+gabc1234.dirty
# No tag (clean): v1.2.1+gabc1234
# No tag (dirty): v1.2.... |
958e2512ffdaf321a584aa8fcfcac28467521c9461db5fe50ff8bb160064b2ca | Shell | 1,806 | 44 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=normal
module add ... |
2bf478a0a96c7364746ea8d591f6da4933eb21431b6ab2447f9c8203ee92c62a | Shell | 1,807 | 68 | #!/bin/bash
set +x
ROOT="."
MRIVOL="$ROOT/mri/crop/mri.crop.mgz"
MRIGM="$ROOT/mri/crop2/gray.crop.nii"
MRIWM="$ROOT/mri/crop2/white.crop.nii"
MRIVSL="$ROOT/mri/crop/vessels.manual.crop.mgz"
OCTVOL="$ROOT/oct/pool3x3x3/oct.win33.nii"
OCTMSK="$ROOT/oct/pool3x3x3/mask.nii"
OCTGM="$ROOT/oct/gray.lowres.mgz"
OCTWM="$ROOT... |
31eb4372c2f367c6e66908afc6050f026ab6368e86886e89c30b5a6d123e9c58 | Shell | 1,816 | 52 | #! /bin/bash
set -e
set -x
RUN_TEST=$1
if [[ $EUID -eq 0 ]]; then
chmod -R 777 /data/helixfold/msa_cache/ind/
fi
# 下载 ccd 库
if [[ ! -f infer_scripts/demo_data/ccd_preprocessed_etkdg.pkl.gz ]]; then
/root/linux-bcecmd-0.5.1/bcecmd bos cp -y bos:/helixvs-temp/backdoor/ccd_preprocessed_etkdg.pkl.gz infer_script... |
1134e0010616af7cb8b4dd0d0c73e231b4598ddb4ef19b721e353b26cb2f53d2 | Shell | 1,817 | 44 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# for STEPS label fusion on foler of images with registration already done
# usage: ./labfusion_batch.sh atlas $1 $2 $3 $4
# $1: folder include all the images for label fusion
# $2: atlas (in_vivo ex_vivo)
# $3: STEPS pa... |
4ab3184d1f2d72064233dcf982cd688c434c410c73cfcdae423244deb04b8b20 | Shell | 1,821 | 65 | #!/usr/bin/env bash
############################################################
# run-rjava.sh
# Java wrapper for legacy R modules, which pre-date the
# Rscript command.
# Usage:
# run-rjava.sh -c env-custom r-version java-flags -cp classpath RunR args
# Example module commandLine
# commandLine=<R2.5> <libdir>... |
45c716f3f01bfc169d9b0745fbddf4b46e3223cdd2a382f5b9d6fc0f51b98f44 | Shell | 1,825 | 59 | #!/bin/bash
#
#SBATCH --job-name=AHRB_ROIest
#SBATCH --array=1 #Only needs 1 job, calculates ROI for all maps within input dir
#SBATCH --time=00:25:00
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=8GB
#SBATCH -p ${PROFILE}
# Outputs ----------------------------------
#SBATCH --output=../logs/ROI.%A_%a.out
#SBATCH --... |
ba2ee200d149cacc5c4257090d544dc1e10525be15fef1fe83a1d1eb20bf3c45 | Shell | 1,825 | 1 | phyloFit --tree "(((((((((((((((((((((White-throated-sparrow,Yellow-rumped-warbler),(Tawny-bellied-seedeater,Medium-ground-finch)),Common-canary),House-sparrow),(White-rumped-munia,Zebra-finch)),((Collared-flycatcher,Siberian-stonechat),(Javan-myna,Common-starling))),(Silver-eye,(Willow-warbler,(Phylloscopus-plumbeitar... |
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