sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
47fbf7904ae32564fbf2990ddb5254a50ae674e3d04f9bf96efb24a6889ce966 | Shell | 1,152 | 41 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_barriers_e2
train_path=../data/barriers_e2/train.csv
val_path=../data/barriers_e2/val.csv
test_path=../data/barriers_e2/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py... |
e48c680ce90d11a64ebef9f484af9eda80a43d1f5fb374b6bd982f139119a693 | Shell | 1,154 | 34 | #!/bin/bash
#This is just an example compilation. You should integrate these files into your build system. Boost jam is provided and preferred.
echo You must use ./bjam if you want language model estimation, filtering, or support for compressed files \(.gz, .bz2, .xz\) 1>&2
rm {lm,util}/*.o 2>/dev/null
set -e
CXX=... |
20dac0d02d0e606c000d81bd040e7bfa9130583dad3efbaf0f73dc991cf6688a | Shell | 1,155 | 36 | #!/bin/bash
##########################################################################
## This script takes two command line arguments (in the below order)
## 1. CellRanger results folder path to be cleaned up
## 2. Temporary or trash folder path
##
## Example run:
## 02_cellranger_count_results_cleanup.sh \
## /glads... |
422b819adc4d8295d716d4bef540d4d91782e2a8a0d7c66279186db63ae6af99 | Shell | 1,156 | 41 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_barriers_sn2
train_path=../data/barriers_sn2/train.csv
val_path=../data/barriers_sn2/val.csv
test_path=../data/barriers_sn2/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimizatio... |
ddf80cd58632f6d7e74966845ee5d8e0352291aea12dfb18f2d643e8179ad52b | Shell | 1,156 | 44 | #!/bin/bash
mkdir -p /cbica/projects/pnc_fixel_cs/scripts/MRtrix_recon/normalise_jobscripts_try1
project=/cbica/projects/pnc_fixel_cs
while read subject
do
echo SUBJECT: ${subject}
OUTPUT_PROOF=${project}/data/MRtrix_recon/sub-${subject}/ses-PNC1/dwi/sub-${subject}_wmfod_new_norm.mif
if [ -f ${OUTPUT_PROOF... |
f7a8582d88a55c61dcf2818e4eae2f0a8a845740752783b479fa3d1e82dcdf0d | Shell | 1,158 | 38 | #! /bin/bash
source activate GloDyNE
mkdir bash/log
echo '......Chengbin HOU @SUSTech 2019 DynWalks 0.1 bash......'
echo '------------ AS733 -----------------------------------------'
bash bash/NE_AS733.sh
echo '......well done......'
mv bash/log bash/log_1
mkdir bash/log
echo '......Chengbin HOU @SUSTech 2019 Dyn... |
899a3aadda4dbb1dfc3eae0bc1184d0fd146c95afc235298813310e274f12959 | Shell | 1,159 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=mcdermott
module ad... |
8eac3e5037eaf31030bc8495c9a1835015aff710d9615196a3e19d6dd9ee97f8 | Shell | 1,159 | 29 | #!/bin/bash
#SBATCH --job-name=null_vgg
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=128000
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=mcdermott
module ad... |
427d8e688c8c520dc0e7192d7b838cf6dde2affc3c7c10e2921645e7dfc82f68 | Shell | 1,162 | 39 | #!/bin/bash
BUILDDIR="../../build/debug" # We use debug to avoid problems from fast-math
TOOLDIR="$BUILDDIR/tools"
# Compile code
CURDIR=`pwd`
cd $BUILDDIR && ./bootstrap.sh && make
cd $CURDIR
make -C $BUILDDIR
# Benchmark parameters
SIMTIME=10
REVISION=`git log --pretty=oneline -1 | cut -d " " -f 1`
TESTNAME=`bas... |
6c32cd92b07bae4ba67977fc3533e4fbc460b6c886e120a2853ceaee3006e127 | Shell | 1,162 | 31 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH predict --test_file data/HLA_I_full_mcpas/test/test_pos.csv \
--hla_class HLA_I \
... |
c6a0d015e34ba5277a83815e6bc0534991496a26f3cc9a413ef095d5615c4a59 | Shell | 1,162 | 45 | #!/usr/bin/env bash
# Build the FA4 Apptainer SIF image.
#
# Usage:
# ./tools/ci/build_sif.sh [OUTPUT_PATH]
#
# Default output: /scratch/user/$USER/attention_fa4_<date>.sif
# All temp/cache dirs are redirected to /scratch to avoid filling the root volume.
#
# Example:
# ./tools/ci/build_sif.sh
# ./tools/ci/build_... |
b361c1920e121dc666866bc2715c5211a760da1919878441cc289a69ee8fa921 | Shell | 1,164 | 29 | #!/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=48:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=mcdermott
module ad... |
ed13c6879f27926ec842c04a8f615efe1b899d73fb2d975b028bd11df1452e0f | Shell | 1,164 | 29 | #!/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=48:00:00
#SBATCH --gres=gpu:GEFORCEGTX1080TI:1
#SBATCH --array=0
#SBATCH --constraint=high-capacity
#SBATCH --partition=mcdermott
module ad... |
6dc3b734be4468af19aa42411ce6c583bf5bbf26618cd04fe62b420584b73b71 | Shell | 1,168 | 34 | #! /bin/bash
#SBATCH --job-name="bone-age_sh"
#SBATCH --partition="ampere"
#SBATCH --mem="30G"
#SBATCH --cpus-per-task="32"
#SBATCH --gres gpu:1,localtmp:25G
#SBATCH --time="22:00:00"
#SBATCH --output=/ceph01/projects/bone2gene/bone-age2/output/slurm/%j.out
#SBATCH --signal=SIGUSR1@90
NAME="masked_effnet_shallow_fancy... |
a26eaa264dc74389ab5435c2208c1f531eb314b1070c56d3f45de2d878f3efb6 | Shell | 1,172 | 33 | # 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_STAPLE.sh $1
# $1: atlas (in_vivo ex_vivo)
ROOT_DIR=$(pwd)
# echo "Bash version ${BASH_VERSION}..."
ATLAS=$(basename $1)
LABEL_NUMBER=80
echo -e "STAPLE\c" >> "$1/Dice_Score/Dice_Score_STA... |
ada42834f85b5e1603bc0d506c44e82981bd0660b68f965947ba6d17ae0d47c3 | Shell | 1,178 | 31 | #!/bin/bash
export MRTRIX_NTHREADS=$1
#Intersection of all masks
mrmath \
/work/data/MRtrix_recon/sub-*/ses-PNC1/anat/sub-*_mask_temp_new.mif \
min \
/work/data/MRtrix_recon/template/template_mask_new.mif \
-datatype bit \
-force
#Compute fixel mask while testing 2 different values of fmls_peak_value that determ... |
4a654f1c1fa8d4c1e04416923a0b85d2a73c2856755617c6dc16825b9bc0248e | Shell | 1,180 | 31 | #!/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... |
8f45e16ab32377eef945705a4065d71fbd79647c1efb0f818f94d44528dda5b6 | Shell | 1,181 | 40 | #!/bin/sh
case "$1" in
galaxy|"")
SCRIPT=./run.sh
PORT=8080
LOGFILE=galaxy.log
GRAVITY_LOGFILE=database/gravity/log/gunicorn.log
SUPERVISORD_LOGFILE=database/gravity/supervisor/supervisord.log
;;
*)
echo "ERROR: Unrecognized app"
exit 1
;;
... |
886713a1e8ad4ce32bb2fe0537327c990cfac55e462f3150bca3eaeb73c33104 | Shell | 1,182 | 38 | #!/bin/bash
# Check for valid directory
DIRNAME=$1
if [ ! -f $DIRNAME/readme.md ]; then
echo "usage: upload_model_to_gist.sh <dirname>"
echo " <dirname>/readme.md must exist"
fi
cd $DIRNAME
FILES=`find . -type f -maxdepth 1 ! -name "*.caffemodel*" | xargs echo`
# Check for gist tool.
gist -v >/dev/null 2>&1 ... |
2bdd2e1b412010b8ee676b931af26e7f550493ea7524d29c8fb2eeea2b4abf74 | Shell | 1,183 | 31 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# $1: folder include all the images to be parcellated
# $2: atlas folder
# $3: parcellation parameter file if exist
export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 1 -R y -l h_vmem=4G -l ... |
a8ee3bc5bc874a3a2aadc4a4de911ab883e875a72fa4b5eb9bb871da0c21c0cb | Shell | 1,183 | 30 | python stat_stop_2_base.py 1.rough.txt 1neg.rough.txt > base_2_count1.txt
python stat_stop_2_base.py 2.rough.txt 2neg.rough.txt > base_2_count2.txt
python stat_stop_2_base.py 3.rough.txt 3neg.rough.txt > base_2_count3.txt
python stat_stop_2_base.py 4.rough.txt 4neg.rough.txt > base_2_count4.txt
#####################... |
33d004e0b207adeddd567aa96199e7989af0a3a901cb10ee757610c636b6ac54 | Shell | 1,188 | 39 | #!/bin/sh
# Script generates auryn_revision.cpp according to the following values
AURYNVERSION=0
AURYNSUBVERSION=8
AURYNREVISIONNUMBER=4
AURYNREVISIONSUFFIX=""
# Do not edit below
OUTDIR=`dirname $0`
HASH=`git log --pretty=format:'%h' -n 1`
AURYNREVISIONSUFFIXANDHASH="$AURYNREVISIONSUFFIX-$HASH"
GITDESCRIBE=`git... |
fdfcf37ad81f9037eddf04e24306e1761f5cc0f21d7dc4142b9051e4b0ddd34e | Shell | 1,188 | 30 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6/out/full_cocaine_dataset_with_naive_rn6_with_sample_covar-X/da_peaks/high_vs_low/negbinom
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $HOME/rat... |
83d8b2db09dd577748103dcf1368c683acd53e3aaa8c05fadb4ec97a5e854a06 | Shell | 1,192 | 34 | #!/bin/bash
# ============================================================
# config.sh – site-specific variables for dwi-dtitk pipeline
# Source this file from every script: source ${scriptdir}/config.sh
# ============================================================
# --- Software module versions ---
export DTITK_... |
dc4ebfd8edfde2d26e4300e874788e2585b39935dc9f7978cc1cb7e19e479652 | Shell | 1,194 | 45 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_bde
train_path=../data/bde/train.csv
val_path=../data/bde/val.csv
test_path=../data/bde/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type regression \
-... |
6514f923fac0edbe30972c9bec2a79c2e7578ecc183a91b09d13f1607d85e8b5 | Shell | 1,195 | 34 | #!/bin/bash
#set -x
# Shows you the largest objects in your repo's pack file.
# Written for osx.
#
# @see https://stubbisms.wordpress.com/2009/07/10/git-script-to-show-largest-pack-objects-and-trim-your-waist-line/
# @author Antony Stubbs
# set the internal field spereator to line break, so that we can iterate easil... |
5a41d4ea566e5dd0d9121e596648972090663e877be83c50c7e1a708758eb56f | Shell | 1,196 | 35 |
#!/bin/bash
# Created by M.Y. WANG
# 15-Feb-2022
# Organize the mrs data
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/Data/Raw_data
cd $filepath
MRS_path=/Users/wang/Desktop/Research_projects/BBSC/MRS/Raw_data
ls | grep -i sub- > ./subjList.txt # command grep is trying to filter the input with 'su... |
50e90adaec67ddcbb8dcff25c3e3e07e256b04295d436fd35ab98c9e03820b47 | Shell | 1,198 | 50 | #!/bin/bash
echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
echo ""
echo 'Performing Unit Tests of Build'
echo ' '
echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
if [ -e "Inchworm/bin/inchworm" ]
then
echo "Inchworm: has been Installed Properly"
else
echo "Inchworm Installation appears to h... |
51a3201c1438515f86bf8142d26e37eca2f2af4f43c889da016eb099e98ee326 | Shell | 1,206 | 43 | #!/bin/bash
BUILDDIR="../../build/debug"
TOOLDIR="$BUILDDIR/tools"
# Compile code
CURDIR=`pwd`
cd $BUILDDIR && ./bootstrap.sh && make
cd $CURDIR
make -C $BUILDDIR
# Benchmark parameters
echo "Getting revision number"
SIMTIME=10
REVISION=`git log --pretty=oneline -1 | cut -d " " -f 1`
TESTNAME=`basename "$0"`
# Vog... |
95c55664c00b230872b1e5528848e0070448d7c4da4fac94c7858efaf777039d | Shell | 1,206 | 30 | #!/bin/bash
#SBATCH --job-name=null_spectemp
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=16000
#SBATCH --cpus-per-task=8
#SBATCH --time=6:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=1-999:4
#SBATCH --exclude=node093,node040,node037,node097,node098
#SBATCH --constraint=high-... |
fd7e6277d52ad9d0a91e191e38588b7d30bb4b6b927d1dc84d2fc184145c4b95 | Shell | 1,206 | 41 | #!/bin/bash
# Default video URL (can be overridden with environment variable)
VIDEO_URL=${VIDEO_URL:-"https://www.youtube.com/watch?v=dQw4w9WgXcQ"}
DEVICE=${VIRTUAL_DEVICE:-"/dev/video10"}
LOOP=${LOOP:-"true"}
echo "Setting up virtual video device: $DEVICE"
echo "Streaming from: $VIDEO_URL"
# Check if virtual device... |
2abcf6a3129a6d255ee8afe01a36d5dd1fae90f278b9f087d9f0b6f452c378ac | Shell | 1,213 | 34 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
ldc93s1_sdb="${ldc93s1_dir}/ldc93s1.sdb"
epoch_count=$1
audio_sample_rate=$2
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -... |
c0fdbef8159a19cb47677234bcf26bfaf25f610b7af6813984cbd4e0fd48d7ac | Shell | 1,215 | 30 | # test pre-trained rnasamba
source venv/bin/activate
source templates.sh
full_train_set="data/mammalian_200-1200_train_RNA_balanced.fa"
pc_train_set="data/mammalian_200-1200_train_PC_RNA.fa"
nc_train_set="data/mammalian_200-1200_train_NC_RNA.fa"
# re-train rnasamba on our data and test
for i in 1 2 3 4 5
do
rnasamba t... |
fd117ae48e46ef5fcd1456f2caf353eff1d84ae291e91bd752ccca2a7b76d674 | Shell | 1,215 | 37 | #!/usr/bin/env bash
set -ex
export PATH=/usr/bin:${PATH}
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2
read -r -d '' CTEST_CACHE << EOM || true
CMAKE_PREFIX_PATH:PATH=${COREBINARYDIRECTORY}
SWIG_EXECUTABLE:FILEPATH=${COREBINARYDIRECTORY}\swigwin\swig.exe
BUILD_TESTING:BOOL=ON
BUILD_EXAMPLES:BOOL=ON
SimpleITK_BUILD_... |
a38c35d2c1f89d1f3520541608b088a5e031e2c669e31a26c323607d86a8edf1 | Shell | 1,217 | 45 | #!/bin/bash
set -e
MARKDOWN_LINK_CHECK=$(which markdown-link-check || echo "")
if [[ -z "$MARKDOWN_LINK_CHECK" ]]; then
echo "❌ ERROR: markdown-link-check command not found. Install it globally via:"
exit 1
fi
CONFIG=".mlc.external.json"
LABEL="external"
echo "🔍 Checking $LABEL Markdown links..."
LOG_FILE=$... |
c026cafcb058713baf6a6c567c6301f7ef4e70eb99a99497c0f505f0da3c2690 | Shell | 1,218 | 46 | #!/bin/bash
# From https://denibertovic.com/posts/handling-permissions-with-docker-volumes/
# Add local user
# Either use the LOCAL_USER_ID if passed in at runtime or
# fallback to 9001
echo "----------------------------------------------------------"
cat<<TF
##### # #### # # ###### #####
# # ... |
15cdfc3d8a27a1d419789bc7965b1880a45a84136eab620006bc4301aeb11733 | Shell | 1,221 | 25 | #!/bin/bash
set -xe
# Will inspect this task's dependencies for one that provides a matching npm package
get_dep_npm_pkg_url()
{
local all_deps="$(curl -s https://community-tc.services.mozilla.com/api/queue/v1/task/${TASK_ID} | python -c 'import json; import sys; print(" ".join(json.loads(sys.stdin.read())["depende... |
39500170e3f498c09669f025691999ed6e2c6b87d3b722c963b7332db0b99a13 | Shell | 1,223 | 42 | GNU nano 2.4.2 File: orthofinder.sh
#!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).... |
7d000e53126d30ed586d1b9492a79323454ed57604ee2f6da63b415d90f395b7 | Shell | 1,223 | 37 | #!/usr/bin/env bash
set -ex
export PATH=/usr/bin:${PATH}
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2
read -r -d '' CTEST_CACHE << EOM || true
CMAKE_PREFIX_PATH:PATH=${COREBINARYDIRECTORY}
SWIG_EXECUTABLE:FILEPATH=${COREBINARYDIRECTORY}\swigwin\swig.exe
BUILD_TESTING:BOOL=ON
BUILD_EXAMPLES:BOOL=ON
SimpleITK_BUILD_... |
86805bc44521e964d86cd35f51226485a3059559277d2174d1ef346e12c7f9cb | Shell | 1,231 | 25 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
b9aa9586538941f53ef846322ce04d5c82fdf8376352072138ef48c28e5e3711 | Shell | 1,236 | 62 | #!/bin/bash
ROOT="."
VERBOSE=4
for i in {08..23}; do
OCT="${ROOT}/oct/slices/unstack/oct.${i}.masked.nii.gz"
OCTVSL="${ROOT}/oct/slices/unstack/vessels.${i}.nii.gz"
LSFM="${ROOT}/lsfm/slide_center_oct/neun.${i}.nii.gz"
LSFMVSL="${ROOT}/lsfm/slide_center_oct/vessels.${i}.float.nii.gz"
LSFMDST="${ROOT}/lsfm/slide_ce... |
036ee41c78a402420cb5b8b06eccadbd113ef3256c8a3a3abb4fe958ab9598d9 | Shell | 1,238 | 31 | #!/bin/bash
#SBATCH --job-name=null_alexnet
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --exclude=node093,node040
#SBATCH --constraint=high-capacity
#SBATCH --partition... |
2bb79fdaf859f963d6932f37a1220dff08e4057cc76928ae48facd6b68af04df | Shell | 1,239 | 20 | #!/bin/bash
# used to make heatmaps of ChIP signal over OR genes
# same parameters are used to make plots in Figure2, Supp Figure2, Figure 6 and Supp Figure 6
# input is bigwig files merged from two replicates (generated with HOMER) and bed regions for OR gene bodies
computeMatrix scale-regions \
-S mergedR... |
4b61b5b2440888d27434cda1359a203e6964819bbd397c75f437675a36a13796 | Shell | 1,243 | 44 | #!/bin/bash
# exit when any command fails
set -e
# load modules on HPC
#module load fsl
#module load R/3.4.1
# subject
subj=$1
## COPY FILES TO NEW DIRECTORY
echo "COPY FILES: subject: " ${subj}
# paths and parameters
proj_dir=/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/
fix_path=${proj_dir}data/deriva... |
1e37ba9477084bc2f522213d7a9ba06299ca9eb853a704485ccbdbf08d7fc51a | Shell | 1,246 | 31 | #!/bin/bash
#SBATCH --job-name=null_alexnet
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --exclude=node093,node040,node094
#SBATCH --constraint=high-capacity
#SBATCH --p... |
871cb6df6284b9db3c29b69630cbd1a38f2f61bd64a3eaab0a88223b65bc3502 | Shell | 1,246 | 46 | #!/bin/bash
ROOT="."
VERBOSE=4
for i in {08..23}; do
OCT="${ROOT}/oct/slices/unstack/oct.${i}.noisify.nii.gz"
OCTVSL="${ROOT}/oct/slices/unstack/vessels.${i}.nii.gz"
LSFM="${ROOT}/lsfm/slide_center_oct/neun.${i}.nii.gz"
LSFMVSL="${ROOT}/lsfm/slide_center_oct/vessels.${i}.float.nii.gz"
LSFMDST="${ROOT}/lsfm/slide_c... |
b046053da043fc1237429a80841df1b1b280a2dad02ba90e6b2047164ec51a1d | Shell | 1,249 | 38 | #!/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... |
78632aa19d0c5e7b510ff1e1fe5b159a5161fcf9d4b07cb6cc6cbaced9393ab3 | Shell | 1,257 | 44 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Segment FOD to fixels - estimated AFD (FD)
fod2fixel \
-mask \
/work/data/MRtrix_recon/template/template_mask_new.mif \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_fod_temp_NR_new.mif \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/fixel_NR_ne... |
caf59ef829f0f0068e64ecbf053e97c0a22a489a9c9d54f196042f39ac48f680 | Shell | 1,258 | 30 | # For writing commands that will be executed after the container is created
# Installs `project_name` as local library without resolving dependencies (--no-deps)
# python3 -m pip install -e ./src/project_name --no-deps
# After the above command is run, the contents of the `project_name`` directory can be imported as ... |
6a1e75af8ea94811c6e2e668fc1a359000b4a4c24b01ec106201f68d3d43308c | Shell | 1,259 | 26 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=02:00:00
#$ -j yes
#make the re... |
593ee17d05866cc173c5669920c4dd5f5d4481d35f697201c4923f30ce159722 | Shell | 1,261 | 37 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
ldc93s1_sdb="${ldc93s1_dir}/ldc93s1.sdb"
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir... |
c4c310e9ac20285a028bc685b50369aa9b49d2e5d18a68648906b9036904ade6 | Shell | 1,261 | 29 | source env/bin/activate
export ADAPET_ROOT=`pwd`
export PYTHONPATH=$ADAPET_ROOT:$PYTHONPATH
export PYTHON_EXEC=python
####### Example: run prompt-based fine-tuning experiments on GatorTron #######
# Please specify your data path to train on full train set or subsets, e.g., data/medical/train_{} (full, 100, 500, 1000,... |
f52d1c9da06ff4d060486cc5455298bd3faea9cdb8ebd004a2204be93e9005dd | Shell | 1,262 | 31 | #!/bin/bash
#SBATCH --job-name=null_alexnet
#SBATCH --output=output/null_%A_%a.out
#SBATCH --error=output/null_%A_%a.err
#SBATCH --mem=64000
#SBATCH --cpus-per-task=20
#SBATCH --time=150:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0
#SBATCH --exclude=node093,node040,node094,node098,node097
#SBATCH --constraint=high-capa... |
5a463c8540b4c28b2dad9b4816e928667483e3d4d46bcc7b614a95f6bc2155e7 | Shell | 1,268 | 46 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-11
#$ -tc 3
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
samples_table=$HOME/realign_snatac_fastqs/sample_names.txt
reference_genome=/iblm/netapp/data1/jezhou/cellranger/rn6
fastqs_dir=/iblm/netapp/data1/jezhou/Telese_Rat_Amygdala/snATAC/fastq
o... |
1872a49857e075dc34a142550c314bf31342ac6aae5f679e1266669d33ac0f76 | Shell | 1,269 | 32 | #!/bin/bash
### reconstruction - feed decoded features to generator
## supp: diffusion
MODEL="--model_path generator/diffusion/generator.pt"
MODEL_FLAGS="--attention_resolutions 16,8 --class_cond True --dropout 0.1
--image_size 64 --learn_sigma True --num_channels 192 --num_head_channels 64 --num_res_... |
5bc1a7b3ef770e693f83660c9a9e9c45ee7d95f1b7ccf59b6c3309978f3eec09 | Shell | 1,271 | 10 | #!/bin/bash
python AG.py F-2-1.sorted.bam.filter.bam.region.bam.pos.sort.bam /home/weiqi/project/01.weiqi/20200929_inosine/process/index/GRCm38.p6.fa /home/weiqi/project/01.weiqi/20200929_inosine/process/index/GRCm38.p6.fa.size F-2-1.pos.AG.bam > 1.rough.txt
python AG.py F-2-2.sorted.bam.filter.bam.region.bam.pos.sort.... |
f12d37081f825599e126cfb9419664427dcde0e4f76effabe2dde8f5a813ab35 | Shell | 1,274 | 47 | #!/bin/bash
#NOTE that to use this outside of travis, you'll want to export BRANCH=master
set -euo pipefail
export base=$(pwd)
BRANCH=devel
sudo apt-get update
sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
curl libssl-dev libtool autoconf... |
53968c59d29a081c6b9620f793be9aac9647e07630bd00a40bbc1e1947ce7511 | Shell | 1,277 | 27 | #bash
# analysis anatomical data only
docker run -ti --rm \
-v /Users/joeywang/Desktop/BBSC/Functional/fmri/rawdata:/data:ro \
-v /Users/joeywang/Desktop/BBSC/Functional/fmri/derivatives/fmriprep-23.2.0:/out \
-v /Users/joeywang/Desktop/license.txt:/opt/freesurfer/license.txt \
nipreps/fmriprep:23.2.0 ... |
2e9cf9847d2caa6f0e15b7c3bab9b63fd677d48c79f688be1077f09ef5b3f53a | Shell | 1,278 | 24 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
33e90f2c18bc5cfbc3ac7eb90fa20751ee741ec4b304114402842edb338ba971 | Shell | 1,279 | 26 | source venv/bin/activate
source experiments/scripts/templates.sh
#input_prefix="mammalian_200-1200_test_RNA_nonredundant_80"
input_prefix="mammalian_200-1200_train_RNA_balanced"
rna="data/${input_prefix}.fa"
#prot="data/mammalian_200-1200_test_PROTEIN_nonredundant_80.fa"
prot="data/mammalian_200-1200_train_PROTEIN_bal... |
51665a28a5c353b94a716b3e3ae6cc274ac38c266a463ab1439d06ecd33188a6 | Shell | 1,279 | 25 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=06:00:00
#$ -j yes
#make the re... |
7b5c21b7368726b26c6c6d44c719f5a86a4f6f7de67c9a89c88775e2fb820f28 | Shell | 1,279 | 53 | #!/bin/bash
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="$ROOT/oct/gray.lowres.mgz"
OCTGM="$ROOT/oct/gr... |
105d0cd742a49d762bc37f01c4322c1247284d17e16b8930546fd2c7f0ba340a | Shell | 1,283 | 31 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# $1: folder include all the images to be parcellated
# $2: atlas folder
# $3: If exist, read the file to load user defined parameters (see file under sample_parameters for examples)
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
#... |
61c441a16e672506ed6d1c221135643d5559ee57580fcdad7301779664e58e88 | Shell | 1,283 | 45 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_barriers_cycloadd
train_path=../data/barriers_cycloadd/train.csv
val_path=../data/barriers_cycloadd/val.csv
test_path=../data/barriers_cycloadd/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperp... |
6092fb3b5d336caa6c2341520dd25ef48c1b353ad9801802946c88a94cbd0d14 | Shell | 1,284 | 45 | #!/usr/bin/env bash
# an example to do pre-training: (not that `/path/to/imagenet` should contain directories named `train` and `val`)
# > cd /path/to/SparK
# > bash ./main.sh experiment_name --num_nodes=1 --ngpu_per_node=8 --node_rank=0 --master_address=128.0.0.0 --master_port=30000 --data_path=/path/to/imagenet --mo... |
7b6d82ca5d350a5a480a379cfed30dc367e3d90cbd453d05514b54314eeec3bd | Shell | 1,287 | 31 | #!/bin/sh
# Move to scripts directory
root_dir="/Volumes/hoycw_clust/PRJ_Error"
out_dir="/Users/colinhoy/Code/PRJ_Error/asymmetric_RPE_paper_data"
cd $root_dir/scripts/
# Load the correct SBJ list
echo "Please enter the desired SBJ list:"
read list_name
declare -a SBJs
SBJs=(`cat "${root_dir}/scripts/SBJ_lists/${li... |
03139bb00f19f1a6f7082a378ec4083df0e0952b1a6e2d777de829bc0cbe14a5 | Shell | 1,288 | 37 | #!/bin/bash
# Usage: bash download_uniprot.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt inst... |
08b8a962b697db22dbc6d175d3a0170bcaa858ff24e323230bfc096eeade3fe2 | Shell | 1,289 | 35 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -tc 4
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
# outdir=${celltype}_... |
0cb82b2ddba98dc1b5975c96874a58fbc33ec772bfc8a1e1e174fec67bcb0672 | Shell | 1,294 | 25 | #!/bin/bash
# Set up source and build directories
build="/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/analysis_hapoe_chr/parameters/adppg-mm10-apoe-chr-mapt-chr-2021-A_build"
# set paths for input files
fasta_transgene="${build}/Mus_musculus.GRCm38.dna... |
5ac3c15f59ad8cac5947dbd7af19c0ef3a44f80347a80b4a37be552ca33562d8 | Shell | 1,294 | 43 | #!/bin/bash
set -ex
curdir=$(dirname "$0")/
pip3 install --quiet --user --upgrade pip
export PATH=$HOME/.local/bin/:$PATH
pip3 install --quiet --user --upgrade -r ${curdir}/tc-decision_reqs.txt
# First, perform dry run for push and pull request
# This should help us track merge failures in advance
for event in pul... |
316b8bb125258388c5c53de52899b7186aff90034a52b8b8ff5a265b8d4a39f2 | Shell | 1,297 | 38 | #!/bin/bash
##########################################################################
## This script takes two command line arguments (in the below order)
## 1. CellRanger results folder path to be cleaned up
## 2. Temporary or trash folder path
##
## Example run:
## 02_cellranger_count_batch1_batch2_merged_results_c... |
7c48b37cb3aace8d8e11df9e6d75336805b18d9f643c73327edfde7638fdb71e | Shell | 1,300 | 46 | #!/bin/bash
set -xe
do_bazel_build()
{
local _opt_or_dbg=${1:-"opt"}
cd ${DS_TFDIR}
eval "export ${BAZEL_ENV_FLAGS}"
if [ "${_opt_or_dbg}" = "opt" ]; then
if is_patched_bazel; then
find ${DS_ROOT_TASK}/tensorflow/bazel-out/ -iname "*.ckd" | tar -cf ${DS_ROOT_TASK}/bazel-ckd-tf.tar -T -
fi;
f... |
7d7850dfec5ece6e8c049d3d5fcf9dbc16dbe96a39fdea4c3007d50d040f5284 | Shell | 1,309 | 10 | #!/bin/bash
python TC.py F-2-1.sorted.bam.filter.bam.region.bam.neg.sort.bam /home/weiqi/project/01.weiqi/20200929_inosine/process/index/GRCm38.p6.fa /home/weiqi/project/01.weiqi/20200929_inosine/process/index/GRCm38.p6.fa.size F-2-1.pos.TC.bam > 1neg.rough.txt
python TC.py F-2-2.sorted.bam.filter.bam.region.bam.neg.so... |
fc8153cd2d48ff4c2df999e9c1f864bc0e068df40165ae3271f410572a71862c | Shell | 1,309 | 31 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-13
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $HOME/rat_snatacseq_analysis/coembed/celltypes.txt`
degs=$HOME/rat_snrnaseq_pipeline/dge_labeled/out/dge-with-batch-percent-sample-covars/MAST/high_vs_... |
62fa81412f6d6be67ab798c46892c612b601d246fdc87b2fe67150a18cab28d9 | Shell | 1,312 | 44 | #!/bin/bash
# From https://denibertovic.com/posts/handling-permissions-with-docker-volumes/
# Add local user
# Either use the LOCAL_USER_ID if passed in at runtime or
# fallback to 9001
echo "----------------------------------------------------------"
cat<<TF
##### # #### # # ###### #####
# # ... |
55132d3e6272fb1cceabab05125a89ea08829dfff67c74846a0aed40e38e0af6 | Shell | 1,313 | 38 | #!/bin/bash
subj=$1
# load modules
module load fsl
module load miniconda3/current
source activate fmriprep-env
# run python script to create 'pseudo-FSL' folders
python create_fix_folders.py ${subj}
## fearRev
fix_dir=/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/data/derivatives/fix/fearRev/
# run feat... |
7935c7635bc8304eed88a1c57b528a342f803457c5eed1728a6153c08b055e2e | Shell | 1,315 | 29 | #!/usr/bin/env bash
#
# Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
e22ac518e7d4011d0dea915ee0d955f65b64fd61780e939f8af0ef083e8f3a3d | Shell | 1,315 | 35 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
ldc93s1_sdb="${ldc93s1_dir}/ldc93s1.sdb"
epoch_count=$1
audio_sample_rate=$2
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -... |
6d2f7403879f13c50b22bab28e8ee0aca87a05938341964bcc72d82077dba7d4 | Shell | 1,316 | 29 | #!/bin/bash -ve
PROG=`dirname $0`/../PtR
if [ -e MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz ] && [ ! -e MLF_ESC_NPC.cuff.genes.fpkm.matrix ]; then
gunzip -c MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz > MLF_ESC_NPC.cuff.genes.fpkm.matrix
fi
# assessing read counts and genes mapped
$PROG --matrix MLF_ESC_NPC.cuff.genes.fpkm... |
fedf19c83fa3c3f13987b61c68383faaf39f4bdff110805d899e90ed72b42fd4 | Shell | 1,318 | 36 | #!/bin/bash
## assume script is launched from vsearch/man/
## usage: bash scripts/generate_news.sh [news_file]
##
## Render NEWS.md -- a short preamble plus the release-history fragment
## that vsearch-history(7) is built from -- as the plain-text NEWS file
## the GNU coding standards ask for. The two therefore canno... |
5aa07d7943a74027dd69089a6b2a0af92a2d924a79dd100e3d47b8e5ec7385e2 | Shell | 1,321 | 48 | #!/bin/bash
# Run denoise.m and unring.m as a step 1 in the pipeline
# Ivan I. Maximov, Skollenborg
# 22.11.2018, ver 1.0
# 11.12.2018, ver. 1.1
# 11.08.2019, ver. 2.0
#SBATCH --account=p33_norment
#SBATCH --time=72:00:00
#SBATCH --job-name=UKB_t1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=8G
source /cluster/bin... |
673483784a55fecf6535dfbccfb61f1f18746eb5d2f2baeb22df448b9fcb71dd | Shell | 1,322 | 38 | #!/usr/bin/env bash
set -ex
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2
echo "COREBINARYDIRECTORY: ${COREBINARYDIRECTORY}"
read -r -d '' CTEST_CACHE << EOM || true
CMAKE_PREFIX_PATH:PATH=${COREBINARYDIRECTORY}
CMAKE_CXX_VISIBILITY_PRESET:STRING=hidden
CMAKE_VISIBILITY_INLINES_HIDDEN:BOOL=ON
CMAKE_OSX_DEPLOYMENT_T... |
7a51c77fc5f8f9c3844c38ac5f19cd88842be20986a9b6be11a17e961dac5489 | Shell | 1,324 | 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... |
d279b45cc46bcc581374c4e23114d898cf80e44475a57277d96d3a7a02b5afe1 | Shell | 1,325 | 37 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Calculate individual subject's FOD warping to the FOD template
mrregister \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_wmfod_new_norm.mif \
-mask1 \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/anat/sub-${bblid}_anatmask_s.mif \
/work/data/MRtri... |
ec6be90caf3c3240da75b64d0fa75155e6f2030e5687193d93d19d2311b8a1c2 | Shell | 1,327 | 58 | #!/bin/bash
ROOT="."
ROOT+="/lsfm/slide_center_oct"
pushd $ROOT
for i in {08..23}
do
nitorch reslice \
../slide/vessels.${i}.distance.moved.slidecrop.nii.gz \
-il neun.${i}.to_center.lta \
-t neun.${i}.nii.gz \
-o vessels.${i}.distance.nii.gz \
--bound replicate --extrapolate
nitorch reslice \
../slide/vessels... |
16eaf5c4a5bc15372510c99031e86c4a9f340c1500b244cac20b4c77e3a7c601 | Shell | 1,329 | 25 | #!/bin/bash
# Set up source and build directories
build="/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/analysis_hapoe_chr/parameters/adppg-mm10-apoe-chr-mapt-chr-2021-A_build"
# set paths for input files
fasta_modified="${build}/Mus_musculus.GRCm38.dna.... |
e8d3f6002615d7e0d2d8925703cac3c514749be1cbe75391509d9e5f16767356 | Shell | 1,334 | 67 | #!/bin/bash
echo "------------------------------------------------------------------------------------"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR="${DIR}/../build"
mkdir -p ${DIR}
cd ${DIR}
echo "++++"
echo "++++ Installing Eigen3"
echo "++++"
mkdir -p ${DIR}/eigen3
cd ${DIR}/eigen3
unzip ${DIR}/.... |
4a8cd952331f0802ea5845e3eda59b8982d9252dbeaaffb39211b39dfb6e99a5 | Shell | 1,339 | 33 | export GALAXY_SLOTS_CONFIGURED="1"
if [ -n "$SLURM_CPUS_ON_NODE" ]; then
# This should be valid on SLURM except in the case that srun is used to
# submit additional job steps under an existing allocation, which we do not
# currently do.
GALAXY_SLOTS="$SLURM_CPUS_ON_NODE"
elif [ -n "$SLURM_NTASKS" ] || [... |
8da3034425d695295a8309919efa9d195b01c95c42125243b2ef14e21ac00e08 | Shell | 1,339 | 29 | #!/bin/sh
############################################################################
###################### PARAMETERS THAT CAN BE CHANGED ######################
############################################################################
# Array that contains the input images to create the atlas
export IMG_INPUT=(`... |
1201ca5bc7675759634d7364d4ce21547df9f321486175416d257f905278e9d3 | Shell | 1,345 | 33 | #!/bin/bash
set -u
set -e
# INPUTS:
# - leg files and associated name files (produced with make_leg_files.py)
# - list of good cells with their sexes (../good_cells.txt)
# - 3DG data (from ../3D.../..cleaned.1.3dg) (e.g. ../3D.merged.z1OMP.10.ca.male/merged.z1OMP.10.20k.1.clean.3dg)
# this analysis produces counts f... |
5fdbd580ea8b1505cf38e307d981a470727e4de47e0156df5bef5cbbec3249dd | Shell | 1,345 | 58 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
save_dir=results_timing
data_dir=../data/timing
#100k
python $chemprop_dir/train.py \
--dataset_type regression \
--data_path $data_dir/qm9_100k.csv \
--save_dir $save_dir/qm9_100k \
--aggregation norm \
--depth 4 \
--ffn_num_lay... |
e41d086c8bf7f1a794420f6c26cba9b651b829e176b5f4c1840b79328328e7e9 | Shell | 1,347 | 46 | #! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html.... |
608c5cfc53c1d35dd43f836d59d370afc54651ed8e9c0dbd65f7bf126b41a3c8 | Shell | 1,348 | 38 | #!/bin/bash
#$ -l mem_free=12G,h_vmem=12G,h_fsize=100G
#$ -cwd
# run on JHPCE cluster
# qsub scripts/spaceranger_memory_error.sh
# ----------------------------------------------------------------------------------------
# Script to reproduce Space Ranger memory error when using module on JHPCE cluster
#
# error OCC... |
21c1cc6c70ac4a2823de884edba174d5c2c0400363cc0801563c75fd6ea77fb3 | Shell | 1,350 | 67 | #!/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... |
32f7c622537b3e12d1af50d7e0c3ab8683032bc1682d241ca40c47dc2ab2dce6 | Shell | 1,352 | 50 | #!/bin/bash
#
# Example site customization script for shunit2 test-cases
# sourced from 'env-test.sh'
#
function initEnv() {
# special-case for .libmesa_from_matlab-2014b
if [ "$1" = ".libmesa_from_matlab-2014b" ]; then
export RGL_USE_NULL=TRUE
fi
# exact copy of env-default.sh
if ... |
10b0b097f9ed83c798cd31e044c604333e96c065cafd8ab22bcae4e84ab1c032 | Shell | 1,354 | 81 | set -ex
CLASS='edges2shoes' # facades, day2night, edges2shoes, edges2handbags, maps
MODEL='bicycle_gan'
CLASS=${1}
GPU_ID=${2}
DISPLAY_ID=$((GPU_ID*10+1))
PORT=2005
NZ=8
CHECKPOINTS_DIR=../checkpoints/${CLASS}/
DATE=`date '+%d_%m_%Y_%H'`
NAME=${CLASS}_${MODEL}_${DATE}
# dataset
NO_FLIP=''
DIRECTION='AtoB'
LOAD_SIZ... |
6c63a8cea23136577f53983ede5b78350a059df470bbdeb6c9662596ca42c60d | Shell | 1,355 | 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... |
90c4de10c9d9b85ef292c0497627645daa127d1e3ac1c55f295fa63efafdebee | Shell | 1,358 | 37 | #!/bin/bash
# Usage: bash download_uniprot.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 inst... |
b7e831321bfab0926a003cff0faf7ad27171094acd5e0d83e8f251f9dc7ebe92 | Shell | 1,359 | 50 | #!/bin/bash
set -e
echo "=== Galaxy GCP Batch Job Execution (Direct) ==="
echo "Job: ${job_id_tag}"
echo "Tool: ${tool_id}"
echo "Timestamp: $$(date)"
echo "Host: $$(hostname)"
echo ""
# Check NFS mount
if [ -d "${nfs_mount_path}" ]; then
echo "✓ NFS mount point exists: ${nfs_mount_path}"
if mount | grep "${n... |
ce9658ce65eed55882c0f41f496d19644991ca1c7d2131f495791705f417bdfb | Shell | 1,360 | 34 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
for leftout in B0702 B0801 C0701; do
DePTH predict --test_file data/HLA_I_leave1out_match/HLA_I_leave1out_matc... |
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