sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f5a53e870f172b29677bdb38719b8dfbaa6c72f754f8cdd71c6ae3316b71d175 | Shell | 640 | 28 | #!/bin/bash
preds=${*:4:$#};
predsSTR=$(printf "_%s" ${preds[@]});
dname_src=$(dirname $1)
if [ -n "$dname_src" ]
then
dname="$dname_src/";
else
dname="";
fi
base_filename="$dname$(basename $1 _part.prdmeasures)_$(basename $3 .cdrform)$predsSTR"
outdir="${base_filename/_part\./\.}"
outfile="${base_filename/_part\.... |
f3b60dfae1709ce6717af71bd85019ff49aa502ba3b5e9ada4b04b3703796d2b | Shell | 644 | 4 | python ./bin/plot_correlation.py -p ./data/continuous-current/17h14m41s_Trial7_pipette_temperature_thermistor_14-09-22.asc -c "0 2" -l "V(mV) Temperature ºC" -sv y -sh n -scx 1000 -sf eps
python ./bin/laser_pulse.py -p './data/continuous-current/17h33m37s_Trial8_pipette_temperature_thermistor_14-09-22.asc' -slope 2.326... |
8ba7eb35c3f73b9af8962898bcc9b2620dff2367835327fb7df1b1504efa5d31 | Shell | 652 | 12 | #use palindrover results to generate palindrome track
rm chrY.palindromes.bed
sed 's/chrY/hs1/' hg002.chrY.palindromes.bed >>chrY.palindromes.bed
sed 's/chrY/hs2/' mPanTro3.chrY.palindromes.bed >>chrY.palindromes.bed
sed 's/chrY/hs3/' mPanPan1.chrY.palindromes.bed >>chrY.palindromes.bed
sed 's/chrY/hs4/' mGorGor1.chrY... |
dff6bbc141e9ce453b80da81282483ecd3f9e2ded2f677ee47835b1d40071243 | Shell | 663 | 14 | #!/bin/bash
# scRNASeq
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81252/suppl/GSE81252_data.cast.log2.lineage.csv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81252/suppl/GSE81252_data.cast.log2.liverbud.csv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81252/matrix/GSE81252_series... |
137975fc5a92338e69e53344f7eacc904e36bc09928186aadb6738b1de94bc51 | Shell | 664 | 21 | python -m nltk.downloader punkt
for seed in 1111 1112 1113;
do
python neural-complexity/main.py \
--emsize 256 \
--nhid 256 \
--epochs 40 \
--batch_size 64 \
--lr 20 \
--dropout 0.2 \
--model_file neural-complexity/models/$... |
0533f1be472de265c7f89ce5ec1e6c66839a6dbde22b4fdc244ff609270d24fd | Shell | 669 | 18 | #!/bin/bash
pyinstaller.exe --noconfirm --onedir --console --runtime-hook=./misc/pyinstaller/hook.py src/main.py &&
mv dist/main/main.exe main-cli.exe &&
pyinstaller.exe --noconfirm --onedir --windowed --runtime-hook=./misc/pyinstaller/hook.py src/main.py &&
mv main-cli.exe dist/main/ &&
mkdir dist/main/numpy/.libs &... |
39267446ba34609727cf36ab4f75cfa79fb45c1ad499836b6c38865557494384 | Shell | 669 | 19 | # Download the reference genome
GENCODE_VERSION=26
FILE="gencode.v${GENCODE_VERSION}.annotation.gtf.gz"
ANNOURL="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_${GENCODE_VERSION}/${FILE}"
URL='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz'
if [ ! -f hg37.fa ]
do
wget -O hg38.fa.gz $URL &... |
46951016ffe5c261645a4b820ba0932c75ae62c47a524877bd449d8a5c994e04 | Shell | 671 | 37 | #! /bin/sh
# Usage: ./e2.sh <esl-seqstat> <stockholm file>
# Example: ./e2.sh ../miniapps/esl-seqstat ../formats/stockholm.1
#
# This tests that % cat foo.sto | esl-seqstat -
# produces an error message: Format of seqfile - unrecognized.
# whereas % cat foo.sto | esl-se... |
6747097e1335378d796b48dd4ea9a9c21993c31cb48ea25d5c123630c6d920e7 | Shell | 673 | 25 | #!/bin/bash
# revision.sh
cd $ULTRASCAN/us_somo
RDATE=`git log -1 --shortstat .|grep Date:|sed -e 's/Date: //'`
SHASH=`git log -1 --oneline .| cut -d' ' -f1`
RNUMB=`git log --oneline | sed -n "/$SHASH/,99999p" | wc -l`
cd develop/include
if [ -f us_revision.h ]; then
HDATE=`grep REVISION_DATE us_revision.h | cut ... |
48cecf54f4c06f16df1c2a405f07c1fb8d5636bea8752bfca872f2f789642559 | Shell | 676 | 18 | mkdir -p data/aggregated/rnng;
for strategy in "top_down" "in_order";
do
for seed in 3435 3436 3437;
do
for beam in 100 200 400 600 800 1000;
do
for unit in "A" "B" "C" "D";
do
python src/aggregate/aggregate_surp_rnng.py \
... |
a426b578ba15b60a576831ab5ec54bbecce1904e3f7e7db15373d78493c693c1 | Shell | 676 | 25 | #!/usr/bin/env bash
# test-docs.sh: Test the examples in the vg documentation and wiki with https://github.com/anko/txm
set -e
# Work out where we are.
# See https://stackoverflow.com/a/246128
HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
# Make sure we have the tester
which txm || npm inst... |
ab63c7304b00bc9e5781a6957f57ac2926331f04439975bcdb6aac8d7d9dcb5f | Shell | 676 | 12 | # Human cerebral organoids + fetal neocortex
# SMARTer
# Camp JG, Badsha F, Florio M, Kanton S et al. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc Natl Acad Sci U S A 2015 Dec 22;112(51):15672-7. PMID: 26644564
# GSE75140
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series... |
809f9b52a6bd21b55e967f4ab8b8909f2962319f5152bb0a7e3fada9e3420355 | Shell | 688 | 22 | #!/bin/bash
#SBATCH --job-name=rg_sumstats
#SBATCH --account=p33_norment
#SBATCH --time=4:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
#SBATCH --array=0-1
set -o errexit
source ../settings.sh
source ${SOFTWARE}/ldsr/bin/activate
which python
LDSR_SRC=${DATA}/ldsc
LDSR_OUT=${OUT}/rg
LDSR_IN=${OUT}/munge
... |
a6435153dee4999b42d0007cdbb179134396ec7a33edc2c7d23a65c67a3148b2 | Shell | 688 | 36 | #!/bin/bash
eval "$(conda shell.bash hook)"
conda activate mrtrix
if [ -z "$1" ]; then
echo 'DATA is not specified.'
DATA='meas_MID00402_FID02551_EPISeg2_67_1p0iso_kyShift'
else
DATA=$1
fi
echo $DATA
if [ -z "$2" ]; then
echo 'FILE is not specified.'
FILE='MUSE'
else
FILE=$2
fi
echo $FILE
... |
6df4687055fd066ca0915f710b557eb925df4bbafb7067069a690be2982b4347 | Shell | 696 | 20 | #####################################################
# Following are the dependencies and the versions
# used in the LLM predictivity project
#####################################################
# go to the (base) environment
conda deavtivate
# create conda env
conda create -n llm-pred python=3.7
# activate cond... |
325e58203fc8209d5021037995686c22622f376046374082cc3658a7c55399f1 | Shell | 704 | 20 | #!/bin/bash
inputdir="../data/"
gene2idfile=$inputdir"gene2ind.txt"
cell2idfile=$inputdir"cell2ind.txt"
drug2idfile=$inputdir"drug2ind.txt"
testdatafile=$inputdir"drugcell_test.txt"
mutationfile=$inputdir"cell2mutation.txt"
drugfile=$inputdir"drug2fingerprint.txt"
modelfile="../pretrained_model/drugcell_v1.pt"
result... |
e7db2aaccfdeb70469dfb0e57ec72f94d9148d03848244fc67976e268587cedd | Shell | 706 | 24 |
#!/usr/bin/bash
if [ $# -lt 1 ]
then
echo "sh $0 <id>"
echo "### please run $0 in the output directory ###"
exit 0
fi
PREFIX=$1
SHELL_FOLDER=$(dirname "$0")
Pwd=`pwd`
source ${SHELL_FOLDER}/config.txt
fai=`ls ${PREFIX}*.fa.fai|head -n 1`
cat ${cutoff} | awk '{print "perl '${markLTR}' '${PRE... |
6e54554dbda0e1901fe9be3c81f11a9aafac02b774574f889b4cfb017259aa47 | Shell | 710 | 29 | #!/bin/bash
mkdir scater-objects
# process files and create scater objects
for f in `ls bash`; do
name=(${f//./ })
echo "processing $name..."
mkdir $name
cd $name
# download and process a dataset; create scater object
bash ../bash/$name.sh
Rscript ../R/$name.R
cp *.rds ../scater-object... |
f286c1bbdfecb0869b47d11f5cce8e39d3d86e49660f73e5cec2d2f24faec727 | Shell | 710 | 27 | #!/bin/bash
set -euo pipefail
readlinkf() { perl -MCwd -le 'print Cwd::abs_path shift' "$1"; }
SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd "$SCRIPTDIR/.."
pwd
# This script installs pheweb in a venv and runs tests there.
# It's helpful for checking that there aren't any un-checked-in files I guess... |
09ffc94b2fcb334c25971a3be4f9f9c0996c6f8179eb031e1fff4035eeacce93 | Shell | 711 | 21 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 20
#SBATCH -t 18:00:00
#SBATCH --job-name star_ref
#SBATCH -o %j.out
#SBATCH -e %j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=ykbabal@gtu.edu.tr
module load star
STAR --runThreadN 20 \
--runMode genomeGenerate \
--genomeDir /usr/users/mmnb1ngs... |
c08690726dea43db04f9be036a7d3f6518a65596ba981b4dec4ca12b49170b49 | Shell | 712 | 25 | #!/bin/bash
# submit after jobs from wrapper_connectivity_matrices.sh are finished
dataset="PNC"
script_dir="/cbica/projects/network_replication/manuscript/code/connectivity_matrices/${dataset}"
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
qsub -l h_vmem=25G,s_vmem=25G \
-N makeConnMatrice... |
dbda6b86b68f7b952b265f8d76c4e388cb70634bf6d067ce3e45d7f23002fd96 | Shell | 713 | 15 | # add bash autocompletion
if [ -n "$BASH" ]
then
_vg_complete()
{
local cur prev
COMPREPLY=()
cur="${COMP_WORDS[COMP_CWORD]}"
opts="add align annotate augment autoindex bench-dist-query benchmark call chains chunk circularize clip cluster combine concat construct convert deconstruct depth describe d... |
2040630b25cb241731071a15faebc35353247861504c3eb60d90b5e20be3ee0d | Shell | 714 | 26 | #!/bin/bash
#SBATCH --partition=p_waksman_0
#SBATCH --job-name=featureCounts
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH --mem-per-cpu=5000
#SBATCH --time=12:00:00
#SBATCH --output=featurecount.slurm.%N.%j.out
#SBATCH --error=featurecount.slurm.%N.%j.err
#SBATCH --export=ALL
module purge
... |
b809c895ac420a2fd4534d8894bc17cb1bdd5a5b3efa651900d99abecf1a2cf6 | Shell | 720 | 39 | #!/bin/bash
COMMENT=" updated "
ONLYTEST=0
if [ $# -gt 0 ] ; then
COMMENT=$1
else
echo "USAGE: ./upload.sh <comment> <only_test>"
echo "if only_test is 1, then upload to only test"
exit
fi
if [ $# -gt 1 ] ; then
ONLYTEST=$2
fi
a=$((`awk -F= '{print $2}' version.py | sed "s/\s*'//g" | awk -F. '... |
9ea88b120116bbd0517b3d58557a966938f89ae9723e8d240ec2d447aafed394 | Shell | 725 | 22 | #!/bin/bash
in_dir=example_workspace
in_valid_bedpe=${in_dir}/example_valid.bedpe #Processed valid pairs in '.bedpe' format.
candidate_loops_bedpe=${in_dir}/example.bedpe #Candidate loops file(in 'bedpe' format) that need to be estimated.
out_prefix=example
cpu=16
python ./src/test_I.py -f ./${in_valid_bedpe}... |
b31b83cd2d17acdf7cca4f8204529ebb5c0a8218a303439176ae7adcebcb1550 | Shell | 725 | 27 | #!/bin/bash
# set the number of nodes
#SBATCH --nodes=1
# set max wallclock time
#SBATCH --time=4:00:00
# set name of job
#SBATCH --job-name=strf
# partition
#SBATCH --partition=short
# set gpu
#SBATCH --gres=gpu:1
# qos
#SBATCH --qos=standard
#SBATCH --account=ndcn-computational-neuroscience
# change the location of ... |
a86bf94766be84287c2ebd842d9466f3ec824d0e760a13cc7035ea72c071b5d3 | Shell | 726 | 24 | #!/bin/bash
WORKSPACE=$1
# Delete every Docker containers
# Must be run first because images are attached to containers
docker rm -f $(docker ps -a -q)
# Delete every Docker image
docker rmi -f $(docker images -q)
# get the docker
docker pull quay.io/hemberg-group/scrna-seq-datasets:latest
# run the docker
docker r... |
4f13dd79facc469e8677da7f4a06c84b66c40a94acf917c5c15fa255ca36b6be | Shell | 728 | 20 | #!/usr/bin/bash
if [ $# -lt 2 ]
then
echo "sh $0 <shell> <id>"
echo "### please use full path of run.blastn.sh and run $0 in the output directory ###"
exit 0
fi
shell=$1
id=$2
SHELL_FOLDER=$(dirname "$0")
Pwd=`pwd`
#faname=$(basename $fa)
source ${SHELL_FOLDER}/config.txt
cat ${shell} | awk -F ';' '{print $1" && ... |
766d5ad283a9f0da19695d915189c6f899768875c193f2580ea56b233d11dc21 | Shell | 735 | 23 | #!/bin/bash
datasets=("PNC" "NKI" "HCPD" "HBN")
measures=("GBC" "BNC" "WNC" "Edge")
script_dir="/cbica/projects/network_replication/manuscript/code/connectivity_measures"
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
# Loop through each dataset
for dataset in "${datasets[@]}"; do
# Loop ... |
b9c6ba63d3efb695cd0fc360fe4cc6bc37b98f0bd684ee452d2983570dc2bd58 | Shell | 739 | 16 | _vg_complete()
{
local cur prev
COMPREPLY=()
cur="${COMP_WORDS[COMP_CWORD]}"
opts="add align annotate augment autoindex bench-dist-query benchmark call chains chunk circularize clip cluster combine concat construct convert deconstruct depth describe dotplot filter find gamcompare gampcompare gamsort gbwt genoty... |
6e69b5b61dca6d0091082d40cb9ac2a28f37a4a8388e829a991d4ab7a35c1082 | Shell | 741 | 20 | #!/bin/bash
home_dir=$(pwd)
csv_dir='/cluster/scratch/lawrancn/csv'
find csv -empty -name "E12x12_${1}" | while read line; do
csv_file=$( basename "$line" | cut -c1-13 )
case=$( echo "$csv_file" | cut -c1-9 )
wind=$( echo "$csv_file" | cut -c12-13 | sed 's/^0*//' )
case_dir="/cluster/sc... |
d3bda564b32f0e51b4104f6ba0f8ce631b487fe8b4eb55e3cfdd1dfc6dad46b4 | Shell | 743 | 17 | # set up the project after cloneing
# Move templates to locations you need them to be
# This is saved for record keeping. To download the files please use command `make data``
#!/bin/bash
# mist
python scripts/mist2templateflow/mist2templateflow.py -d -o inputs/custome_templateflow
# difumo
python scripts/difumo_segm... |
9319811e5b96f1e6f58e66d3de39d763e7d68e13df8e17f0077d7247842f4e53 | Shell | 746 | 41 | #!/bin/sh
#
# Install Intan RHX build dependencies
#
set -e
set -x
export DEBIAN_FRONTEND=noninteractive
# update caches
apt-get update -qq
# install build essentials
apt-get install -yq \
eatmydata \
build-essential \
gcc \
g++
# package build essentials
eatmydata apt-get install -yq --no-install-r... |
f7fedae0c0b15204248ba5ae958f3bdadfb27382e7ccbb9081387135e59596d1 | Shell | 752 | 20 | GENCODE_VERSION=26
FILE="gencode.v${GENCODE_VERSION}lift37.annotation.gtf.gz"
ANNOURL="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_${GENCODE_VERSION}/GRCh37_mapping/${FILE}"
# Download the reference chromosomes and concat into single file
if [ ! -f hg37.fa ]
do
URL='ftp://hgdownload.cse.ucsc.edu/goldenPa... |
16609db34e1364a69513ace8a1037469c4257f066a2898f23938063eb4ec6f35 | Shell | 757 | 34 | #!/bin/bash
RUN_SCRIPT=$1
JOB_NAME=$2
function localRun {
if [[ $# -lt 2 ]] ; then
echo "localRun <from> <to>"
exit 1
fi
declare -i from=$1
declare -i to=$2
for ((currindex=${from}; currindex<=${to}; currindex++)) ; do
${RUN_SCRIPT} ${currindex}
done
}
function gridRun... |
7dd6b37db9524b05a8b1eaeb0d14d9c8d42fe94bcf6e49c6eb96e0c743364aa7 | Shell | 759 | 19 | export S3_BUCKET=${S3_BUCKET:="janelia-neuronbridge-data-devpre"}
export S3_DATA_VERSION=${S3_DATA_VERSION:="${DATA_VERSION//\./_}"}
export LOCAL_DATA_VERSION=${LOCAL_DATA_VERSION:="${DATA_VERSION}"}
export LOCAL_DATA_DIR=${LOCAL_DATA_DIR:="/nrs/neuronbridge/${LOCAL_DATA_VERSION}"}
export AWSRUNNER=${AWSRUNNER=echo}... |
ebf23de5b2410f70f4677fef3c579f3b1d6b812c2d13da43d87dcb36e8a24f54 | Shell | 761 | 27 | #!/bin/bash
inputdir="../data/"
gene2idfile=$inputdir"gene2ind.txt"
cell2idfile=$inputdir"cell2ind.txt"
drug2idfile=$inputdir"drug2ind.txt"
testdatafile=$inputdir"drugcell_test.txt"
mutationfile=$inputdir"cell2mutation.txt"
drugfile=$inputdir"drug2fingerprint.txt"
modelfile="../pretrained_model/drugcell_v1.pt"
resul... |
03bbadf94467aa8132e3d74532740421af8f5d7dc75a55103eca6799f85674d0 | Shell | 764 | 32 | # load the modules
module load gcc/4.8.5
module load boost/1.63.0
module load eigen
module load hdf5
# create the software directory
cd ~
mkdir software
cd software
# clone ompl and create the build directories
git clone https://github.com/ompl/ompl.git
cd ompl
git checkout 1.1.1
mkdir -p build/Release
cd build/Relea... |
1caae1ef0801ad832ea37ae8490868e5fc34648f6b2d0c2d7ce57388f25ec0f8 | Shell | 766 | 25 | #!/bin/bash
#SBATCH --job-name=munge_sumstats
#SBATCH --account=p33_norment
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
#SBATCH --array=0-400
set -o errexit
source ../settings.sh
source ${SOFTWARE}/ldsr/bin/activate
which python
GWAS_DIR=/cluster/projects/p33/users/elizabept/multimo... |
7e513218cca703284675f1430c6a46c496e0f4164a616058733f8d6cc4487830 | Shell | 768 | 18 | # parameter exploration settings
# select params
export run_on_hopper=0 # run from hopper's system
export hopper_run=1 # hopper run number
# Note: set number of vals in for statement {1..<count>} below
p1_v=(-60.0000 -42.5000 -25.0000 -7.5000 10.0000 27.5000 45.0000 62.5000 80.0000)
p2_v=(-64.5300 -63.0300 -61.5300 -... |
cd71c369e2979eec660cf6de18c5315cb94102256b45fb08be5ca890aaaa2578 | Shell | 768 | 18 | # parameter exploration settings
# select params
export run_on_hopper=0 # run from hopper's system
export hopper_run=1 # hopper run number
# Note: set number of vals in for statement {1..<count>} below
p1_v=(0.01 37.5000 75.0000 118.0000 150.0000 187.5000 225.0000 262.5000 300.0000)
p2_v=(-66.5300 -64.5300 -62.5300 -... |
5c1b633e6590438b8278463fab9b13e341665f1d18c74014500200e8a27fa62a | Shell | 771 | 32 | #!/bin/bash
what=$1
shift
IMAGE_NAME=ghcr.io/janeliascicomp/colormipsearch-tools:3.1.1
case $what in
--build-image-with-docker)
# Run this using `./build-docker-image.sh --load|--push`
docker buildx build --platform linux/arm64,linux/amd64 --tag ${IMAGE_NAME} . $*
;;
--build-local-podman-image)
echo "Cre... |
52604f60aa32558bdd74d8b33c4766866636dd6f21d6647f8103af1716ac27cb | Shell | 773 | 21 | #!/bin/bash
inputdir="../data/"
gene2idfile=$inputdir"gene2ind.txt"
cell2idfile=$inputdir"cell2ind.txt"
drug2idfile=$inputdir"drug2ind.txt"
traindatafile=$inputdir"drugcell_train.txt"
valdatafile=$inputdir"drugcell_val.txt"
ontfile=$inputdir"drugcell_ont.txt"
mutationfile=$inputdir"cell2mutation.txt"
drugfile=$inputdi... |
967887171c7f767deba7da77963fe2f0eff197ca402712456486fea0c54a0fa8 | Shell | 789 | 23 | #
# combine plot videos
#
# reference: https://trac.ffmpeg.org/wiki/Create%20a%20mosaic%20out%20of%20several%20input%20videos
#
ffmpeg \
-i firing_neuron_space.avi -i firing_physical_space.avi -i animal_postrack.avi -i animal_postrack_all.avi \
-filter_complex "
nullsrc=size=1700x1246 [base];
[0:v] setpts=PTS-S... |
0c869786bbeba331bf1f3e6b21d428a13744ceaedec8c4d79f7728468bcf0ad7 | Shell | 792 | 20 | #!/bin/bash
if [ "$#" -lt 2 ]
then
echo "Missing parameters"
exit
fi
SLIDE=$1
SAMPLE=$2
#python3 ../../reports/bin/sample_status.py --slide ${SLIDE}
python3 delete_cdm.py --verbose --manifold prod --version 3.7.2 --library FlyLight_Split-GAL4_Omnibus_Broad --accept --write --template JRC2018_Unisex_20x_HR --sampl... |
49a3e151e747a2cd19c5d22d3f419d89913e0920aee8799643bde1a3f9ec842d | Shell | 809 | 31 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# Function description
# Benchmark of HiChIP tools
#===============
# Running FitHiChIP tool
input_dir=$1
for data in $input_dir/*
do
bash /home/tangli/tools/FitHiChIP/FitHiChIP_HiCPro.sh -C /home/ta... |
e43df93bd3aa10a06edbb4ba323d3178eb16f395bc10eb47275a0ccfc60f16a1 | Shell | 814 | 13 | echo "Creating janelia-neuronbridge-published-stacks"
aws dynamodb create-table \
--table-name janelia-neuronbridge-published-stacks\
--attribute-definitions AttributeName=itemType,AttributeType=S \
--key-schema AttributeName=itemType,KeyType=HASH \
--billing-mode PAY_PER_REQUEST \
--tags Key=PROJEC... |
3625004003a146068d2367c7f20a9a497727fe5e34b16b6c2b88789f0cf3059c | Shell | 817 | 26 | # pre-install cpu-version of torch by default
# either use the 1st argument as specifier (cu118, cu124 or cu126)
python -m pip install --no-cache-dir torch torchvision --index-url https://download.pytorch.org/whl/${1:-cpu}
#parse dependencies
python -m pip install --no-cache-dir toml
dependencies=$(python -c "
import ... |
62db212657eea3d5314177d6ad5e10a4b6a990be10de4f680f3993d707d885f4 | Shell | 819 | 25 | #!/bin/bash
dry_run=false
LOCAL_DATA_DIR=v3.8.0-fixed-cns
AWS_DATA_DIR=3.8.0
bucket=janelia-neuronbridge-data-dev
nextflow run workflows/step9-upload.nf \
--dry_run ${dry_run} \
--upload_anatomical_areas brain+vnc \
--upload_type "EM_MIPS,LM_MIPS" \
--release_dirname ${LOCAL_DATA_D... |
57187779b040fac9f7db33a9642517e494feecc771c9955c0e6d0bac02980172 | Shell | 833 | 42 | max=`grep "Max Latencies" $1 | tr " " "\n" | sort -n | tail -1 | sed s/^0*//`
grep -v -e "^#" -e "^$" $1 | tr " " "\t" >histogram
cores=12
for i in `seq 1 $cores`
do
column=`expr $i + 1`
cut -f1,$column histogram >histogram$i
done
echo -n "set title \"Latency plot\"\n\
set terminal png\n\
set xlabel \"Latency (u... |
acace81e4be6eb863c9727c81516a55350bd3599e2627c774fa6895e0acb8a73 | Shell | 853 | 29 | #! /bin/bash
kshrinkDir=$1
trees=$2
nw_labels -I $trees | sort | uniq -c | sed "s/^[ ]*//g" > $kshrinkDir/species_occ.txt
#for x in $kshrinkDir/*.ratios; do
# echo $x
# base=$kshrinkDir/`basename $x .ratios`
# paste $x $base.removals | sed "s/k=.*://g" | tr -d "\t" > $base.ratio.RS
# get_species_max_val... |
3c070df46396bdc204295adec385b9cad4991f7f9f9be21652ed7c692bcff4f0 | Shell | 858 | 27 |
#This code has been adapted from the BOLT-LMM v2.3.5 User Manual available at: https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html
/home/BOLT-LMM_v2.3.5/bolt \
--bed=ukb_chr{1:22}.bed \
--bim=ukb_chr{1:22}.bim \
--fam=ukb_fam_file.fam \
--phenoFile=Phenotypes_BOLT.txt \
--phenoCol=... |
bba38abf5d3da1b822c434504472922f45aef889d6d3394aaacf9e4633e373d2 | Shell | 871 | 36 | localip=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')
xhost + $localip
FB_MODE_PARAM="-e DISPLAY=$localip:0"
if [ "$#" -ge 1 ]; then
DATA_FILE=$1
shift
else
DATA_FILE=JRC_SS04989-20160318_24_A3-f_40x.h5j
fi
LOCAL_DATA=local/testData
INPUT="/data/vncData/${DATA_FILE}"
OUTPUT="/data/vncOutput/... |
be015b42494830676c1c0a173a1ef22a02fc32298f95ab8f1f4ed2a19b874f0a | Shell | 874 | 33 | #!/usr/bin/env bash
# On CI, we want to cache deps/ and avoid rebuilding unmodified submodules, but
# we also want to make sure every build has the right source code for all the
# submodules.
#
# This script will start with the version of deps/ fetched from the cache, and
# put in place only the differing source files... |
f527363eb44b918059c481e27f2c99ef530b2f15daf13bf384e4781def4c1bd3 | Shell | 875 | 33 | #!/bin/bash
set -e
if [ -z "$1" ]; then
echo "Usage: $0 <number_of_neurons>"
exit 1
fi
EDEN_REPO_PATH=$(realpath ../eden)
THIS_PATH=$(realpath .)
NML_FILE=
export BUILD=release
rm -f matrix.txt nml2flexhh nml_projector model.json model.json_simhh sandbox/*
mkdir -p sandbox
sh -c "cd $EDEN_REPO_PATH && BUIL... |
cce8856d956fab9df4c55dfb82e6827a0c557b34497a90e96864a07c05b1b3ca | Shell | 879 | 33 | #!/bin/bash
# Run the nextflow workflows. Usage:
# ./run-workflows.sh -p <local|cluster> [-w <workdir>] [-n <nextflow exe>]
OPTIND=1 # Reset in case getopts has been used previously in the shell.
NEXTFLOW=nextflow
# Initialize our own variables:
while getopts "p:w:n:" opt; do
case "$opt" in
p) PROFILE=$OPTA... |
e28381deb7314440a9ab0d7312ae8eb15e3079bd5c748750acb9c036f490c7a9 | Shell | 881 | 48 | #!/bin/bash
SRC_DIR=""
DST_DIR=""
SCOUR_ARGS="--strip-xml-prolog --enable-viewboxing --enable-id-stripping --enable-comment-stripping --shorten-ids --no-line-breaks --strip-xml-space"
while [ $# != 0 ]; do
case "$1" in
-s) SRC_DIR=${2}
shift
shift
;;
-d) DST_DIR=${2}
shift
... |
3e7358584798363e7b236817b444d08d1b20886dbfaa4a2ea48f86dd41868a51 | Shell | 885 | 33 | #!/bin/sh
set -e
#
# This script is supposed to be run by the GitHub CI system.
#
if [ -z "$CI" ]; then
echo "Not in a CI build environment. This script should not be run manually!"
exit 1
fi
#
# Build Debian package
#
git_commit=$(git log --pretty="format:%h" -n1)
git_current_tag=$(git describe --abbrev=0 ... |
960d1ba4db3b61452a39850be9ae4d2f1a741cdbcfe6f90a0bf3b07d8f350bc4 | Shell | 886 | 6 | #!/bin/bash
#python inference/predict_simple.py -i /home/nykim/NeuroApexInput/snuh/post -o /home/nykim/NeuroApexOutput/mk4/snuh/post -t Task03_HELP_mk4 -tr nnUNetTrainer -m 3d_fullres -f all
#python inference/predict_simple.py -i /home/nykim/NeuroApexInput/snuh/pre -o /home/nykim/NeuroApexOutput/mk4/snuh/pre -t Task03_... |
05ca53d1f9329b5720f6904c5280b03d58a64e547a326cffbcf59acc8dc52904 | Shell | 899 | 33 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
d9269da0e118b903b690ab71633f638405167fb70154a465174d4d8c60a2c14c | Shell | 901 | 24 | for strategy in "top_down" "in_order";
do
for seed in 3435 3436 3437;
do
python rnng-pytorch/train.py \
--train_file rnng-pytorch/data/npcmj-train.json \
--val_file rnng-pytorch/data/npcmj-val.json \
--sp_model rnng-pytorch/data/npcmj-spm.model... |
1d820d8454cdb8a2b86d0c745fa4b90f57c58e59ab7699125e7038fed4c07a61 | Shell | 909 | 24 | #!/bin/bash
#
#batch job script for a typicall cellranger count run
#SBATCH --job-name=cellranger_count_HPKcd45_hp38
#SBATCH --partition=largemem
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --cpus-per-task=12
#SBATCH --mem-per-cpu=32GB
#SBATCH --error=job.err
#SBATCH --output=job.out
#SBATCH --mail-ty... |
2302cd00e65d96f4c4e438c962cba38826c01bcdc6fb2e43c394cf94d82ad13d | Shell | 911 | 30 | home_dir=$(pwd)
w=2
wind_delta=1
csv_dir="$home_dir/csv"
case_dir=$1
casename=$(basename "$case_dir")
python_directory="$home_dir/python"
reGrid_dir="../reGrid"
cd $home_dir
for (( w=$w; w<=15; w+=$wind_delta )); do
./reuse_wind_case -c "${case_dir}/W1" -v 1 -o "$case_dir" $w
if [ "$?" -eq 0 ]
then
... |
82bd7b495abfe67a845997fb649e73dcfb31d70e6edbebd99f145743c56557e5 | Shell | 919 | 23 | mkdir -p rnng-pytorch/outputs;
for strategy in "top_down" "in_order";
do
for seed in 3435 3436 3437;
do
for beam in 100 200 400 600 800 1000;
do
for unit in "A" "B" "C" "D";
do
word_beam=`expr ${beam} \/ 10`
fast_tra... |
647718d5b443233d29148758a23c6825447c5943e895ca114e253d7f8b3e8c3b | Shell | 923 | 32 | #!/bin/bash
set -euo pipefail
# update to use most recent genome release
s3_base=s3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-103
# run R in the scpca_r dockerfile
# docker pull ghcr.io/alexslemonade/scpca_r
# rdocker="docker run --mount type=bind,target=/home/rstudio,source=$PWD ghcr.io/alexslemonade/scpca-... |
dedcf6bb29ffc9d13369113b622b2b0f9179e3a9aaabd27a616eaa985cfe7275 | Shell | 925 | 8 | #!/bin/bash
s1r1='/cis/home/kstouff4/Documents/MeshRegistration/TestImages/MERFISH/cell_S1R1_mesh100.vtk'
s1r2='/cis/home/kstouff4/Documents/MeshRegistration/TestImages/MERFISH/cell_S1R2_mesh100.vtk'
s2r1='/cis/home/kstouff4/Documents/MeshRegistration/TestImages/MERFISH/cell_S2R1_mesh100.vtk'
s2r2='/cis/home/kstouff4/... |
7b21479f7a606e81f95feab27342c47e1155797e8af65e2b427411529fc38244 | Shell | 934 | 18 | #!/bin/bash
# run velocyto for the Wild-type data
# The input data for this analysis are available on Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) (see associated publication)
velocyto run --outputfolder RNAVelocity/DataObjects/Wildtype/ \
--samtools-threads 16 --samtools-memory 2000 \
--bcfile WT_barc... |
173f265611103a6443705182923a7a5cf7143376306638a86b0a850e796497f0 | Shell | 937 | 36 | #!/bin/bash
#SBATCH --job-name=workflow-NS-LDA-PCT
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --account=iacc_nbc
#SBATCH --qos=pq_nbc
#SBATCH --partition=IB_40C_512G
# Outputs ----------------------------------
#SBATCH --output=log/%x_%j.out
#SBATCH --error=log/%x_%j.err
# ------------------... |
737842688d101824f93d66104cb63d0141a490d29f27ea59bf99f3053bc3c9b3 | Shell | 937 | 24 | source /home/laura/anaconda3/etc/profile.d/conda.sh
conda activate bioinformatics
cd /media/laura/MyBook/ADNI-WGS
mkdir selected_variants
for i in {1..23}; do
echo chr$i
bcftools view --include ID=@/home/laura/Documents/CODE/APP_genetics/genetic_profiles/data/associated_variants.txt ADNI.808_indiv.minGQ_21.... |
6a45bc6fb5cf5f94d6830ff860da6f69b02d2d50d182c27f535205c0aabb4e0a | Shell | 939 | 19 | #!/bin/bash
echo "These scripts expect that you have run identify_stim_neurons.py"
full_array=(
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211128/pumpprobe_20211128_112504/
...and other folders
)
for folder in "${full_array[@]}"
do
echo ""
echo "##################"
echo "processing $folder"
... |
c39d9d6b59e0afff1de8a3b6a3e13a8f9603bf0fc40fea34ad290a1f82329de9 | Shell | 947 | 33 | mkdir -p agc1_OliNeu/data/salmon
cd data/salmon
curl -OL http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
cd ../../
# You need an environment with salmon installed, if you don't have it, run:
# conda create -n salmon -c bioconda salmon
conda activate salmon
salmo... |
7161301775540618b61a048ad2a3c7f233b508246b2edfe76610e1045f906898 | Shell | 949 | 33 | get_base ()
{
basename $1 | rev | cut -d. -f2- | rev
}
get_suffix ()
{
echo "$1" | rev | cut -d. -f1 | rev
}
config_path="$1_outdir/config.ini"
pred_partition=$(get_base $2);
pred_partition=$(get_suffix $pred_partition);
pred_partition="${pred_partition/_part/}"
#pred_partition=$(echo $pred_partition | sed 's/fit/... |
bf3c884085ec509b638537a745eae6717c35abdd8324a495a9bd294d67d7734c | Shell | 951 | 18 | for file in *-1_R1_Full_Normalized.bedGraph
do
base="${file%-1_R1_Full_Normalized.bedGraph}"
cut -d$'\t' -f4 $PWD/$base"-1_R1_Full_Normalized.bedGraph" > $PWD/$base"_1_Signal.bed"
cut -d$'\t' -f4 $PWD/$base"-2_R1_Full_Normalized.bedGraph" > $PWD/$base"_2_Signal.bed"
paste $PWD/$base"_1_Signal.bed" $PWD/$base"_2_Signal... |
ffa58c2c3e853749952a01e779c3801fa7e0dd7454e51b97a31b93edc84884f8 | Shell | 957 | 23 | #!/bin/bash
# Original works: https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd RAW;
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83139/suppl/GSE83139_tbx-v-f-norm-ntv-cpms.csv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83139/matrix/GSE83139-GPL11154_series_matrix.txt.gz
wg... |
b1cf8157707a53fbc7eea3c4328a43caae1dea7ec70934a4bd8087f3fa3a6d23 | Shell | 968 | 38 | #!/bin/bash
#SBATCH --job-name=uinv_gwas
#SBATCH --account=p33_norment
#SBATCH --time=36:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
#SBATCH --array=1-22
set -o errexit
source ../settings.sh
PHENO=$1 # a file in PHENO_DIR
COVAR=$2 # a file in COVAR_DIR
RES=$3 # prefix of a file to create in OUT_DIR
RO... |
511d67235cf1902d0d2cc235c644f2fd3f9480827919a18e0d6d70eb30624653 | Shell | 970 | 31 | #!/bin/bash
#SBATCH --job-name=metrics_highdem
#SBATCH --time=24:00:00
#SBATCH --account=rrg-pbellec
#SBATCH --output=logs/metrics_highdem.%a.out
#SBATCH --error=logs/metrics_highdem.%a.err
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --array=0-3
source /lustre03/project/6003287/${USER}/.virtualenvs/fmr... |
727ef072552d3fd397f8827d93ec15a3c36b2af623d937293a1b1b3461682dbb | Shell | 970 | 38 | #!/bin/bash
if [ $# -lt 5 ]; then
echo usage: $0 [ref] [num samples] [coverage] [readlength] [fragment length]
exit
fi
reference=$1
n=$2 # number of samples
coverage=$3
readlength=$4
mfl=$5
echo
echo generating test data
echo
answers=answers.vcf.gz
seed=$(od -An -N2 -i /dev/urandom)
mutatrix -s 0.05 -i 0.01... |
1c669731055a693c25bf11e3bb277d2b368047e6a664d92a9673e6d76008e17e | Shell | 977 | 30 | #!/bin/bash
# make connectivity matrices - rest only
datasets=("PNC" "HCPD" "HBN")
script_dir="/cbica/projects/network_replication/manuscript/code/connectivity_matrices"
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
# Loop through each dataset
for dataset in "${datasets[@]}"; do
qsub -l h... |
bded6fed5194e55e8a776f4adec9d7f19d4360c5ad4affc02fdf049ea053a54d | Shell | 981 | 12 | ### overlapped the repeatmasker result with ltr havest and using cd-hit to reduce redundancy
id=$1
fa=$2
SHELL_FOLDER=$(dirname "$0")
source ${SHELL_FOLDER}/config.txt
grep -v "#" ${fa}.ltr.gff | awk '$3=="long_terminal_repeat"' | awk '{gsub("Parent=","",$9);print $1"\t"$4-1"\t"$5"\t"$9"_D"2-NR%2"\t0\t+"}' > ${id}.ltr... |
3c146b8f73671b8917ae0d5c56a2e5eb1ff16809ece08f3bb0c32ab20c983385 | Shell | 982 | 37 | #!/bin/bash
#SBATCH --job-name=uinv_gwas_perm
#SBATCH --account=p33_norment
#SBATCH --time=36:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
#SBATCH --array=1-22
set -o errexit
source ../settings.sh
PHENO=$1 # a file in PHENO_DIR
COVAR=$2 # a file in COVAR_DIR
RES=$3 # prefix of a file to create in OUT_DI... |
a9b6a89f0d225ed2e5693402b975ff351519f780c7d1eb240960ee80649b548c | Shell | 992 | 27 | #!/bin/bash
JOB_TYPE=${JOB_TYPE:=ga-em-vs-lm}
export JOB_LOGPREFIX=${JOB_LOGPREFIX:=${LOGS_DIR}/${JOB_TYPE}}
export TOTAL_MASK_NEURONS=$((${TOTAL_MASK_NEURONS:=${MASKS_COUNT}}))
export START_MASK_NEURON_INDEX=$((${START_MASK_NEURON_INDEX:=0}))
export NEURONS_PER_JOB=$((${NEURONS_PER_JOB:=${MASKS_PER_JOB}}))
export T... |
a4ba136a3081075e8818335c81e9fb5ab5279c3fcf9ebae59812a19d8113b624 | Shell | 998 | 29 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 18:00:00
#SBATCH --job-name bcl2fastq
#SBATCH -o %j.out
#SBATCH -e %j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=ykbabal@gtu.edu.tr
module load gcc
module load bcl2fastq
bcl2fastq --use-bases-mask Y*,I8n*,I8n*,Y* \
--create-fastq-for-index-... |
50ebde0fc3c008575337b63f662c7368ccd90c5740676f026302d8b9a55f33a5 | Shell | 1,018 | 22 | PKG_NAME=mne-foo
PYTHON_NAME=mnefoo
GH_NAME=my_github_user
unameOut="$(uname -s)"
if [[ "${unameOut}" == "Linux" ]]; then
git grep -l 'mnetemplate' | xargs sed -i 's/mnetemplate/'"${PYTHON_NAME}"'/g'
git grep -l 'mne-template' | xargs sed -i 's/mne-template/'"${PKG_NAME}"'/g'
sed -i 's/mne-too... |
767ac74862b0f9e57d8ef1ed2317391c0975c27ea255b9fd9e321a9c9d5dbf00 | Shell | 1,022 | 49 | #!/bin/bash
#SBATCH --partition=p_waksman_0
#SBATCH --job-name=hisat2
#SBATCH --nodes=1
#SBATCH --ntasks=3
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4000
#SBATCH --time=12:00:00
#SBATCH --output=hisat2.slurm.%N.%j.out
#SBATCH --error=hisat2.slurm.%N.%j.err
#SBATCH --export=ALL
set -x
cd /scratch/hht25/gse101/tr... |
83013f08c5e07c8e6f00b2dc95a776483b2eee96cc9db7b7597b96a2324aac30 | Shell | 1,022 | 23 | # Note: The index commands require ~32G free memory -- more than we have on a
# desktop -- and Singularity can't mount Docker data volumes. Thus, we don't
# currently use this script. Instead, we copy the reference fasta to the
# cluster rather than getting it from the container. The Singularity command is:
# singular... |
743701bc87baf5f7bc01398eb9a6c8dbaf40b3ad5e484b11ad9c330856d0f36f | Shell | 1,029 | 35 | #!/bin/bash
#SBATCH --job-name=make_bfile_chunks
#SBATCH --account=p33_norment
#SBATCH --time=6:00:00
#SBATCH --mem-per-cpu=8GB
#SBATCH --cpus-per-task=1
#SBATCH --array=0-906
source /cluster/bin/jobsetup
module purge
source ${HOME}/.profile
source ${HOME}/cluster/bin/activate
module list
which plink2
which python
... |
581bf90e50a68e784a0ba7bb6cdfe92f29cef61940a2a38242be7fc06e226902 | Shell | 1,038 | 23 | #!/bin/bash
#HOMER motif analysis
# data generation for Fig3 c & d, S3 b & c
# all MEIS2 peaks, centered on peak summit (determined by MACS2)
# MEIS2, 200bp window, 6,8,10,12 bp motifs
nohup findMotifsGenome.pl ./meis2_e14_mm10_500bp_summit.bed mm10 ./HOMER/MEIS2_200bp_new -size 200 -len 6,8,10,12 > output.txt &
... |
401184dbf69efa3841fe86469cfbd0329662d510348732cfd975d20c67055f07 | Shell | 1,044 | 23 | # Note: The index commands require ~32G free memory -- more than we have on a
# desktop -- and Singularity can't mount Docker data volumes. Thus, we don't
# currently use this script. Instead, we copy the reference fasta to the
# cluster rather than getting it from the container. The Singularity command is:
# singular... |
7363559e137687259692435a21fc910104c1bf1c573034605ece8a69e6a41f05 | Shell | 1,045 | 24 | # Note: The index commands require ~32G free memory -- more than we have on a
# desktop -- and Singularity can't mount Docker data volumes. Thus, we don't
# currently use this script. Instead, we copy the reference fasta to the
# cluster rather than getting it from the container. The Singularity command is:
# singular... |
7162927eb0377de9a33c995fcb7c825323de8734f146b3910e592010706cbfa5 | Shell | 1,047 | 21 | # Note: The index commands require ~32G free memory -- more than we have on a
# desktop -- and Singularity can't mount Docker data volumes. Thus, we don't
# currently use this script. Instead, we copy the reference fasta to the
# cluster rather than getting it from the container. The Singularity command is:
# singular... |
b3e4a0fcb2b589e9ab1aa51670e5cfc59b36e9607fa48f50934805c032392af8 | Shell | 1,051 | 29 | LIBNAME=$1
JACS_LIB_DIR=/nrs/jacs/jacsData/filestore/system/ColorDepthMIPs
export LIBDIR=${LIBDIR:=${JACS_LIB_DIR}/${ALIGNMENT_SPACE}/${LIBNAME}}
export JACS_URL=${JACS_URL:="http://<host>/api/rest-v2"}
export JACS_AUTH_TYPE=${JACS_AUTH_TYPE:="APIKEY"}
export JACS_AUTH_TOKEN=${JACS_AUTH_TOKEN:="tokenvalue"}
if [[ -... |
0c94bb1246558b9b65c81a6d047eee6efee7c06ccbc1399e8805e2ecb03b86a6 | Shell | 1,056 | 31 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 18:00:00
#SBATCH --job-name bcl2fastq
#SBATCH -o %j.out
#SBATCH -e %j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=ykbabal@gtu.edu.tr
module load gcc
module load bcl2fastq
bcl2fastq --use-bases-mask Y*,I8n*,I8n*,Y* \
--minimum-trimmed-read-le... |
cf05eac85a3d9bbc1da705076cb9f2e89ca91e4e8e7306ec0d9aaf9d657383dd | Shell | 1,069 | 15 | # Mouse (adult & embryo), Human embryo, & human ipsc-derived dopaminergic neurons
# La Manno G, Gyllborg D, Codeluppi S, Nishimura K et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell 2016 Oct 6;167(2):566-580.e19. PMID: 27716510
# GSE76381
wget ftp://ftp.ncbi.nlm.nih.gov/geo/seri... |
e1c645e12ee7c5416097037beb48f86ec350a4205735f60e986aa0cd8e8993bd | Shell | 1,074 | 37 | #!/bin/bash
JAR_VERSION=3.1.0
ALIGNMENT_SPACE=JRC2018_VNC_Unisex_40x_DS
LIBNAME=flylight_split_gal4_published
AS_ARG=
LIB_ARG="-l flywire_fafb_783"
VALIDATED_SAMPLES_ARG=
APPLY_ERROR_TO_LMCDS="--apply-error-tag-to-lm-cdmatches"
APPLY_ERROR_TO_EMCDS="--apply-error-tag-to-em-cdmatches"
ERROR_TAG_ARG="--error-tag valid... |
2cfa025011128f612a3e1baf32e655215998fbd6ceb7ec7ee686ff6c21873934 | Shell | 1,078 | 44 | #!/bin/bash
SCRIPT_DIR="$(dirname "$0")"
CDSPARAMS=${CDSPARAMS:-${SCRIPT_DIR}/cdsparams.sh}
source ${SCRIPT_DIR}/cdsparams.sh
source ${CDSPARAMS}
export TOTAL_JOBS=$(((TOTAL_MIP_IDS - START_MIP_ID_INDEX) / MIP_IDS_PER_JOB))
function localRun {
if [[ $# -lt 2 ]] ; then
echo "localRun <from> <to>"
... |
b788026bf13f4828718f75bcbfe12581600219de8655cb6a370fbcab6355d56f | Shell | 1,096 | 27 | #!/bin/bash
#
#batch job script for a typicall spaceranger count run
#
#SBATCH --job-name=spaceranger_count_D4BX1R_ph38
#SBATCH --partition=largemem
#SBATCH --ntasks=1
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=64GB
#SBATCH --error=job.err
#SBATCH --output=job.out
#SBATCH --mail-t... |
2c41245658c6dd3481be611f1fa0e8255e817f93960efec9b725e0533a20ef79 | Shell | 1,106 | 33 | #!/bin/sh
# Fix Makefile in gui for Mac (add qrc_images lines)
if [ `grep -c 'qrc_us3_gui_images' Makefile` -eq 0 ]; then
# This Makefile is missing qrc_images: insert lines
# Count lines to 3 insertion points
LINE1=`sed -n '1,/^SOURCES/p' Makefile|wc -l`
LINE2=`sed -n '1,/^OBJECTS /p' Makefile|wc -l`... |
58dc1ab1e59c023858023b59e6d94dd983220625725ab0edbce448c7518b85ac | Shell | 1,107 | 16 | # param expoloration params
# select params
export paramexp_type=" \"iz\""; # choose iz (izhikevich) or tm (tsodyks-markram) parameters exploration
export fdr_prefix="param_explore_iz_" # folder name prefix
export local_run=1 # local run number
export run_on_hopper=1 # run from hopper's system
export use_hopper_data=... |
95e4c2d020ffe2275c5c3b90020e730f58d19c856c1b9f3df0ceb04fb8a0ec39 | Shell | 1,109 | 38 | #!/bin/bash
OUTPUT="inputs/denoise-metrics/"
echo "gordon333"
for ds in ds000030 ds000228; do
build_features inputs/giga_timeseries/${ds}/fmriprep-20.2.1lts/ \
${OUTPUT} \
--atlas gordon333 --dimension 333 --qc stringent --metric qcfc
done
echo "mist"
for N in 7 12 20 36 64 122 197 325 444 ROI; ... |
585e12b481f975196c7f4e47838779f53ebdc206602e15a19126f596c26b80a5 | Shell | 1,112 | 21 | #!/bin/bash
xNPZ='/cis/home/kstouff4/Documents/MeshRegistration/Particles/AllenAtlas10um/Sub_300-400_XnuX.npz'
pref='200-300'
znpz="/cis/home/kstouff4/Documents/MeshRegistration/Particles/AllenAtlas10um/Experiments/Sub_${pref}__0__optimalZnu_ZAllwC1.2_sig0.05_Nmax5000.0_Npart1000.0.npz"
python3 -c "import visualizeR... |
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