sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f7c2d0dda71f903baad3525e47c6966a58eab34cc24f4e035fa1eefe399b101a | Shell | 442 | 13 | #!/bin/bash
cd app
sudo dpkg -i veyon_1.1.0_amd64_NO_MASTER.deb
sudo veyon-cli config clear
sudo veyon-cli config import default.config
sudo veyon-cli config set Service/Autostart false
sudo veyon-cli config set Authentication/Method 1
sudo veyon-cli config set Master/ConfirmUnsafeActions true
sudo veyon-cli authkeys i... |
078358474b1b34daa64cfbf1e0215eccbc6fbe6e96e29c2655b967d694fe3edf | Shell | 443 | 24 | #!/bin/bash
# Siwei 13 Sept 2021
# count both total and unique reads of each .bam file
rm read_sum.txt
for eachfile in *.bam
do
echo $eachfile
printf "$eachfile\t" >> read_sum.txt
samtools view -@ 40 $eachfile | wc -l >> read_sum.txt
# move back to the end of the previous line
# echo -e '\e[1A'
# print a secon... |
c568e9291a28b97c9e1eba8798e612c62a09675738c82537f0d1a0a5e42cee0d | Shell | 444 | 19 | #!/bin/bash
# Siwei 04 Jul 2023
# move all BAM files of Het 10792832 to downsample folder
target_folder="downsample_100M"
mkdir -p $target_folder
het_list_file="General_rs10792832_het_list.list"
readarray -t het_file_names_array < $het_list_file
for ((i=0; i<${#het_file_names_array[@]}; i++ ))
do
echo ${het_file_... |
7cb84e23fcc6254f77e35b2645d28e424741214de81f83b02fa2e08a415f3c87 | Shell | 446 | 24 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
action () {
if (test $mode = 0) then
rm -f ../$1
fi
}
# only uninstall
for file in *.cpp *.h; do
action ${file}
done
if (test $1 = 1 || test $1 = 2) t... |
443216bc14b084e5bb393fa5b8fb900a13972e67b0f16dd06165480303ec193a | Shell | 448 | 14 | #!/bin/bash
set -e
# If HOST_UID/HOST_GID are set, ensure /output is owned by the host user
# then drop privileges and run the command as that user.
# This avoids output files being owned by root without requiring the user
# to pre-create the output directory.
if [ -n "${HOST_UID}" ] && [ -n "${HOST_GID}" ]; then
... |
49e106fb04cd3e4cceff653b063200ad1ab0a5b192fd5346661b353518d2e81d | Shell | 449 | 25 | #!/bin/bash
# Siwei 14 Feb 2018
# Siwei 22 Dec 2019
# Siwei 04 Jul 2023
# Genotype CLU
output_file_name=$1"_rs1532278_CLU_genotyping.txt"
date > $output_file_name
echo "All genomic coordinates are based on GRCh38p7." >> $output_file_name
for EACHFILE in *.bam
do
echo $EACHFILE >> $output_file_name
echo $EACHFI... |
67d011ebca0b7207f0fecde3368f9ca50fefad5631f9643514dae2bae3be42bb | Shell | 450 | 18 | #!/bin/bash
# Siwei 2 Jun 2021
# concacenate fastq files generated from two
# flow cells into one by a list,
# input file names from the first two columns,
# output files by the third column
# note use IFS= to preserve white space issue for fail-safe
while IFS=$'\t' read -r part_1 part_2 output_file; do
echo "$pa... |
cbe7097137fa607dca754c3815530abbd4c87832911c4dd7e7eaab1db4e23e76 | Shell | 451 | 23 | #!/bin/bash
source $HOME/.bashrc
source $HOME/.bash_profile
MATDIR=$1
RESOL=$2
BIN=$3
OUTDIR=$4
LIBID=$5
mkdir -p $OUTDIR
LIBIDs=(${LIBID})
for LIBNAME in "${LIBIDs[@]}"; do
# see this: https://unix.stackexchange.com/questions/426748/cat-a-very-large-number-of-files-together-in-correct-order
find $MATDIR/ -maxdep... |
0a348c25fa5383d59b8b2ee21200ac9d7b780ae2909139fb8380efab73cbb723 | Shell | 455 | 19 | #!/bin/bash
chr_num=$1
notebook_path="notebooks/wes/variant_annot/chr${chr_num}.ipynb"
dx login --token TOKEN
my_cmd="papermill chr${chr_num}.ipynb chr${chr_num}_out.ipynb"
dx run dxjupyterlab_spark_cluster \
-ifeature="HAIL-VEP" \
-icmd="$my_cmd" \
-iin="${notebook_path}" \
-iduration=120 \
... |
82e24ce27d240035203371658584050f3e1360cd50a5f46326e169f38d64dff3 | Shell | 455 | 25 | #!/usr/bin/env bash
set -e
set -o pipefail
err() { echo -e >&2 ERROR: $@\\n; }
die() { err $@; exit 1; }
SCRIPT_DIR=$(cd $(dirname $0) || exit 1; pwd)
cd $SCRIPT_DIR/../
if [ ! -d .git ]; then
die "Failed to locate the root of the current git-versioned project"
fi
SOURCE_SHA_REF=$(git rev-parse --short HEAD)
p... |
e8d08349f339c97caf5c0108b4ce3c388201ed0cdbd9c8aa416ecf5762b5705e | Shell | 455 | 15 | #!/bin/bash
# Run catch22 feature extraction over every test-data subdirectory.
# Each subdirectory of testData holds a set of .txt time-series files;
# outputs are written back alongside the inputs with an "_output" suffix.
testdir="$(dirname -- "$0")"
runner="${testdir}/../C/runAllTS.sh"
for dir in "${testdir}"/*/... |
4bb8158473b9513468c8beb024503412565809dda7ae59c99976095ba5d57386 | Shell | 456 | 10 | #!/usr/bin/env bash
echo -e "\n\nINSTALLING BRAVEHEART CSV FILES TO ~/braveheart\n"
currentdir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
echo -e "Current Directory = $currentdir\n"
mkdir -p ~/braveheart
cd $currentdir
mv *.csv ~/braveheart
echo -e "CSV FILE INSTALL COMPLETE!"
echo -n -e "\033... |
c98ae57a3df616a1cb1f7f8675d342b21dac06d7e4ab0361f3408c7fae5fdab3 | Shell | 456 | 27 | #!/bin/bash
# Siwei 10 May 2022
# use the improved method as in
# https://www.biorxiv.org/content/10.1101/496521v1
mkdir -p ldsc_peakset
for eachfile in *.bam
do
echo $eachfile
samtools index -@ 20 $eachfile
done
macs2 callpeak \
-t *.bam \
-f BAMPE \
-g 2.7e9 \
-q 0.05 \
--keep-dup all \
--... |
d671813a21f4c9f36371671d913d2b6dc0e42a8174f3c9e34b2a72082b359e52 | Shell | 458 | 10 | # cd to the main rosettafy directory (using a absolute path here...)
# alternatively, make sure this script is run from the main directory
cd /Users/sg/PycharmProjects/rosettafy
#for i in $(cat "pdb_files/KosciolekAndJones/ready_set_1.txt");
for i in $(cat "pdb_files/KosciolekAndJones/ready_set_4.txt");
do
echo "$i"... |
5febdbc7feb9e456f6201f1f10b023dacba87b4774a22f7503a5201c415f2864 | Shell | 459 | 14 | #!/bin/bash
#SBATCH --job-name=zip
#SBATCH --output=/data/p_02915/SPOT/logs/%x_%A_%a.out
#SBATCH --error=/data/p_02915/SPOT/logs/%x_%A_%a.err
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=16
#SBATCH --mem=500G
INPUT_DIR = "/data/p_02915/dhcp_derivatives_SPOT/HCP-D/hcp_surface"
OUTPUT_FILE = "/data/dept_transfer-3/hc... |
25d8d6c1be32d38db3e035484598814f1d17d0310224503577c93a4cf4cebe6e | Shell | 460 | 15 | # Source this file to setup running environment for CNRGH's cluster
hn=$(hostname)
if [[ ${hn#*.} =~ ^(cnrgh|cng)\.fr$ ]] ; then
echo "Purging modules"
module purge
echo "Loading required modules"
module load extenv/ibfj python/3.11
toolchain --for-python
module load mpi/openmpi/4.0.4
fi
[[ -d ... |
a765bab71716c868891ae494d49cd513825cde222ccb4df6d7a44161d6f3742a | Shell | 461 | 18 | #!/bin/bash
set -e
DOCSPATH="$( cd "$(dirname "$0")" ; pwd -P )"
echo "DOCSPATH:" $DOCSPATH
if python -c "import sphinx" &> /dev/null; then
echo 'Python requirements already present...'
else
echo 'Install python requirements...'
python3 -m pip install -r $DOCSPATH/requirements.txt
fi
set +e
make -C $DOCS... |
40acc18e338572cb01c3a4ad5413b24f944fd5a7be4a2ca0abe8428ac0c8613a | Shell | 463 | 27 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=4G,h_vmem=4G,h_fsize=100G
#$ -N read_twas
#$ -j y
#$ -o logs/read_twas.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
echo "Task id: ${SGE_TASK_ID}"
## ... |
1f077591b22ea8191e3a189c5e14f9446700028c8e38424ab7a5f90236b6cfbb | Shell | 465 | 17 | #!/bin/bash
echo "Activate <conda_env> conda environment ..."
export PYTHON_EXEC="$HOME/miniconda3/envs/<conda_env>/bin/python"
echo "Start experiments via slurm ..."
$PYTHON_EXEC -c "import exputils
exputils.start_experiments(directory='./experiments/',
start_scripts='run_experiment.py',
start_comman... |
44c79fc49ba7d6459ad0ffaf84060143b310a279e51696db45414e71219c6ce7 | Shell | 465 | 20 | #!/bin/bash
#
#this_work_dir=$1
this_scripts_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
dtn=`date +%Y%m%d.%N`
pwd="$(pwd)"
this_work_dir="/home/sespy/work/proteomics/jump-search"
echo "start (steps) $this_scripts_dir"
echo "pwd $pwd"
echo "this_scripts_dir $this_scripts_dir"
echo "this_work_dir $this_work... |
3c23c9effd398cc51bdd7d2c132ad72e9760c7758643066c5cee5aa2e6ef08bf | Shell | 466 | 18 | #!/bin/bash
case "$DCMQI_COMMAND" in
'itkimage2segimage')
echo "COMMAND: $DCMQI_COMMAND"
python3 -u itkimage2segimage.py
;;
'segimage2itkimage')
echo "COMMAND: $DCMQI_COMMAND"
python3 -u segimage2itkimage.py
;;
'tid1500writer')
echo "COMMAND: $DCMQI_COMMAND"
... |
6c28876c898c287cf099d9637c15be80fc87d6692a2a5992c2ee2ec99ae82dbc | Shell | 466 | 12 | # ----------------------------------------
# This just serves as an example for how
# to run the container by mounting folders
# and opening up a port (to use with)
# jupyterlab, for example.
# ----------------------------------------
docker run -u 0 \
-v /home/nzolman/projects/sindy-rl:/home/firedrake/sind... |
ab3d368be44c7dddf3965f6915dd0fbd8800c06f7e4f14db23f9136985f554a4 | Shell | 468 | 15 | #!/bin/bash
for cluster in *.tck # EDIT HERE
do
tckresample -endpoints $cluster ${cluster%%.tck}_endpoints.tck # EDIT HERE
tckconvert -scanner2voxel $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz ${cluster%%.tck}_endpoints.tck ${cluster%%.tck}_endpoints_[].txt
cat -v ${cluster%%.tck}_endpoints_???????.txt ... |
0b3ac0c09820bac12d4da31d138477d2face456c2441121f2cf76c5172c7108d | Shell | 469 | 25 | #!/bin/bash
# Siwei 14 Feb 2018
# Siwei 22 Dec 2019
# Siwei 04 Jul 2023
# Genotype PICALM rs10792832
output_file_name=$1"_rs10792832_PICALM_genotyping.txt"
date > $output_file_name
echo "All genomic coordinates are based on GRCh38p7." >> $output_file_name
for EACHFILE in *.bam
do
echo $EACHFILE >> $output_file_... |
3b3bf1c1f83c38a2979b7334f0f8052ce318807d4ea001bee18ffcbbf330bb56 | Shell | 469 | 29 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -N parse_star_junctions_nosub
#$ -cwd
#$ -V
#$ -l h_vmem=6G,tmem=6G,h_rt=24:00:00
#$ -pe smp 2
#$ -R y
# join stdout and stderr output
#$ -j y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME="run"
fi
FOLDER=submissions/$(date +"%Y... |
b41b881d49b1a7420f62c18a188c884be392ce28250f696cd9d974c32ee8547f | Shell | 470 | 24 | #!/bin/bash
#Script to perform alignment using mafft
#COPYRIGHT 2022
#Created by Mike Mwanga
#mikemwanga6@gmail.com
#SBATCH -J Mapping
#SBATCH -p batch
#SBATCH -n 5
#SBATCH --mem-per-cpu 8000
#SBATCH -o job.%j.out
#SBATCH -e job.%j.err
#SBATCH --mail-type=ALL
ali
module load mafft/7.475
mafft --auto --reorder --an... |
d8816a8c23bf46c4f41787b2c46ca3ae5c8fd7579765b799e7813fe63f7fe25a | Shell | 471 | 18 | #!/bin/bash -l
#SBATCH --account=proj85
#SBATCH --partition=prod
#SBATCH --nodes=40
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate hippocampus
module load... |
4427e3a532bc4af92ba3e52027a2345f86515ee568337db8a7fc0367549155be | Shell | 472 | 17 | #!/bin/bash
ENV_NAME="dockbiotic"
CURRENT_DIR=$(dirname "$(readlink -f "$0")")
MODELS_DIR=$CURRENT_DIR/../../saved_models
export DEEPCHEM_DATA_DIR="$CURRENT_DIR"/../../deepchem_data_dir
COMMAND="""
python $CURRENT_DIR/script.py \
--model_type attentive_fp \
--dataset stokes \
--mode regression \
--mo... |
b294aed5bc6e5ded1aa43f58d3ab3339171518f95fdc66658b4e140a9158e86b | Shell | 472 | 17 | #!/bin/bash
notebook_path="notebooks/bmi/14a_proteomics_protein_assoc.ipynb"
dx login --token TOKEN
my_cmd="pip install openpyxl statsmodels scikit-learn && papermill 14a_proteomics_protein_assoc.ipynb 14a_proteomics_protein_assoc_out.ipynb"
dx run dxjupyterlab \
-icmd="$my_cmd" \
-iin="${notebook_path}"... |
175bd64a0bdc07c2364367b4700ca194835d7088811edf8e78817acd1d6f211a | Shell | 474 | 26 | #!/bin/bash
#$ -cwd
#$ -l mem_free=20G,h_vmem=20G,h_fsize=100G
#$ -pe local 6
#$ -N process-hg19-gwas
#$ -j y
#$ -o logs/process-hg19-gwas_$JOB_ID.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: \${USER}"
echo "Job id: \${JOB_ID}"
echo "Job name: \${JOB_NAME}"
echo "Hostname: \${HOSTNAME}"... |
15fb92d499bf99a6abc65ca423fd77fdcde08feb8a60b8262acbbf0e7c548abe | Shell | 475 | 23 | #!/usr/bin/bash
DATA_NAME=oanet_data
FILE_NAME=$1
OUTPUT_NAME=$2
if [ ! -d download_data_$DATA_NAME ]; then
mkdir -p download_data_$DATA_NAME
fi
let CHUNK_START=$3
let CHUNK_END=$4
for ((i=CHUNK_START;i<=CHUNK_END;i++)); do
IDX=$(printf "%03d" $i)
URL=research.altizure.com/data/$DATA_NAME/$FILE_NAME.tar... |
2bbd4aabd428af5f6b40683ffba6a814f19ef61aa73d04d8932b11e33c960124 | Shell | 475 | 18 | #!/bin/bash -l
#SBATCH --account=proj85
#SBATCH --partition=prod
#SBATCH --nodes=40
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate hippocampus
module load... |
59d23d74bcbae15a819a053c23b317ed1ec92611fb4a2afa1ffc62dc6f486025 | Shell | 475 | 14 | #!/usr/bin/env bash
# Disable everything related to fusions to potentially avoid issue
# common_utilization <= producer_output_utilization
# export XLA_FLAGS=""
/usr/bin/env
jupytext --output ../docs/examples/execute_TI.ipynb AT_titanium_fused_training.md
cd ../docs/examples && papermill execute_TI.ipynb AT_titani... |
829950c7018d55d179b23f056a3b4d33c4d3a2db60ca05a3ab1c6501b77073c9 | Shell | 476 | 6 | echo "Starting download of ABC MERFISH data:"
mkdir -p abc_dataset
wget -P abc_dataset/ https://allen-brain-cell-atlas.s3-us-west-2.amazonaws.com/expression_matrices/MERFISH-C57BL6J-638850/20230830/C57BL6J-638850-log2.h5ad
echo "Started downloading metadata:"
wget -P abc_dataset/ https://allen-brain-cell-atlas.s3-us-... |
cfedfc8f0980e9d8997390c8c4bd81940aaa3fae7f20513c476f01deb962f599 | Shell | 476 | 18 | #!/bin/bash -l
#SBATCH --account=proj85
#SBATCH --partition=prod
#SBATCH --nodes=400
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate hippocampus
module loa... |
47361f909466c3de7c9ab30b04708e98484366dd69381cbcd012f1e7099012fb | Shell | 477 | 18 | #!/bin/bash -l
#SBATCH --account=proj85
#SBATCH --partition=prod
#SBATCH --nodes=40
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate hippocampus
module load... |
a0506f8c0917da69bc4d225ee204fd7a4f7bc1f71b025ee4111d78b51bfab87d | Shell | 478 | 25 | #! /bin/bash
# Siwei 26 Mar 2024
# convert the BAM files used to bigwig for GEO submission
mkdir -p bigWig
for eachfile in *.bam
do
echo $eachfile
samtools index -@ 20 $eachfile
bamCoverage \
--bam $eachfile \
-o "bigWig/"${eachfile/%.bam/.bw} \
-of bigwig \
-bs 50 \
--normalizeUsing None \
--effecti... |
d2034c92f327b68e9ca1f8fa4165bf0811826faeeeea6b3955a568ebfbb66445 | Shell | 479 | 16 | set -ex
for MODEL in char_rnn vae aae
do
for SEED in 1 2 3
do
mkdir -p checkpoints/$MODEL/$MODEL\_$SEED
python scripts/run.py \
--model $MODEL \
--data data \
--checkpoint_dir checkpoints/$MODEL/$MODEL\_$SEED \
--device cuda:$SEED \
--m... |
d66dc8cdbde8a1f2ccccbce2769a7a5d1f80fe08057234482ce1715774bcf847 | Shell | 479 | 28 | #!/bin/bash
#$ -cwd
#$ -l mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -pe local 4
#$ -N "build_bims_NAc_genes"
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
echo "Task id: ${SGE_TASK_ID}"
## Load... |
3d2916c8ecad57e26603d675f32294585a4e5c48fad61ece0a9c6642ea12392b | Shell | 481 | 14 | #!/bin/bash -x
#SBATCH --nodes=6
#SBATCH --ntasks-per-node=3
#SBATCH --cpus-per-task=1
#SBATCH --output=c-out.%j
#SBATCH --error=c-err.%j
#SBATCH --partition=debug
#SBATCH --distribution=cyclic:*:*
#SBATCH --hint=nomultithread
cd /home/cluster/imartin/tvb-cpp/projects/cmake-build-relwithdebinfo
./prepro_cluster --da... |
b41c58c89dbbf89f62c3b29c0c4a27f5281def2e571338ef0fcb4e0ee96293c6 | Shell | 482 | 18 | #!/bin/bash
# Siwei 2 Jun 2021
# concacenate fastq files generated from two
# flow cells into one by a list,
# input file names from the first two columns,
# output files by the third column
# note use IFS= to preserve white space issue for fail-safe
while IFS=$'\t' read -r part_1 part_2 output_file; do
echo "$pa... |
de003f81a055a2a9b7eadf26244b3b0fad2af45e34d0916c0c390d30c80d3751 | Shell | 483 | 14 | #!/usr/bin/env bash
# Disable everything related to fusions to potentially avoid issue
# common_utilization <= producer_output_utilization
# export XLA_FLAGS=""
export DATA_PATH="../../examples/data"
/usr/bin/env
jupytext --output ../docs/examples/execute.ipynb CG_alanine_dipeptide.md
cd ../docs/examples && paperm... |
5bba702885cf1c9b5dda438cea2d98998da99ba2bc7c86d8996f2b6d9d909ae3 | Shell | 484 | 12 | #!/bin/sh
set -e # Exit immediately if a command exits with a non-zero status
export PYTHONPATH="$PWD"
if [ -z "${DEV_FILES}" ]; then
# Production
exec uvicorn main:app --workers 4 --host 0.0.0.0 --port 8000 --root-path $APPLICATION_ROOT --access-log --use-colors --forwarded-allow-ips '*'
else
# Develop... |
13dc5db8abaf125513e6d95fc7d2996203337831929d5ced92b81d475950c673 | Shell | 486 | 27 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -N generate_twas_plots
#$ -j y
#$ -o logs/generate_twas_plots.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
echo "Task id... |
ef474b0ee5876f282893d0a13aa3be0ff5f0242cd7ebcc516b1d1d1d597a8863 | Shell | 490 | 9 | # USAGE example
#sh run_fMRIprep.sh run_fMRIprep_sbatch.slurm
###############################################################
export STUDY=/work/swglab/data/R61rtsz/analysis/proj_franci_selfref
which_sbatch=$1
# generates a job array containing n jobs. n is determined by counting up every first field of each line in ... |
71cb22f161746c67127ddd8b5b097b5a6ce3048b202023900e75aedc5045c04e | Shell | 491 | 23 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=12
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#S... |
c681222cf712936f29d5ba7272d748e2a80c0f6908824bea362b45510e5b8972 | Shell | 491 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=14
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#S... |
df7e876388b3d523d76be2687b1f1d4e251bd38b280f7430fd4ffdb0e80b8527 | Shell | 492 | 27 | #!/bin/bash
# Siwei 14 Feb 2018
# Siwei 22 Dec 2019
# Siwei 04 Jul 2023
# Genotype PICALM rs10792832
output_file_name=$1"_rs2027349_VPS45_genotyping.txt"
date > $output_file_name
echo "All genomic coordinates are based on GRCh38p7." >> $output_file_name
for EACHFILE in *.bam
do
echo $EACHFILE >> $output_file_na... |
4f1be395e54e1f9d59f98860f61429f75df61221cf40004ad886497cd62e9ebf | Shell | 494 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=12
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#S... |
0f111f28482237cd799c3e52b6e5011840c944a758938283ff7e24a56896e9a2 | Shell | 495 | 13 | #!/bin/bash
# File: buildExtLib.sh
# SPDX-License-Identifier: GPL-3.0
# This file is part of NetInf (https://github.com/neuro8000/NetInf),
# developed by Peter M. Rasmussen, Aarhus University, Denmark.
# It is distributed under the terms of the GNU General Public License v3.0.
# See the LICENSE file or https://www.gnu.... |
467757283b43ee2856750769792f3238700570ed8482520966d5af5e44d6d614 | Shell | 497 | 12 | set -e
module load R/4.0.3 bedtools2/2.27.0
read introns_out_bed intron_size_thrs genes exons <<< "$@"
while read line;
do
gid=$(echo -e $line | awk '{print($4)}')
bedtools subtract -s -a <(echo -e "$line") -b <(grep "$gid" "$exons")
done < <(cat $genes) | bedtools sort | bedtools merge -s -c 4,5,6 -o distinct 1... |
8aed55f563c87d3bc15b981848f7a4d2f263867842abe87bc0e29bd193db15b4 | Shell | 497 | 13 | #!/bin/bash
./venv/bin/python ./LFCNN_decoder.py -cmb "RI" "RM" "LI" "LM"
# ./venv/bin/python ./LFCNN_concatenated.py -cmb "RI" "RM" "LI" "LM"
# ./venv/bin/python ./LFCNN_decoder.py -cmb "RI RM" "LI LM"
# ./venv/bin/python ./LFCNN_concatenated.py -cmb "RI RM" "LI LM"
# ./venv/bin/python ./LFCNN_decoder.py -cmb "LI" ... |
ec7deede4461a6de4f1163dd5c00f7608f8aa689e02fa0126e7b528e86e51283 | Shell | 497 | 9 |
nanopolish eventalign --reads control_1.fastq--bam sort_dmel-all-transcript-r6.43_control_1_Nanopore.bam --genome dmel-all-transcript-r6.43.fa --scale-events --signal-index --summary summary.txt --threads 50 > /path/to/control1_eventalign.txt
m6anet dataprep --eventalign /path/to/m6anet/m6anet/tes... |
3c7c5b33e21d66cf777836345509454b6e82a03d9c6a1ed55ffb360de4a78505 | Shell | 499 | 14 | ## This script will copy all quantification files from their MCMICRO subfolders into one central folder for easy downstream analysis
project_dir="Melanoma_Brain_Metastasis"
main_mcmicro_folder="$project_dir/mcmicro"
quant_folder="$project_dir/mcmicro_quants"
for FILE in $main_mcmicro_folder/*
do
if [ ! -f $quan... |
68a524712cc1e326c43e12984163796f7f9bb29436675fcaf5c7a334e5105faa | Shell | 500 | 26 | #!/bin/bash
set -e
# activate the metl-sim environment
. env/bin/activate
# change directories to the root (metl-sim)
cd ../..
# Read parameters from command line arguments
ROSETTA_MAIN_DIR=$1
PDB_FN=$2
RELAX_NSTRUCT=$3
OUT_DIR_BASE=$4
CONDA_PACK_ENV=$5
# Run the Python script with the specified parameters
python... |
6f6152a1c31b6822c5661d7b5fe0a033ad1726929720ec4a8c5c1cd7c8798279 | Shell | 500 | 4 | #get name synonyms for FBte IDs in flybase_fbte.txt
for i in `cut -f1 flybase_fbte.txt`; do
echo "SELECT distinct f.uniquename, f.name, s.name FROM cvterm cvt, feature f, feature_synonym fs, synonym s WHERE f.feature_id = fs.feature_id AND fs.synonym_id = s.synonym_id AND s.type_id = cvt.cvterm_id AND cvt.name = 'full... |
fb74f095e2dfa0de414590223ce524406dc9036291033c6f62c2fd5bc4684d67 | Shell | 501 | 19 | # Train models later evaluated in papers
# Large model ~ VAE 128
train () {
rm -rf /data/cache
rm -rf $HOME/cache/
python3 -m scripts.train_model +dataset=alpha_multiscene ++dataset.root_folder="/data/local/worldfloods_change_no_duplicates/train" \
+normalisation=log_scale +channels=high_res +trai... |
4bc2baca990296f97e1836129d2c70c6511838f6182a21a457371e6972a401cf | Shell | 502 | 32 | #!/bin/bash
function mean_seed_map {
seed=$1
seed_name=$(basename $seed .nii.gz)
echo $seed_name
fslmerge -t ${seed_name}_4D.nii.gz $PWD/subject_maps/*${seed_name}_z.nii.gz
fslmaths ${seed_name}_4D.nii.gz -Tmean $PWD/mean_seed_maps/${seed_name}_mean
rm ${seed_name}_4D.nii.gz
}
export... |
536a5c2f4924b98a9104c14e743a86b293845889cd80e134c74f7c3f83634fb2 | Shell | 502 | 21 | #!/bin/bash
for c in 1
do
for L in 81
do
for l_l in 0.1
do
for l_z in 0.001
do
for l_r in 1.0
do
for l_a in 1.0
do
python train.py -c config.json --L $L --l_l $l_l --l_z $l_z ... |
aa601d5f849b0b6bcb59db5f2f8f3f3010cd98c75f9f3665d6b0833973fef660 | Shell | 502 | 4 | #get symbol synonyms for FBte IDs in flybase_fbte.txt
for i in `cut -f1 flybase_fbte.txt`; do
echo "SELECT distinct f.uniquename, f.name, s.name FROM cvterm cvt, feature f, feature_synonym fs, synonym s WHERE f.feature_id = fs.feature_id AND fs.synonym_id = s.synonym_id AND s.type_id = cvt.cvterm_id AND cvt.name = 'sy... |
a1ca4500d87b5a50821517d752b1776abcd741bf2b171d44100d090bb853ad71 | Shell | 503 | 22 | #!/bin/bash
subj_ids=$1
ses=2YearFollowUpYArm1 #2YearFollowUpYArm1 #baselineYear1Arm1
count_start=0
if [ -z "$1" ]; then
echo
echo "Error: Missing list. Provide subject list w 'sub-' prefix in positon 1."
echo
exit 1
fi
n=${count_start}
cat $subj_ids | while read line ; do
subj=$(echo $line | awk -F" " '{ print... |
d9c49705eee0979d72b06d40382f9f14f7b3c79912ddc71bed5df0275b0b13fe | Shell | 503 | 21 | #!/bin/sh
set -x
CMD=""
if [ -n "$MAX_QUERY_SIZE" ]; then
CMD="$CMD --max-query-size $MAX_QUERY_SIZE"
fi
if [ -n "$START_DATE" ]; then
CMD="$CMD --start-date $START_DATE"
fi
if [ -n "$END_DATE" ]; then
CMD="$CMD --end-date $END_DATE"
fi
mkdir -p /$WORKFLOW_DIR/$BATCH_NAME/query/$OPERATOR_OUT_DIR/
CMD... |
f175ecb8d893f3107b2b0653d88900d87c4a81b9e85cbba5d51ba3e7223c8a79 | Shell | 503 | 12 | #!/usr/bin/env bash
# Reproduce every simulation-based panel. Population runs (N = 3000) take
# 5-10 min each; the whole script needs ~1-2 h on a laptop. Results are cached
# in cache/ so re-running only re-plots. Add --quick for a fast smoke test.
set -e
cd "$(dirname "$0")/scripts"
python fig2_single_neuron.py "$@"
p... |
6c913f6adbf7f80653c4a76b9660a77d69428eb46d2134fcc181eed2a6b69d3c | Shell | 504 | 18 | #!/bin/bash -l
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --nodes=400
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate neurodamus
module load ... |
bc53fc2baf82e7f86ed01570df2c1ee7b69a8c1a17b80cb60b96038c7bb931f2 | Shell | 504 | 34 | #!/bin/bash
# Kokkos
if [ ! -d "kokkos" ]; then
git clone https://github.com/kokkos/kokkos
fi
cd kokkos
git checkout develop
git pull
cd ..
# KokkosKernels
if [ ! -d "kokkos-kernels" ]; then
git clone https://github.com/kokkos/kokkos-kernels
fi
cd kokkos-kernels
git pull
cd ..
# MiniMD
if [ ! -d "miniMD" ]; then
... |
c2a22b7b433aaa4e0419cd1907941d5b16891943342521f170657aef1cf265b4 | Shell | 504 | 22 | #!/usr/bin/bash
#SBATCH --job-name=gnnenrich
#SBATCH --mail-type=END,FAIL
#SBATCH --mem=32000MB
#SBATCH --time=10:00:00
#SBATCH --output=gnnenrich_%j.log
#N=${1:-10}
N=100000
pwd; hostname; date
# Setup environment
source setup_env.sh
mpirun --tag-output python demo.py -vv -n "$N" -d \
"./databases" -w "./wrk1" -... |
3f9144047f8d96941a842e39f30c243097e220f8063fbf4b27ce6a71a39d3020 | Shell | 506 | 17 | #!/bin/bash -l
#SBATCH --account=proj83
#SBATCH --partition=prod_small
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=2:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate neurodamus
module loa... |
d6000d69e6fcfda2f6bd2513c16c8fac9c595fa1634c80b044543b9a2f10240e | Shell | 508 | 17 | #!/bin/bash
# Converts dicom images in current folder to NIFTIs using dcm2niix. The dicom
# images are assumed to have the signature 001_0%s_0%p. The converted images
# are stored in a subfolder called "converted".
# Get the current directory
input_folder=$(pwd)
# Define the subdirectory
output_folder="${input_folde... |
4addbd5b2d282ee5e442581e3a2bb09b102c37ac7e3d700ebb9b4ea582532595 | Shell | 509 | 18 | #!/usr/bin/bash
# Example script for generating contact information.
get_dynamic_contacts.py \
--topology 5xnd_topology.pdb \
--trajectory 5xnd_trajectory.dcd \
--ligand "CA" \
--itypes all \
--output 5xnd_all-contacts.tsv
get_contact_trace.py \
--input_contacts 5xnd_all-contacts.tsv \
--interactions ... |
7518f6ea990dd03025a3d8ac8e00b556bf126274fa60b8713a122f02cf804f43 | Shell | 509 | 18 | #!/bin/bash
#SBATCH --mem=50G # 请求 50GB 内存
#SBATCH --job-name=letsgo
#SBATCH --ntasks=28
#SBATCH --time=24:00:00 # 最大运行时间
#SBATCH --partition=normal
#SBATCH --output=/scratch/groups/yyanmin/zongmingnew2/NeuronTransportIGA/nsvms_src/letsgo_$
#SBATCH --error=/scratch/groups/yyanmin/zongmingnew2/NeuronTransportIGA/nsvm... |
ae574a18554279fd88b6b659bc75ceccff1691db77774f620cb3da26b257e64b | Shell | 510 | 16 | #!/usr/bin/env bash
set -xe
SIMDIR=$1
CONFIG_FILE=${2:-BlueConfig}
mpi_launcher=${3}
#srun --pty python -m pdb $NEURODAMUS_PYTHON/init.py --configFile=${SIMDIR}/BlueConfig --verbose
$mpi_launcher neurodamus ${SIMDIR}/${CONFIG_FILE} --verbose
if [ -d "${SIMDIR}/results/" ]; then
sort -n -k1,1 -k2 < output/out.dat >... |
0a4be1cf96495660353c9dd21f2be3ee5264d39537fdb079ab6bd62514c8e080 | Shell | 515 | 24 | #!/bin/bash
# Set variables from external file
source batch_run_parameters.txt
# Compile simulation script and run batch of simulations
if g++ -o ./spatial_ecDNA_patterns_2D ./spatial_ecDNA_patterns_2D.cpp
then
for k in $all_k
do
for s in $all_s
do
for q in $all_q
do
printf "Running %s simulations wit... |
11b38e030deca1f2b5cb6aa725c287b7605fc25a7f9b9c0cebabaa125a313181 | Shell | 515 | 19 | export TMPDIR='/home/user/temp' #Adjust this path to your temporary directory
output_dir='./results' #Adjust this path to your output directory
#Running the command
python3 ../peka.py \
-i './inputs/K562-TIA1-chr20.xl_peaks.bed.gz' \
-x './inputs/K562-TIA1-chr20.xl.bed.gz' \
-g './inputs/GRCh38.p12.genome.masked.fa' \... |
7388f171fcabfd2821172462541d3791743d716bbb7fa69d3755823af16b5630 | Shell | 516 | 19 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --exc... |
10cd91ac35d6e5029e164ae9d6ebfd51ac7ecef374277cd39820ec7a524a916b | Shell | 518 | 25 | #!/usr/bin/env bash
# Check status of Slurm job
jobid="$1"
if [[ "$jobid" == Submitted ]]
then
echo smk-simple-slurm: Invalid job ID: "$jobid" >&2
echo smk-simple-slurm: Did you remember to add the flag --parsable to your sbatch call? >&2
exit 1
fi
output=`sacct -j "$jobid" --format State --noheader | head -n... |
a76bb0b4edcfe2de2380f1bce8de9c7ed7b4b2376e730683d6a7b44a49dc63c8 | Shell | 519 | 18 | ##!/usr/bin/env bash
## This script loops through all scaffolds in the dunnart genome and
## generates a separate RepeatMasker command for each scaffold
## These commands are then used in a slurm array script to run jobs in parallel
TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
echo ${TRA[@]}
for t... |
6887b1310358f656c010d85ddce3853fd0c30e47b75f064e4030cb1a7dfe036d | Shell | 520 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=12
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#... |
721d22bc9b569990166fe16a5956b8a511957fc56570fe263b71404663472436 | Shell | 520 | 34 | #!/usr/bin/env bash
set -e
SRC=$1
BUILD=$2
CPUS=$(nproc)
mkdir -p $BUILD
cd $BUILD
cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=/usr -DLTO=ON $SRC
echo Building on $CPUS CPUs
if [ -z "$3" ] ; then
make -j$CPUS
fakeroot make package
LIBDIR=$(grep VEYON_LIB_DIR CMakeCache.txt |cut -d "=" -f2)... |
d1c534e4f631d5b5b1dd4625d1f1f4fea668b36e14a3e091c2024c67a45d7b3b | Shell | 521 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=14
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#... |
f1644b31fd50cf0b37a0b81358aa0aab941fb6a087f956be7cb31353932d83e2 | Shell | 521 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=2
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#SB... |
3661e944ef429dc3a8c7edc35f2a47f4a75b5abe01358dfc5fc0ba16124ceb8c | Shell | 522 | 21 | #!/bin/bash
notebook_path="notebooks/wes/sample_qc/sample_qc.ipynb"
dx login --token TOKEN
my_cmd="pip install gnomad && papermill sample_qc.ipynb sample_qc_out.ipynb"
dx run dxjupyterlab_spark_cluster \
-ifeature="HAIL" \
-icmd="$my_cmd" \
-iin="${notebook_path}" \
-iduration=600 \
--destina... |
01ab60ebb80075990b95d4a3ca62fef91ac488798767b6412ab3279e7ea50dea | Shell | 523 | 25 | #!/usr/bin/bash
#SBATCH --job-name=gnnenrich
#SBATCH --mail-type=END,FAIL
#SBATCH -N 1-1
#SBATCH -n 12
#SBATCH --mem=32000MB
#SBATCH --time=10:00:00
#SBATCH --output=gnnenrich_%j.log
N=${1:-10}
pwd; hostname; date
# Setup environment
source setup_env.sh
fg_sar start GNN_ENRICH
srun python demo.py -vv -n "$N" \
-d... |
1ac609608cacaf37fdff965ed6a266c04238db7d0fb1cf71da9ed1ea5126b279 | Shell | 524 | 18 | #!/bin/bash -l
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --nodes=40
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate neurodamus
module load u... |
51bc6cd2bb27b937794fdbe1e620938ae84b31f16633f54d0586228ca0b34848 | Shell | 525 | 6 | export MYBASEDIR="$HOME"
export ISF_HOME=$MYBASEDIR/project_src/in_silico_framework
alias source_isf='source $MYBASEDIR/anaconda_isf2.7/bin/activate; export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH; cd $MYBASEDIR'
alias source_3='source $MYBASEDIR/anaconda_isf3.8/bin/activate; export LD_LIBRARY_PATH=$CONDA_PR... |
e9e2e66a2234a9b64e97a93f3cd7f44c2aeb8e088cf3394ee22d8b776c8281d6 | Shell | 525 | 18 | #!/bin/bash -l
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --nodes=400
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=24:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate neurodamus
module load ... |
1c6567c93a8340b773bfa92da97c050f0e88eb5b6c43311ef1ee891820cc0e15 | Shell | 526 | 23 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
#SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
#SB... |
3d8b60dba99802bc56074e8d4b4ea828cda3c3d3809acea7f87dedfe406e46de | Shell | 526 | 13 | #!/bin/bash
source ~/00envs/anaconda3/bin/activate /work/home/sdxgroup01/00envs/anaconda3/envs/sc_cellchat
wpath='~/Cellchat'
rdspath='~/rds_label_add'
IFS=$'\n'
files=$(find ~/rds_label_add -name "*.rds" -exec basename -s .rds {} \;)
for i in ${files}
do
opath="${wpath}/output/$i" && mkdir -p "${opath}"
sbat... |
55462720229a2a342ee78d07d424256aab5db1294a575eb8d05fbf1590820c23 | Shell | 526 | 26 | #!/bin/bash
source $HOME/.bashrc
source $HOME/.bash_profile
MATDIR=$1
BIN=$2
LIBID=$3
BINNAME=`expr $BIN \* 2`
LIBIDs=(${LIBID})
COUNT=0
## create output file
OUTFILE=$MATDIR/all_sparse_matrices_${BIN}.txt
touch $OUTFILE
## add to output file
for LIBNAME in "${LIBIDs[@]}"; do
awk -v count="$COUNT" '{print ($1+cou... |
28a2a96bb1fa9bf32d964ae60d1f88e9c3234dc737ab5f27eb3e076602c3ffd0 | Shell | 527 | 16 | # --- Might need to sudo bash run this script
# This script downloads the main datasets for our experiments
# from the google bucket
mkdir -p /data/local
# for alpha_multiscene
gsutil -m cp -r gs://fdl-ml-payload/worldfloods_change_no_duplicates /data/local/.
# for alpha_singlescene
gsutil -m cp -r gs://fdl-ml-pay... |
86c23265178b39b6667a7073f7caf9b0292b9ef2f673713ff91258f677f85f2c | Shell | 527 | 17 | #!/bin/bash -l
#SBATCH --account=proj83
#SBATCH --partition=prod_small
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=0
#SBATCH --constraint=cpu
#SBATCH --exclusive
#SBATCH --time=2:00:00
#SBATCH --job-name=CortexNrdmsPySim
# SPDX-License-Identifier: GPL-3.0-or-later
spack env activate neurodamus
module loa... |
4d1365dbe2b8024c74a4d863f623d1a93d6dbd20ce99615c18c409e85ce454dd | Shell | 528 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=12
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#... |
4ddd98ed21be5533c3fcf13c21b1df60d36bfd77ef48a49bcdedcc564c1c621f | Shell | 528 | 15 | #!/bin/bash
echo User: "$(id -un "$USER")" && echo Group: "$(id -gn "$USER")" &&
. "$FSLDIR/etc/fslconf/fsl.sh" &&
export && \
echo "SHELL: $SHELL" && \
echo "PATH: $PATH" && \
. activate "${CONDA_ENV}" &&
xvfb-run -s "-screen 0 900x900x24 -ac +extension GLX -noreset" \
-a coverage run --rcfile="/app/.coveragerc" \
/ap... |
0089ff7f9d172c7b0f196fdf5ed2432eb76dab107d214d9cb444c51dca1b60dd | Shell | 530 | 19 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --exc... |
85e1bd3423258e679917f64cb71f29b5491b3bb147433ff273290b7a850c860d | Shell | 530 | 30 | #! /bin/bash
# Siwei 19 May 2021
mkdir merged
## list all .bam files
shopt -s nullglob
bam_array=(*.bam)
echo "${bam_array[@]}"
date
echo "merging..."
samtools merge \
-l 9 -@ 40 -f \
-h ../DN-19_S11_WASPed.bam \
merged/merged_unsorted.bam \
${bam_array[@]}
# samtools index -@ 40 merged/merged_unsorted.bam
da... |
ebaed09de555e3186ec191e76a9a38cef53cb27a22d8380936c7b055a16b8d6f | Shell | 530 | 19 | #!/bin/bash
chr_num=$1
notebook_path="notebooks/wes/variant_qc/0_initial_variant_qc_chr${chr_num}.ipynb"
dx login --token TOKEN
my_cmd="pip install gnomad && papermill 0_initial_variant_qc_chr${chr_num}.ipynb 0_initial_variant_qc_chr${chr_num}_out.ipynb"
dx run dxjupyterlab_spark_cluster \
-ifeature="HAIL" \... |
f6f69c11bec27afb4d4d6891c0369ee4f249072f97fbbfc8d1aec314df834da3 | Shell | 533 | 13 | #!/bin/bash
#SBATCH --job-name=noise_injection
#SBATCH --output=/data/p_02915/SPOT/logs/%x_%A_%a.out
#SBATCH --error=/data/p_02915/SPOT/logs/%x_%A_%a.err
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=16
#SBATCH --mem=900G
#SBATCH --array=1-228:2
/data/u_yoos_software/miniforge3/envs/SPOT/bin/python /data/p_02915/SPO... |
27b41a0f5a46272f18ccd36adeeaeb12fc5c827496f05b0128f82058e6692d30 | Shell | 534 | 15 | #!/bin/sh
set -e # Exit immediately if a command exits with a non-zero status
export PYTHONPATH="$PWD"
APPLICATION_ROOT="/aii"
python3 alembic/migrate.py
if [ -z "${DEV_FILES}" ]; then
# Production
exec uvicorn app.main:app --workers $WORKERS --host 0.0.0.0 --port $PORT --root-path $APPLICATION_ROOT --acce... |
63240398dc18588e2e0abc79b0928ea82a369701fc0293e142fea2bcd29c3d19 | Shell | 537 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=2
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#SB... |
683df178bce153e94478bb4a5b0706acfbe0fdfe4684465ece289e208a629807 | Shell | 538 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=2
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#SB... |
0b4d15ace9010c826379311a8a65f3b188c01f4d0232a37fb35b1ecfb9aadb4e | Shell | 539 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=10
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#... |
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