sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6c39bc54184ff5eb1636e5e3e6296a7e7a77725295b210e4d5706667f681acfc | Shell | 539 | 5 |
fslswapdim $STUDY_DIR/derivatives/$subj/rest/001/f_st_mc_regout_bp_m_2MNI.nii.gz x -z y $STUDY_DIR/derivatives/$subj/rest/001/f_st_mc_regout_bp_m_2MNI_LIA.nii.gz
fslroi $STUDY_DIR/derivatives/$subj/rest/001/f_st_mc_regout_bp_m_2MNI_LIA.nii.gz $STUDY_DIR/derivatives/$subj/rest/001/f_st_mc_regout_bp_m_2MNI_LIA_crop.nii... |
9e78ccc4ea5d907d311cd79234faea0d734b725c51f17eaa4a80207b0e538d72 | 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=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... |
cc791828230575c914365ab26d10bd629eca260d45a1dcf7879c933fb9679c16 | Shell | 539 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=20
#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... |
fac1e786a104fae83eda27cdd059087bca9c7eed2f6ec8aeb5612dd4a16e3e32 | Shell | 539 | 23 | #!/bin/bash
set -e -u
TEST_CASE_NAME=$1
ENV_NAME=$2
SHORT_SHA=${3:-sha_na}
BRANCH_NAME=${4:-branch_na}
cd e2e_tests
conda run -n $ENV_NAME --no-capture-output python prepare_test_data.py $TEST_CASE_NAME
ls */*
cat $TEST_CASE_NAME/config.yaml
TIMESTAMP_START=$(date +%s)
conda run -n $ENV_NAME --no-capture-output alp... |
2bf9a0acbe323629f629fd89b63f55317bc93893f970a4e17ca496db0ab1a484 | Shell | 540 | 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
#... |
5534b7d25c531a68935cd779c15ac1128676464b846b1ed4d1e2a2787d004877 | Shell | 546 | 28 | #!/bin/sh
## 5 Jul 2017 Siwei
## modified on 2 Oct 2017
## This script takes one vcf input file and generate WASP-compatible txt inputs of chr 1-22 (gz compressed)
INPUT_VCF=$1
OUTPUT_DIR=$2
k=1
char_chr='chr'
rm -r $OUTPUT_DIR
mkdir -p $OUTPUT_DIR
while [ $k -lt 23 ]
do
echo $char_chr$k
k_chr=$char_chr$k
ech... |
02cd5de476b4aae632785c915e5d9f3efb2e1553dbc6bdc061d3ca4c50b5b293 | Shell | 547 | 8 | fslswapdim $subj/rest1_1.25mm/001/fmcpr.sm0.mni305.1mm.nii.gz x z -y $subj/rest1_1.25mm/001/fmcpr.sm0.mni305.1mm_LAS.nii.gz
fslroi $subj/rest1_1.25mm/001/fmcpr.sm0.mni305.1mm_LAS.nii.gz $subj/rest1_1.25mm/001/fmcpr.sm0.mni305.1mm_LAS_crop.nii.gz -15.5 182 -16 218 -15.5 182
mri_convert $subj/rest1_1.25mm/001/fmcpr.sm0... |
5593a21f641de3d36202bf08258a09c75bddc790150de4ce8e03e311e873991b | Shell | 547 | 18 | set -eux
#1. Train franken
cd tests/lammps/metatomic/
franken.autotune \
--train-path ../train4.xyz \
--l2-penalty="1e-8" \
--force-weight="0.999" \
--jac-chunk-size 16 \
--run-dir "./" \
--backbone=pet --pet.path-or-id "PET_MAD/xs_1.5" \
--rf=gaussian --gaussian.num-rf "256" --gaussian.le... |
b56a7437e1efcc3d112a47b437d93d9dc15a75c7b4e461892167ad8cf93c08c5 | Shell | 548 | 11 | conda install -c conda-forge r-base # install R (>=4.0)
# for some reason certain R dependencies cannot be installed using install.packages('.')
# run this before trying to install BandNorm and/or cisTopic
conda install -c conda-forge r-gert
conda install -c conda-forge r-rgeos
conda install -c conda-forge r-devtools
... |
b95fcc3e5d7fb7f2fca974de385c9a72311d063e62f805a6de22731ea55a87d5 | Shell | 548 | 16 | #!/bin/sh
set -e # Exit immediately if a command exits with a non-zero status
export PYTHONPATH="$PWD"
APPLICATION_ROOT="/dicom-web-filter"
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 $APPLICATI... |
11740bbe135ee598316dc7bd6aed141abf3d33766d1284cec1384b6e14706aa8 | Shell | 552 | 15 | #!/bin/sh
set -e # Exit immediately if a command exits with a non-zero status
python3 alembic/migrate.py
export PYTHONPATH="$PWD"
python3 scripts/create_kaapana_instance.py
if [ -z "${DEV_FILES}" ]; then
# Production
exec uvicorn app.main:app --workers $WORKERS --host 0.0.0.0 --port $PORT --root-path $APPLI... |
eee293cd2e4ab43fc2bde14cc0b88ef8ec36234b378dad900a9b1eeeef253544 | Shell | 552 | 13 | #!/bin/bash
# Orftcr.sh
export NA=$1
export TF=$2
cd ${NA}
printf "${NA}_dipy_bk_inbetween_Pugh.txt\n100\n${TF}\n${NA}_dipy_inbetween_bk_plus.wig\n${NA}_dipy_inbetween_bk_minus.wig\n\n" | perl ../uvpp_offset_yeastbs_inbetween.pl
#printf "${NA}_dipy_bk_inbetween_Pughindiv.txt\n100\n${TF}\n${NA}_dipy_inbetween_bk_plus... |
37360969af2d34a936d57dd15c47712af068d0e37bf9fb545c32711063959aed | Shell | 554 | 25 | #!/bin/bash
#SBATCH -p shared
#SBATCH -c 1
#SBATCH --mem=5G
#SBATCH --job-name=01_sra_metadata
#SBATCH -o ../../processed-data/11_raw_data_upload/01_sra_metadata.log
#SBATCH -e ../../processed-data/11_raw_data_upload/01_sra_metadata.log
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ... |
52c72913bd8350760b632a970ea34e4b7d9254c718b87c9c576da7ef87289f27 | Shell | 555 | 14 | #!/bin/bash
# File: setupNetInfPaths.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... |
2d5112eea9f9ecf5fd0958300302d13fb13d3f09195c16efc7942fb74f3eaa97 | Shell | 557 | 18 | ## Command to subsample bam files
TRA=($(for file in *_downSampled_q30.sorted.dedup.bam; do echo $file |cut -d "_" -f 1-3;done))
echo ${TRA[@]}
for tr in ${TRA[@]};
do
echo ${tr}
samtools index ${tr}_downSampled_q30.sorted.dedup.bam ${tr}_downSampled_q30.sorted.dedup.bai
#frac=$( samtools idxstats ${tr}_PPq30.sor... |
844a215b5833309d7810b62cc17dc39644fc518b7327cde17c91e3b89d09ca49 | Shell | 558 | 10 | CURRENT_DIR=$(dirname "$(readlink -f "$0")")
# Download whole dataset
wget https://zenodo.org/record/2543724/files/pubchem.chembl.dataset4publication_inchi_smiles_v2.tsv.xz
# Decompress (required space ~18GB)
unxz pubchem.chembl.dataset4publication_inchi_smiles_v2.tsv.xz
# Get desired columns (SMILES, gene name and ac... |
8f806a3b46ae3c85b940d3832c57859cfc06b770ce0bba092e253196fb42c57d | Shell | 558 | 24 | #!/bin/bash
function invert_linear_reg {
matrix_original=$1
sub_name=$(basename $matrix_original _to_MNI.mat)
fold_name=$(dirname $matrix_original)
convert_xfm -omat ${fold_name}/${sub_name}_from_MNI_to_sub.mat -inverse $matrix_original
}
export -f invert_linear_reg
#### Script ... |
9fdf23a5bcfeb7da2129d0a1d89bb73b26b919f87ea587426a032ba83b267f9b | Shell | 558 | 25 | #!/bin/bash
#SBATCH -p shared
#SBATCH -c 1
#SBATCH --mem=5G
#SBATCH --job-name=02_sra_biosample
#SBATCH -o ../../processed-data/11_raw_data_upload/02_sra_biosample.log
#SBATCH -e ../../processed-data/11_raw_data_upload/02_sra_biosample.log
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "Use... |
40cd5c92b4f29cd12bd57b99684ca03fc1e73c399b2978eca8b3de02eb85e39f | Shell | 559 | 7 | for i in {1..3}; do
bash bash_scripts/libri.sh --seed $i --experiment_name libri_delta8_pred_$i --loss pred --prediction_target enc --pred_steps 8;
bash bash_scripts/libri.sh --seed $i --experiment_name libri_delta8_inv_sg_$i --loss inv --prediction_target pred --pull_coef 1.0 --push_coef 2.0 --decorr_coef 20.0... |
d711821b5a19733a51f8a740414e9469ea8beb7bf4369e7df0635c34c483eacf | Shell | 562 | 10 | #!/bin/bash
source_folder=
mkdir -p ${source_folder}/04.Subsampled
cp -r ${source_folder}/03.LanesMerged/* ${source_folder}/04.Subsampled
seqtk sample -s 2025 ${source_folder}/04.Subsampled/C1/C1_L001_R1_001.fastq.gz 20000000 > ${source_folder}/04.Subsampled/C1/C1_L001_R1_001.fastq
pigz -p 24 ${source_folder}/04.Subs... |
4da05b07cabec3763f9d7fee6df12662cfc6a36fb56f8d0c834ac5cc3971a5dc | Shell | 563 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=6
#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_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
ec0cb106a476b86f8a71f21174f88ccc1e1c7979cf20c96a5f4bef80e7dbe14f | Shell | 563 | 7 | for i in {1..3}; do
bash bash_scripts/mnist_triplets.sh --seed $i --experiment_name mnist_triplets_pred_$i --loss pred --prediction_target enc;
bash bash_scripts/mnist_triplets.sh --seed $i --experiment_name mnist_triplets_inv_sg_$i --loss inv --prediction_target pred --pull_coef 1.0 --push_coef 1.0 --decorr_co... |
309b70db55efc892f8febbc5d855be23e7f7029cb060a17dcb975455dcd15628 | Shell | 564 | 20 | #!/bin/bash
ENV_NAME="dockbiotic"
CURRENT_DIR=$(dirname "$(readlink -f "$0")")
MODELS_DIR=$CURRENT_DIR/../../saved_models
DATA_DIR=$CURRENT_DIR/../../data
export DEEPCHEM_DATA_DIR="$CURRENT_DIR"/../../deepchem_data_dir
COMMAND="""
python $CURRENT_DIR/script.py \
--model_type attentive_fp \
--dataset stokes ... |
de55131fe5f32874b314502a3f940036691f7e1fa166d17941eccb869a139d92 | Shell | 564 | 32 | #!/bin/bash -e
# Copyright (c) Facebook, Inc. and its affiliates.
{
black --version | grep -E "23\." > /dev/null
} || {
echo "Linter requires 'black==23.*' !"
exit 1
}
ISORT_VERSION=$(isort --version-number)
if [[ "$ISORT_VERSION" != 5.12* ]]; then
echo "Linter requires isort==5.12.0 !"
exit 1
fi
echo "Run... |
522965e494cbdd0c19bfed66cfef134627003db5cfbf8ae8b7e32fcb92a07472 | Shell | 566 | 25 | #! /bin/bash
# Siwei 09 Jul 2021
# added nolambda parameter to make output comparable to previous core calls
# Siwei 18 May 2021
# Call peaks use MACS2
# use conda environment encode-atac-seq-pipeline (python 3.7)
# appearently there are compatibility issues with python 3.8.8
## list all .bam files
shopt -s nullglo... |
e2cc71e59c2d1233007677860a546fbd2e950f3120b7933764283db76936a64e | Shell | 566 | 18 | #!/bin/bash
#SBATCH --account=IscrB_ProAmmo
#SBATCH --time 24:00:00 # format: HH:MM:SS
#SBATCH --nodes=1 # node
#SBATCH --ntasks-per-node=1 # tasks out of 32
#SBATCH --gres=gpu:1 # gpus per node out of 4
#SBATCH --cpus-per-task=10
#SBATCH -p boost_usr_prod
##SBATCH -... |
55d4c6a563ec63d2bf3fb01b975e6232e57ba9a6df444b9c5d44fa0b9e830f89 | Shell | 567 | 17 | #!/bin/bash
#SBATCH --job-name=prechunk.job
#SBATCH --time=8:00:00
#SBATCH --export=ALL
#SBATCH --output logs/prechunk-%j.out
#SBATCH --nodes=1 # Use 1 node
#SBATCH --ntasks=1 # 1 task
#SBATCH --cpus-per-task=32 # Allocate N CPUs for the task
#SBATCH --mem-per-cpu=30G ... |
893a0830ddecd302a48ac635e4e7bcc4b3294fc2fd29e39c84ef10b2effd4e96 | Shell | 568 | 21 | #!/bin/bash
# clean old res
rm res_*.dat
# test standard Lammps
../../../../src/lmp_serial -in in.spin.iron-nve
# test spin/kk with Kokkos Lammps
# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
# -k on -sf kk -in in.spin.iron-nve
# extract data from Lammps run
in="$(grep -n Step log.lammps | awk -F ':' '{p... |
bbe4e07037847b618f586723040c16457f40f3df1adb1db2e40ab7c615f8771a | Shell | 570 | 24 | #!/bin/bash
function invert_linear_reg {
matrix_original=$1
sub_name=$(basename $matrix_original _to_MNI_2mm.mat)
fold_name=$(dirname $matrix_original)
convert_xfm -omat ${fold_name}/${sub_name}_from_MNI_to_sub_2mm.mat -inverse $matrix_original
}
export -f invert_linear_reg
####... |
1cb24efc2b641ac5ad1c3aca33d9fe45fb81a3447f8987cf5a5091175dfe112d | Shell | 572 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=6
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
e30b8aac17d3774c47d01912d88ea3549f5f96281fe6438b6b0257b947d7bd39 | Shell | 572 | 19 | #!/bin/bash
# Create reaction core dataset split.
DATA_PATH="data/RDB7"
FULL_CSV="$DATA_PATH/raw_data/rdb7_full.csv"
RXNS_CLS_CSV="$DATA_PATH/raw_data/rxn_core_classified.csv"
RXN_TYPES_CSV="$DATA_PATH/raw_data/reaction_types.csv"
python data_processing/classify_by_reaction_core.py \
"$FULL_CSV" \
--out_file... |
460c9ce0e972420907ab802d2505d813a06cc723f6dd27d54370d57b828844dc | Shell | 573 | 18 | #!/bin/bash
source_folder="01.RawData"
target_folder="03.Renamed"
for sample_name in $(ls $source_folder); do
echo "Renaming $sample_name"
i=1
mkdir -p $target_folder/$sample_name
for fl in $(ls $source_folder/$sample_name/*1.fq.gz | rev | sort | rev); do
new_name="${sample_name}_L00${i}_R1_00... |
93ea9f7da973f2526e3e69c0f0c19fa131e4ab724a8bd17a3c15735689a27f90 | Shell | 573 | 15 | #!/bin/bash
# File: getExtLib.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.or... |
b0813e23d818dac92c0d552a256ff66e447c5aec5f74667e87d89225e7aaaaae | Shell | 574 | 15 | # conda activate ciriquant
set -e
read workdir circles fastq_dir samplelist_dir params <<< "$@"
[ ! -d "$(realpath $fastq_dir)" ] && { echo "Required input fastq dir. Exit..."; exit; }
# Update your <conda prefix>
conda="--use-conda --conda-prefix <conda prefix>"
echo "Update your <conda prefix>"
exit
config="sampl... |
c79be2968aa4fd5adea5cf08305aac5a7fb6d4d93ff4190d192a384431354638 | Shell | 575 | 21 | #!/usr/bin/env bash
BVp="/hpc/soft/brainvisa/brainvisa/bin/"
FSLPREFIX="fsl5.0-"
mkdir surfaces
OUTp="surfaces/"
IN="sub-Musly_ses-01_T1w_Mean_denoised_debiased_in-inia19_grey_white"
cIN=$OUTp$IN
"${FSLPREFIX}fslmaths" $IN $cIN -odt short
"${FSLPREFIX}fslmaths" $cIN -mul -1 $cIN -odt short
"${FSLPREFIX}fslmaths" $cI... |
41042998b1677757ab8e4a3a238f70bbd6fcd7be9bbacc10a0052febcd62561f | Shell | 577 | 13 | #!/bin/sh
# PulseAudio for Selkies audio. The container has no sound hardware, so create a virtual
# null sink named "output"; its ".monitor" source is what pcmflux captures (Selkies'
# audio_device_name defaults to "output.monitor"). Start with -n (no autodetect) and load
# only what we need to keep container logs cl... |
fe04a6b82a7895a5d14305e0feb419b36e50f50277945186b91be03ad8e6aa60 | Shell | 577 | 11 | FILE=$1
echo "Note: available models are apple2orange, orange2apple, summer2winter_yosemite, winter2summer_yosemite, horse2zebra, zebra2horse, monet2photo, style_monet, style_cezanne, style_ukiyoe, style_vangogh, sat2map, map2sat, cityscapes_photo2label, cityscapes_label2photo, facades_photo2label, facades_label2photo... |
61fb5d25ef8aa93a998a2568bac2dbe5759ff81cd2b90580322b75a49b3e8132 | Shell | 578 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=20
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_0_CoordsV.out
#SBATCH --error=EEG_0_CoordsV.err
#SBATCH --exclusive
#S... |
883891020338bca38d49dac6260ff5cdbe3364585888bbae753556cdb994765f | Shell | 578 | 17 | #!/bin/bash
set -e
# setup ros environment
# source "/opt/ros/$ROS_DISTRO/setup.bash"
source "/root/ros_catkin_ws/install_isolated/setup.bash"
# set environment variables
export ROS_PORT_SIM="11311"
# export GYM_GAZEBO_ENV_SCARA3="/Users/victor/gym-gazebo/gym_gazebo/envs/assets/worlds/scara_basic.world"
export GYM_GA... |
e4ad361633769f1fcb7ba388a46abd68629d21a58b6639578947c2a4d86669f8 | Shell | 578 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
f073e43d49bd89fc978446bb85175590c4045f5b1fc7bd8cbddc98eb031128d9 | Shell | 579 | 26 | #!/bin/bash
#SBATCH -p shared
#SBATCH -c 1
#SBATCH --mem=2G
#SBATCH -t 10:00
#SBATCH --job-name=04_prepare_fastqs
#SBATCH -o ../../processed-data/11_raw_data_upload/04_prepare_fastqs.log
#SBATCH -e ../../processed-data/11_raw_data_upload/04_prepare_fastqs.log
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE ... |
d2f2aa3ce8360e7a18f45ab3cab9038c668eff906503899066ea64e8072d2752 | Shell | 580 | 19 | #!/bin/bash
#SBATCH --job-name=bowtie2-index
#SBATCH --output=./out/bwt.%j.out
#SBATCH --error=./out/bwt%j.err
#SBATCH --cpus-per-task=16
#SBATCH --mem=100G
#SBATCH --time=1-00:00:00
#SBATCH --partition=XXX
#SBATCH --output=./bowtie2build_%j.out
#SBATCH --error=./bowtie2build_%j.err
module load bowtie2
# Path to the ... |
c30430d1f70145a26af8e95bc4f338f870f2301e443dd48e00f2ddbbe3364ec2 | Shell | 582 | 20 | #!/bin/bash
# Confirm that we are in the neuroscan directory and that the neuroscan binary exists
if [ ! -d ".git" ]; then
echo "This script must be run from the root of the neuroscan repository."
exit 1
fi
if [ ! -f "./neuroscan" ]; then
echo "The neuroscan binary does not exist. Please run the build scri... |
6cf83a7512d279359873914533d05f5db499793b8d62bac362ceab755d7d90ad | Shell | 583 | 9 | #!/usr/bin/env bash
python train.py vae --train_load ../lincs_trapnell_zinc.csv \
--val_load ../zinc_smiles_test.txt \
--config_save /storage/groups/ml01/projects/2021_chemicalCPA_leon.hetzel/embeddings/chemvae/config.txt \
--model_save /storage/groups/ml01/... |
632ccd89786f42204deeb6a01929dc832a5e9ae624500ba18a96ef4927343ea9 | Shell | 584 | 18 | path=$1
ref=$2
sample=$3
echo ${sample}
ln -s ${path}/${sample}_R1.fq.gz ./01.rawdata/${sample}_R1.fq.gz
ln -s ${path}/${sample}_R2.fq.gz ./01.rawdata/${sample}_R2.fq.gz
cd 01.rawdata/
nohup fastqc ${sample}_R1.fq.gz 2>&1 > ../log/fastqc_log.log &
nohup fastqc ${sample}_R2.fq.gz 2>&1 > ../log/fastqc_log.log &
reach... |
c4ea80f489adef6c8025a4111f02f1dce0b5dc269253146b957313924d6937e3 | Shell | 584 | 11 | # Split BAM into uniquely mapped and multi-mapped reads
samtools view -@ 5 -q 255 -o Aligned_unique.bam -U Aligned_multi.bam Aligned.out.bam
# For multi-mapped reads, count the number of primary alignments (-F 0x100)
samtools view -@ 5 -F 0x100 Aligned_multi.bam | cut -f1,12,14 | uniq -c > count_primary_alignments.txt... |
213a149f846ec4b4718e8fa7b5c5c0ccbc739143802a860ecab947752008b362 | Shell | 585 | 17 | #!/bin/bash
set -e -u
# Build the installer for MacOS.
# This script needs to be run from the root of the repository.
# Prerequisites: wheel has been build, e.g. using build_wheel.sh
rm -rf dist_pyinstaller build_pyinstaller
export EAGER_IMPORT=true # TODO check if this can be removed with newest peptdeep version w... |
9ae3a042533ecd8b5139f01595886b7e963948f065420e59c6a272814399bb34 | Shell | 586 | 25 | #!/bin/bash
subj_ids=$1
ses=2YearFollowUpYArm1 #2YearFollowUpYArm1 #baselineYear1Arm1
out_dir=/scratch.global/${USER}/mid_rt_mod
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 $subj_ids | while read line ;... |
46e7cb4dbaa8938f87f675d17d69ca2dd2d871f919319c8aa59583eca986db14 | Shell | 587 | 24 | #!/bin/bash
ENV_NAME="dockbiotic"
CURRENT_DIR=$(dirname "$(readlink -f "$0")")
for ORIGIN in stokes coadd ; do
for TARGET in stokes coadd ; do
# skip intra-dataset similarities
if [[ "$ORIGIN" == "$TARGET" ]]; then
continue
fi
printf "\nCalculating similarities for:... |
b0fa11f33559e60cd02754538d3a465b58b17c1002f041277ba5b0adef0ac7a1 | Shell | 588 | 18 | #!/bin/bash
#SBATCH --job-name=extract_sections.job
#SBATCH --time=3:00:00
#SBATCH --export=ALL
#SBATCH --output logs/extract_sections-%j.out
#SBATCH --nodes=1 # Use 1 node
#SBATCH --ntasks=1 # 1 task
#SBATCH --cpus-per-task=1 # Allocate N CPUs for the task
#SBATCH --mem-pe... |
2187a48ae499f76f98703232a47ea2a506259b809eddf5e3f2c9739232aedeff | Shell | 589 | 20 | #!/bin/bash
# Siwei 6 Aug 2021
# Siwei 7 Nov 2018
# Siwei 28 Dec 2018
# remove chromosomes of alternative assembly,
# decoy, chrUn. Anything with chr name includes "_", HLA
# and sex chromosomes
for eachfile in *.bed
do
echo $eachfile
cat $eachfile | \
grep -v "_alt" | grep -v "_random" | grep -v "chrEBV... |
732a18b7c452f7a5926b99cff877a0f27f8c08c9c048588bd8e6b9554f9663d1 | Shell | 589 | 17 | #!/bin/bash
#SBATCH --job-name=decsummary
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodinggendf.%A.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodinggendf.%A.err
#SBATCH --partition... |
2e270ca22e6de229b5ef2027d6bfc7545f7507762f96c6cf212f625512e15a3a | Shell | 591 | 34 | #!/bin/bash
cp /staging/{chtc_id}/metl.tar.gz ./
ENVNAME=metl
# if you need the environment directory to be named something other than the environment name, change this line
ENVDIR=$ENVNAME
# these lines handle setting up the environment; you shouldn't have to modify them
export PATH
mkdir $ENVDIR
echo "un taring en... |
56c1b59f4add9daadbf3137f19292cafc42e946d4f3ec12b183cfbd14459217c | Shell | 591 | 22 | #!/bin/bash
chrnum=$1
notebook_path="notebooks/wes/sample_qc/repartition/chr${chrnum}.ipynb"
dx login --token TOKEN
my_cmd="pip install gnomad && papermill chr${chrnum}.ipynb chr${chrnum}_out.ipynb"
dx run dxjupyterlab_spark_cluster \
-ifeature="HAIL" \
-icmd="$my_cmd" \
-iin="${notebook_path}" \
... |
a13652afb7c0fdedc4b815f3643bf24b0ca6187a00e52d1adfce7a4614797ab7 | Shell | 593 | 27 | #! /bin/bash
set -e
TARGET_DIR="$(pwd)"
REPO_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd .. >/dev/null 2>&1 && pwd )"
BUILD_DIR="$(mktemp -d)"
cleanup () {
rm -rf "$BUILD_DIR"
}
trap 'cleanup' EXIT
cd "$BUILD_DIR"
echo "Building .dmg in $(pwd)"
qmake "$REPO_DIR/labelbuddy.pro" "CONFIG +... |
b72af652dcb2cacec046e6d6045f516ecbe766cd15c4ed58dcce1281c434abf6 | Shell | 593 | 19 | # Train models later evaluated in papers
# Medium model ~ VAE 128 with 0 skip connections
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... |
3a28781aa41822350bceb0f4ea7f200c6c804a3b42f18cd2aa45bf6fc6c2c5ec | Shell | 594 | 21 | #!/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=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj83
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
e7a56bbe35d51f3fce66724a39923846b9d2352193bfd0d1452b8a074001a116 | Shell | 597 | 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... |
591c7d4e32ca977fc262af260291e7ad0a3225d6a99620e7214946847d29fd1b | Shell | 598 | 20 | #!/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... |
74764132a3866e41c870d90a272248c90c68316c17e7cc00b44b7d6ad00f7e34 | Shell | 598 | 17 | #!/bin/bash
#SBATCH --job-name=decsummary
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingsummary.%A.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingsummary.%A.err
#SBATCH --parti... |
9f8de75823e23ad4c5d400b3893230faec7fa090f6e8942cb1800ab14fdc52e7 | Shell | 598 | 22 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-deb.sh "debian-stretch"
# generate source tarball
cd /veyon
VERSION=$(git describe --tags --abbrev=0 | sed -e 's/^v//g')
cp /build/CONTRIBUTORS .
.ci/common/strip-kitemmodels-sources.sh
.ci/common/strip-kldap-source... |
fc1175ed31fe9bb5652bf9a39ad4afe2b9d56c6b72010ec413b306d261ed4608 | Shell | 599 | 17 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingimposterdf.%A.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingimposterdf.%A.err
#SBATCH --p... |
2119995655fb806fa02952e3ebc0226ac5fa2086d932e7dbd59691204dcdc9ea | Shell | 601 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=submissions/$(date +"%Y%m%d%H%M")
mkdir -p $FOLDER
cp single_ste... |
81949d9353ce98cfd73f6fe316558c7b5477934d6d16e09330e0fe2b6d4c9565 | Shell | 601 | 21 | #!/bin/bash
#SBATCH -N 1 # number of nodes
#SBATCH -c 2 # number of cores
#SBATCH -G a100:1 # number of GPU
#SBATCH --mem=12G # memory requested
#SBATCH -t 0-4:00:00 # time in d-hh:mm:ss
#SBATCH -o slurm.%j.out # file to save job's STDOUT (%j = JobId)
#SBATCH -e slurm.%j.err #... |
88717d75d736686dccb10e22c9632379c876a3acf1fa2dc715626c78d6411429 | Shell | 602 | 17 | #!/bin/bash
set -e -o pipefail
shopt -s nullglob
EXCLUDE=(BareTraining.slurm SparsityOnly.slurm FRMagnitudeOnlyOnly.slurm BareTrainingMemoryAntiAngle.slurm SparsityAndFRMagnitudeMemoryAntiAngle.slurm SparsityAndFRMagnitude.slurm SparsityAndFRMagnitudeAlphaBetaSweep.slurm Dropout.slurm) # <-- add files here (exact nam... |
3ee506529556fa827516e97f0fdaa5cd03bb26c7886d9862c207fd7f0a5710e5 | Shell | 603 | 16 | #!/bin/bash
# Note: Be sure package already in PyPI
conda install anaconda-client &&
conda install conda-build &&
# TODO: allow user-specified version and append this to next line: --version x.x.x
conda skeleton pypi accelerometer --output-dir conda-recipe &&
conda build -c conda-forge conda-recipe/accelerometer
pri... |
65b3df6acca316dc81b7a400a1eba77c91f755b08eb0215d1727f382fc5974fd | Shell | 604 | 20 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod_small
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH... |
df7debf2e13a8b82e5ef666a81cab4b6cbf9f5c166db73bc7a8fc6eb402177be | Shell | 604 | 21 | # Brain extraction for the T1 structural image
# Author: Valeria Oliva
echo -n "sub? Only insert number >"
read subject
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/sub-NSPilot${subject}/ses-${ses}brain/anat
# Running ants
antsBrainExtraction.sh -d 3 -a sub-NSPilot${subject}_ses-${s... |
1d7a05515b8e62b8d10f98d2609dfaedd374dd687a7a33339a39abe9c75491dd | Shell | 605 | 35 | #!/bin/bash
# Siwei 03 Jun 2022
# !!! input SAF file is the first parameter
# @@@ output file name is the second parameter
# will count all bam files under the current directory
mkdir -p featurecount_output
saf_reference=$1
output_file_name=$2
# make index for all BAM files in case
#for eachfile in *.bam
#do
# e... |
ed5293865d84f4b3d32d929283cfa7b6a53548a00e453e9dab69b87aa8707abe | Shell | 606 | 15 | #!/bin/sh
set -e # Exit immediately if a command exits with a non-zero status
export PYTHONPATH="$PWD"
# Apply all migrations once here, before launching the (multi-worker) server
python3 alembic/migrate.py
if [ -z "${DEV_FILES}" ]; then
# Production
exec uvicorn app.main:app --workers $WORKERS --host 0.0.... |
a5d9147f29bd3a012de20a4239c562aee149458bbad53b11c5c3312202329ca2 | Shell | 607 | 15 | #!/bin/bash
# SetBackground.sh
#Code adapted from code on Taylor lab github site
export NA=$1
cd ${NA}
# calculate inbetween position for wig
# set backbground for dipyrimidine reads
printf "${NA}_minusstrand_inbetween.wig\n../initial_minus_inbetween_dipy.wig\n" | perl ../set_background.pl >${NA}_dipy_inbetween_bk_m... |
ab33e6b4440c11699db29a6bb866efa002a55e6025873b724f510fa50a299b8d | Shell | 607 | 5 | cd PCR1
~/.local/bin/bbmap/bbduk.sh -Xmx6g in=R1.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered interleaved nodisk outu=unmapped.fq.gz scafstats=scafstats.txt 2> log_mapping.out
cd ../PCR2
~/.loc... |
3b41cdb6342f0d404b0b26e979a60740b13a9c5e28b9c94a655109c2284db7aa | Shell | 608 | 24 | #!/bin/bash
MYIPADDRESS=`ifconfig en0 | grep 'inet ' | awk '{print $2}'`
VERSION=latest
docker pull fredericklab/capcalc:${VERSION}
docker run \
--rm \
--ipc host \
--mount type=bind,source=/Users/frederic/code/capcalc/capcalc/data/,destination=/data \
-it \
-v /tmp/.X11-unix:/tmp/.X11-unix \
... |
132206015bbf09891f0430bde9ac6965f57bff32bfd055b8cdff4820410dd319 | Shell | 609 | 24 | #!/bin/bash
# Install Tensorflow with CUDA support
pip install tensorflow==2.8.4
# Install the learned optimization package from GitHub
pip install git+https://github.com/google/learned_optimization.git
# # Install Jax
pip install -U "jax[cuda11_pip]==0.4.23" -f https://storage.googleapis.com/jax-releases/jax_cuda_r... |
5f212145b7c0cc5ec73d1f3d5dd7008c27024ae163d7257f419a8b8e707e484f | Shell | 613 | 24 | #!/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=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --ex... |
8bc9be51bf33ec97ecd2ac74e65bcaaa3f2f726218253cc12aaa8d4adc5d2c3c | Shell | 614 | 17 | # Install miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
# Configure ~/.bashrc
echo alias p=\"ps -aux|grep zhangjq|grep 'python -u'\" >> ~/.bashrc
echo alias n=\'nvidia-smi\' >> ~/.bashrc
echo alias d=\'du -hs * | sort -h\' >> ~/.bashrc
echo al... |
681ad0d608bf45e93ff38f7fbcf7ab1d4c1fe0a2cf52142edde3902953139ba5 | Shell | 616 | 18 | #!/bin/bash
#SBATCH -N 1 # number of nodes
#SBATCH -c 2 # number of cores
#SBATCH -G a100:1 # number of GPU
#SBATCH --mem=12G # memory requested
#SBATCH -t 0-4:00:00 # time in d-hh:mm:ss
#SBATCH -o slurm.%j.out # file to save job's STDOUT (%j = JobId)
#SBATCH -e slurm.%j.err #... |
d4ac42a167e1dedb8cd80cc0baabffab0d1a65d74203d2a59236e6cfe19a39aa | Shell | 617 | 22 | #!/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
printf "\n\nFinetune on stokes after pretraining on dockstring\n"
COMMAND="""
python $CURRENT_DIR/script.py \
--random_seed 42... |
09d026605bedf7805385ff54b40e30f942da0f1dc90e102799f879d9fec60d50 | Shell | 619 | 19 | path=$1
ref=$2
sample=$3
echo ${sample}
bzcat ${path}/${sample}_R1.fastq.bz2 | gzip - > 01.rawdata/${sample}_R1.fq.gz &
bzcat ${path}/${sample}_R2.fastq.bz2 | gzip - > 01.rawdata/${sample}_R2.fq.gz &
wait
cd 01.rawdata/
nohup fastqc ${sample}_R1.fq.gz 2>&1 > ../log/fastqc_log.log &
nohup fastqc ${sample}_R2.fq.gz 2... |
daf5750b96d8590ecd097859b428c8ea4dccc6b167f09705c34e4945e2a31660 | Shell | 620 | 17 | #!/bin/bash
# SetBackground.sh
#Code adapted from code on Taylor lab github site
export norm=$1
export NA=$2
cd ${NA}
# normalize wigs
perl ../norm_wigs.pl ${norm} ${NA}_dipy_inbetween_bk_minus.wig >${NA}_dipy_inbetween_bk_norm_minus.wig
perl ../norm_wigs.pl ${norm} ${NA}_dipy_inbetween_bk_plus.wig >${NA}_dipy_inbe... |
cf5c553fef5f371dc32c27310502f43d6e77f001dde64f811e6a4090ef8c13d9 | Shell | 621 | 20 | #! /bin/bash
set -eu -o pipefail
ROOT_INPUT_NRRD_DIR="/kaapana/app/nrrd"
ROOT_REFERENCE_DIR="/kaapana/app/reference"
ROOT_OUTPUT_NRRD_DIR="/kaapana/app/dicom"
echo "Start conversion"
for INPUT_NRRD_FILE in $( find ${ROOT_INPUT_NRRD_DIR} -mindepth 2 -maxdepth 2 -type f -name *.nrrd ); do
IDENTIFIER=$( basename $(... |
4913f67c885ba24eb8297d4c6011b66c494b4c02800f3f1cf106236fe49002bb | Shell | 623 | 20 | #!/bin/bash
# please follow magma instructions to create the correct dir structure
traits=("scz" "bpd" "asd" "epilepsy")
celltypes=("astro" "endo" "micro" "oligo" "opc" "vlmc" "excitatory" "inhibitory") # for major cell type class
celltype_dir="./"
for celltype_file in ${celltype_dir}*; do
celltype=$(basename ${... |
f3932d16a5d506da027063df01f54c53864a4374d50a90a1ed159bfb2217d9a1 | Shell | 624 | 12 | # ===== Build packages =====
# For CPU
sed -i'' -e 's/\_\_preferred_device\_\_[ ]*=[ ]*\"[A-Za-z0-9]*\"/__preferred_device__ = "CPU"/g' anylabeling/app_info.py
python -m build --no-isolation --outdir wheels_dist
# For GPU
sed -i'' -e 's/\_\_preferred_device\_\_[ ]*=[ ]*\"[A-Za-z0-9]*\"/__preferred_device__ = "GPU"/g' a... |
7594475c80c22198ec7046ef0c6e733cec81b5580d4dcaece8680b9a1a754f43 | Shell | 627 | 25 | #!/bin/bash
# EXPECTED INPUT:
# One nifti image per functional category containing the union of all seeds/stimulation points
echo $PWD/*.nii.gz | tr " " "\n" > file_list.txt
struct=(`cat "$PWD/file_list.txt"`)
# create strings for fslmaths add commands and add images (Implementation: remove the loop)
for (( i = 0 ... |
a31514d0aa9387108f263d4673051a08f3e8038612d7684fb0b3f6536ade3bce | Shell | 627 | 5 | perl /home/yli4/bin/customizedDB/MFM_junction/select_novel_junctions.pl $1.txt 3 3 $1_novel.txt
perl /home/yli4/bin/customizedDB/MFM_junction/extractFlankingGenomicSeq.pl /home/yli4/genomes/hg19_genome_raw.fa $1_novel.txt 66 $1_novel.fas
perl /home/yli4/bin/customizedDB/MFM_junction/junction_seq_translation.pl $1_novel... |
b42fb9a82d855ae7ae5606585325d80e1d3fc0a3a453a66a60050d4c3a9d4ef8 | Shell | 627 | 26 | #!/bin/bash
new_sample_dir=
sample_name="105_2g_DMSO"
sub_factor=0.4
seed=2025
# go through the fastq files with sample nimse
for i in $(ls ${new_sample_dir}/${sample_name}_*.fastq.gz)
do
base_name=$(basename $i)
base_name=${base_name%.fastq.gz}
first_part=${base_name%_S*_L*_[RI][123]_001}
second_pa... |
e43b4c1aa848abe32c500458b4e1f56aacc3ed9c394b4cff605eb32767078f6d | Shell | 628 | 21 | #!/bin/bash -e
NT=$1
PROG="./KokkosCore_PerformanceTest_Mempool"
COMMON_ARGS="--kokkos-threads=$NT --fill_stride=1 --alloc_size=10027008 --super_size=65536 --repeat_inner=100 --chunk_span=4 --repeat_outer=10"
postproc() {
cat log | grep "fill ops per second" | rev | cut -d ' ' -f 2 | rev >> yvals_fill
cat log | grep "... |
3bd5df83752ffb8300082b127275355ba8f02eff6831f67d6263bac72fe22b31 | Shell | 631 | 26 | #!/bin/bash
# check if we are in the root of the neuroscan repository
# if not, exit with an error message
if [ ! -d ".git" ]; then
echo "This script must be run from the root of the neuroscan repository."
exit 1
fi
echo "Building frontend"
cd frontend || exit 1
yarn
cp ./overwrite/Canvas.js ./node_module... |
62682d8cadbc41ad06048e2e3e91121d8250b742fea307faac80748020b6a928 | Shell | 633 | 30 | #!/bin/bash
#$ -cwd
#$ -l mem_free=4G,h_vmem=4G,h_fsize=100G
#$ -pe local 10
#$ -N compute_weights_full_NAc_genes
#$ -j y
#$ -o logs/compute_weights_full_NAc_genes_$JOB_ID.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: \${USER}"
echo "Job id: \${JOB_ID}"
echo "Job name: \${JOB_NAME}"
echo... |
c7fd28e9a5508cc3ada799bf283fb3d771a69733492b8644c9e33dbc4db6b79b | Shell | 635 | 27 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=8
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive
#... |
04eee314c3ad3027c02d7f393347fdcb722c0c57ccdff414b97e78550a999d7a | Shell | 636 | 31 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=10G,h_vmem=10G,h_fsize=100G
#$ -pe local 10
#$ -N "build_bims_NAc_genes"
#$ -m e
#$ -j y
#$ -o logs/build_bims_NAc_genes_$JOB_ID.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "H... |
6f03cc63e5ddb44778e78a3321e1ddf32e307389ae4a2ac63f9ff64ae1362769 | Shell | 638 | 25 | #!/bin/bash -e
NT=$1
PROG="./KokkosCore_PerformanceTest_Mempool"
COMMON_ARGS="--kokkos-threads=$NT --fill_stride=1 --fill_level=70 --chunk_span=5 --repeat_inner=100"
postproc() {
cat log | head -n 1 | rev | cut -d ' ' -f 1 | rev >> xvals
cat log | tail -n 1 | rev | cut -d ' ' -f 1 | rev >> yvals
}
for yset in 1 2 3
d... |
c132edc30f77df85b52c5fb03eb88f3d88d640517cefebc3620bf210605c5868 | Shell | 638 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=200
#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_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
... |
5345cbfb65267bf93cafc6b7f32a897f6859a8654bc59c2bea74dea8208e07fc | Shell | 639 | 32 | #!/bin/bash
# Define variables
URL="https://zenodo.org/records/15032263/files/test_structures.tar.gz?download=1"
FILE_NAME="test_structures.tar.gz"
download_dir="../data"
mkdir -p "$download_dir"
cd $download_dir
# Download the file using wget
# wget -O "$FILE_NAME" "$URL"
curl -L -o "$FILE_NAME" "$URL"
# Check if ... |
8752927d361328911932026ef22372a8488de68e28734149b648bc4a87ea4e5e | Shell | 640 | 30 | #!/bin/bash
set -ex
# SET THE FOLLOWING VARIABLES
# docker hub username
USERNAME=fredericklab
# image name
IMAGE=capcalc
# ensure we're up to date
git pull
# bump version
version=`cat VERSION | sed 's/+/ /g' | sed 's/v//g' | awk '{print $1}'`
echo "version: $version"
# run build
docker build . -t $IMAGE \
--bu... |
b3b874810243f3b479cd83635848617fd851f463ac67063e1432c7ea6fb9ada8 | Shell | 640 | 17 | #!/usr/bin/env bash
# Need this conda env active - envs/papa_r.yaml - papa_pipeline_r
script="scripts/tx_to_polya_quant.R"
sample_tbl="data/liu_facs/liu_facs_papa_sample_sheet.tdppos_first.csv"
salmon_dir="data/liu_facs/2024-11-20_decoys/salmon_quant/"
tx2le="processed/decoys/2024-11-20_decoys_novel_ref_combined.quan... |
4a4650777705b0d9ce64295daf24e5f61a2f8985ffc1deb30f9feea8540622b0 | Shell | 641 | 35 | #!/bin/bash
# Process COSMIC data
cd scripts/cosmic
python3 generate_cell_line_mutations_files.py
cd ../..
# Process COSMIC data
cd scripts/drugbank
python3 get_drug_targets.py
cd ../..
# Process PPI data
cd scripts/ppi
python3 export_ppi_all_genes.py
cd ../..
# Process LINCS data
cd scripts/lincs
python3 process... |
12e14666edab8e84d7f6bc92766ed99a72ebb37ac3187e9796ad2af3522b471c | Shell | 644 | 24 | #!/bin/bash
# Install Tensorflow with CUDA support
pip install tensorflow==2.8.4
# Install the learned optimization package from GitHub
pip install git+https://github.com/google/learned_optimization.git
# # Install Jax
pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.... |
da9b6be0872d50076f1c8a74b584c13e592475a809baf955ab860e825c400359 | Shell | 644 | 24 | #!/bin/bash
set -euo pipefail
APP_NAME=lammps
DOCDIR="$1"
DESTDIR="${PWD}"
echo "Delete tar files, if they exist"
rm -rvf "${PWD}"/lammps-src-*.tar.gz
pushd "${DOCDIR}/.."
VERSION=$(grep LAMMPS_VERSION src/version.h | sed 's/^.*LAMMPS_VERSION //' | tr -d \" | tr -d \ )
TARNAME=lammps-src-${VERSION}.tar
TARPATH="${DES... |
3674c3ccfd3df795729468de1e5898b6e0a6f0783f73d06cf68adb64e63bfe4b | Shell | 645 | 17 | #!/usr/bin/env bash
# create minimal empty files for testing pipeline plumbing
# required dirs
mkdir -p testdata_empty/aligned_bams
mkdir -p testdata_empty/star_sj_tabs
# required input files
touch testdata_empty/input_junctions.bed
touch testdata_empty/annotation.gtf
touch testdata_empty/aligned_bams/control_1.Alig... |
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