sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
32a374858d2b4290da5309bc1d5ba0a794e406b0df84ad5851d31989cb853242 | Shell | 683 | 29 | export IPYTHONDIR="`pwd`/.ipython"
export IPYTHON_PROFILE=default
echo "This code assumes you have BasalGangliaData installed"
# ipcluster start -n 2 --profile=$IPYTHON_PROFILE --ip=127.0.0.1&
# sleep 20
for sim_size in 1000 5000 10000 50000; do
sim_name=networks/arvind-$sim_size
snudda init $sim_name --s... |
f672c2e067fd9f5ea4e27378f2a987836efc901804041a627ffcd86caf5bc1bd | Shell | 683 | 36 | #!/bin/bash
#SBATCH --time=0-00:30:00
#SBATCH --mem-per-cpu=4000
#SBATCH --output=./slurm_logs/slurm-%A.out
INPUT_DIR=/scratch/n/tbi/meg
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "INPUT_DIR set as $INPUT_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
SUBJECT=$1
ml purge
module load teflon
ml anaconda3
source activa... |
aca52ceda3c45e3628d2db916aed6c53b74d18eea3ae239ced65376c587fd228 | Shell | 688 | 19 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Spherical deconvolution
ss3t_csd_beta1 \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_ses-PNC1.mif \
/work/data/MRtrix_recon/template/av_wm_response_new.txt \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_wmfod_new.mif \
/work/data... |
e7bc129a7f1e5d131d43e5b7b31eb577e63f3f88488ce89b609b4510023981f6 | Shell | 688 | 18 | sbatch --wait << EOF
#!/bin/bash
#SBATCH -o logs/%j.job
#SBATCH -e logs/%j.job
#SBATCH -J snakemake
#SBATCH -p cpu_p
#SBATCH -c 8
#SBATCH --mem=15G
#SBATCH -t 06:00:00
#SBATCH --nice=10000
source $HOME/.bashrc
conda activate bert-rbp
python3 ../../methods/bert-rbp/examples/run_finetune.py --save_steps 1000000 --mode... |
c0602315ade8acc19b4f074c9373dbad82064fcc6078d8089f52ade8e5a43093 | Shell | 690 | 38 | #!/bin/bash
BAM=$1
BW=$2
factor=$3
TMPD=$(mktemp -d -p .)
mkdir -p $TMPD
samtools idxstats $BAM | cut -f 1,2 | grep -v \* | grep -v ERCC > $TMPD/chrom.sizes
BDGS=""
echo $(date --rfc-3339=seconds) Converting chroms to bedGraph...
for chrom in $(cut -f 1 $TMPD/chrom.sizes);
do
BDG=$TMPD/$chrom.bedGraph
BDGS="... |
7216d9d18f71e5367b55035607342c056e190e65823746d538da90f7b2fe5930 | Shell | 691 | 21 | #!/bin/sh
# The SGE_TASK variable specifies the data sets, as in $HOME/test.qsub
cd /home/knight/hoycw/PRJ_Error/scripts/utils/
# don't change this variable, used by the submit script to define which data sets to analyze
SBJ="${SGE_TASK}"
# define function
FUNCTION='fn_elec_match_atlas'
# set up matlab function cal... |
49a5f8fa84ae4398fb6567bf93a8d6508eacbfb1247d52c2fbfc295f4af4d5aa | Shell | 692 | 24 | #!/bin/bash
# Usage: bash download_small_bfd.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt in... |
dea298309969d43b34376af2e6e55c03c162acbeee3040358f8f1025bf68a12d | Shell | 693 | 6 | #PBS -l walltime=72:00:00
#PBS -l select=1:ncpus=32:mem=124gb
#PBS -J 1-3
module load anaconda3/personal
python2 RunRFMix.py PopPhased /rds/general/project/human-popgen-datasets/live/HGDP_1000g/${PBS_ARRAY_INDEX}/HGDP_1000gNYC_3pop_target_ref_rfmix154_short_B_${PBS_ARRAY_INDEX}.phased.alleles /rds/general/project/human... |
b8cf4bd450a52a28c8db41d87d8ead45513d6042ba4f24db00731534bf0967a0 | Shell | 695 | 26 | #!/bin/sh
gp_output_check=/ncf/hcp/data/analyses/myelin/Adversity_Project/results/output_check/missing_regional_gp_model_output.txt
rm $gp_output_check
touch $gp_output_check
kfold_output_check=/ncf/hcp/data/analyses/myelin/Adversity_Project/results/output_check/missing_regional_kfold_output.txt
rm $kfold_output_chec... |
7aff8fa40c2f700036e0cfd05fda9e8b0a3a084df3eb0a431db20ea2aefe0e71 | Shell | 698 | 30 | set -ex
# models
RESULTS_DIR='./videos/edges2shoes'
G_PATH='./pretrained_models/edges2shoes_net_G.pth'
# dataset
CLASS='edges2shoes'
DIRECTION='AtoB'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=1
# misc
GPU_ID=0
NUM_TEST=5 # number of input images duirng test
NUM_SAMPLES=20 # number of samples per input images
# command
CU... |
2195f0d0885c8a34a677797c6c4f20b2ae186625f68e0ad04533202a8d26e19a | Shell | 699 | 31 | #!/bin/bash
# much slower than perl version
# read jobnumbers in current directory (and directory passed as variable) and kill them (start at the last job and move to oldest)
if [ $1 ]; then
if [ -e "$1/jobnumbers.out" ];then
tac "$1/jobnumbers.out" |
while read line
do
echo "$1/jobnumbers.out": Stopping $... |
6b58d379de1e7ebdacf4f05d72197e859307701f1512156c0619fb6ea098e57d | Shell | 701 | 31 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
e3ca6e769a4915474e4b4daf6f6ca4015c58c229b72d910f7866dae8b4792697 | Shell | 701 | 15 | #!/bin/bash
# Run Jupyter in foreground if $JUPYTER_FG is set
if [[ "${JUPYTER_FG}" == "true" ]]; then
jupyter-lab --allow-root --ip=0.0.0.0 --no-browser --NotebookApp.token=''
exit 0
else
nohup jupyter-lab --allow-root --ip=0.0.0.0 --no-browser --NotebookApp.token='' > /dev/null 2>&1 &
echo "Notebook ser... |
0b2139088b0f3011bfcb3e89e98e380edffb635dd6434c86350dc25871c82b2b | Shell | 702 | 30 | #!/bin/bash
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
CDIR="$( cd ${IDIR}/../compiletools && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
# Cleanup some old stuff
rm -rf ${BDIR}/install
rm -rf ${BDIR}/doc
echo ""
echo "**********************************************... |
8118ae89646464dd05e2abf3769c310ac0bd1d67ea14f53a134cec8244f489dd | Shell | 702 | 23 | #!/bin/bash
# Usage: bash download_helixfold3_checkpoints.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c... |
f089bfd3ce6bd446a0c32cd0638f6d89496d09c476a7e79a382b99c354a7407e | Shell | 702 | 38 | #!/bin/bash
BAM=$1
BW=$2
factor=$3
TMPD=$(mktemp -d -p .)
mkdir -p $TMPD
samtools idxstats $BAM | cut -f 1,2 | grep -v \* | grep -v _ | grep -v ERCC > $TMPD/chrom.sizes
BDGS=""
echo $(date --rfc-3339=seconds) Converting chroms to bedGraph...
for chrom in $(cut -f 1 $TMPD/chrom.sizes);
do
BDG=$TMPD/$chrom.bedGr... |
a26752850ec7af19c8f8cd269c112efe75531d11322a25316453dfd213b34bf5 | Shell | 706 | 25 | #!/bin/bash
## assume script is launched from vsearch/man/
## usage: bash scripts/visualize_manpage.sh commands/vsearch-cut.1.md
##
## Render one markdown source and page through it, without writing
## anything: the quickest way to see the effect of an edit.
## the path is computed, so only "shellcheck -x" can follo... |
e8c9200ff957a8d0c4cd7e683f3142e685e1a79bd055c9575c461ce26db7847e | Shell | 706 | 37 | #!/bin/bash
ROOT="."
MRI="$ROOT/mri/crop/mri.crop.mgz"
INFRASUPRA="$ROOT/mri/crop/infrasupra.smooth.crop.mgz"
MRI2OCT="$ROOT/mri2oct/affine/affine.lta"
for i in {08..23}
do
AFFINE="$ROOT/oct2lsfm/nonlin/$i/affine.lta"
NONLIN="$ROOT/oct2lsfm/nonlin/$i/svf.nii.gz"
TARGET="$ROOT/lsfm/slide_center_oct/neun.${i}.nii.gz"
... |
c9503503a76efbf1246b73ea04b3bed82acefb88338eea48dc1c8fd5591d52fe | Shell | 708 | 26 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --time=48:00:00
#SBATCH --mem=60GB
#SBATCH --account=bbenayou_34
#SBATCH --partition=epyc-64
#SBATCH --mail-type=all
#SBATCH --mail-user=alanxu@usc.edu
# Author: Alan Xu
# Software Used: fastp version 0.23.2
WORKDIR=/scratch2/alanxu/2... |
7143902f0ade3b02c407522f6c30389bc76c1d5f50abdfcbbbbcfa91046a2b4d | Shell | 710 | 19 | #!/bin/bash
#--- Switch to the correct path (where the script is in)
backpath=`pwd`
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd $DIR
#--- Download the compressed file
wget -nc http://www.acfr.usyd.edu.au/papers/data/sydney-urban-objects-dataset.tar.gz #This is the original dataset (we just need some li... |
0eb96fa79aed867df55b67ff94266ae0d7cb7c247010e6947d4cae6799acbaed | Shell | 711 | 17 | #!/bin/bash
#set -x
NAME="primary alignment test"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`
PARAME... |
fa488f4474bad18d0b66353dab72b61e955e530333a8cb60aebf3b0a9f901026 | Shell | 712 | 9 | #!/bin/bash
bedtools intersect -a F-2-1.sorted.bam.filter.bam -b 31RPMF_out.txt_final.bed > F-2-1.sorted.bam.filter.bam.region.bam
bedtools intersect -a F-2-2.sorted.bam.filter.bam -b 42RPMF_out.txt_final.bed > F-2-2.sorted.bam.filter.bam.region.bam
bedtools intersect -a F-2-3.sorted.bam.filter.bam -b 31RPMF_out.t... |
fdf2e5f0f709f8ce36fbaacde6efeb35b11f3a6ea809eaac85734948ce95357c | Shell | 715 | 19 | # set -ex
config_file='Image_translation_codes/MUNIT/configs/SEN1_2_20%_summer.yaml'
input_folder='Image_translation_codes/MUNIT/datasets/SEN1_2/20%_train/ROIs1868_summer_20%_train/testA/'
output_folder='Image_translation_codes/MUNIT/results/SEN1_2_20%_summer/images/'
checkpoint='Image_translation_codes/MUNIT/outputs/... |
8c7d80cacbdcb596a3d04cf4ff4263fb0ec9fb1e7e1e693a792836446db27c93 | Shell | 717 | 20 | # set -ex
for ((i=1; i<=5; i++));
do
echo "Processing"$i"th epoch..."
# --- pix2pix ---
# python Image_translation_codes/pytorch-CycleGAN-and-pix2pix/test.py \
# --dataroot Image_translation_codes/pytorch-CycleGAN-and-pix2pix/datasets/combined_sar2opt \
# --name sar2o... |
def07310bcd22667ce44b02aa5ac1bb6915a2a3b88250f0e4ffda2dc6084342b | Shell | 719 | 25 | #!/bin/bash
echo "Copying binary builds"
echo "------------------------------------------------------------------------------------"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR="${DIR}/../../build"
cd ${DIR}
WASMDIR=${DIR}/../various/wasm/
cp ${DIR}/web/libbiswasm_wasm.js ${WASMDIR}
cp ${DIR}/web/li... |
46f1b55ea7fd788ebc26db0e96083e07e589ce15a40fe125025f16b0c229ed42 | Shell | 721 | 6 | #PBS -l walltime=72:00:00
#PBS -l select=1:ncpus=32:mem=62gb
#PBS -J 4-22
module load anaconda3/personal
python2 RunRFMix.py PopPhased /rds/general/project/human-popgen-datasets/live/HGDP_1000g/${PBS_ARRAY_INDEX}/HGDP_1000gNYC_3pop_target_ref_rfmix154_short_B_${PBS_ARRAY_INDEX}_AFRAME.phased.alleles /rds/general/projec... |
a913cc4ff4bda4c69d8b95cd64bc68304f54c6fb6a744740d576f03e1e7c1914 | Shell | 723 | 19 | #!/bin/bash
#base project path
base_dir=/gladstone/bioinformatics/adnetworksppg/Project_1_Huang/NK01
# path to the cell ranger script
cellranger_script=$base_dir/scripts/YH_NK01/HMGB1_snRNA_mm10/cellranger_count_batch1_batch2_merged/cellranger_count_batch1_batch2_merged.sh
#make the results output directory
mkdir $b... |
fd34663527972626e5f424da2d8b8cd300092cc0d56d209f4bd5751ba354e0cb | Shell | 723 | 30 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
f8bd3dadc17c0b2477d8d44ccdc880836875bd202b15526847c057e50a79188b | Shell | 726 | 28 | #!/bin/bash
#
#SBATCH -J anat # A single job name for the array
#SBATCH -n 1 # Number of cores
#SBATCH -p medium # Partition
#SBATCH --mem 8000 # Memory request
#SBATCH -o LOG/anat_%A_%a.out # Standard output
#SBATCH -e LOG/anat_%A_%a.err # Standard error
# Ensure there is a LOG directory
export FSLOUTPUTTYPE=NIFTI_... |
6194246378806fd1166c1e410b8380bf089ef61895b1511837e3984c3be222a9 | Shell | 727 | 21 | #! /bin/bash
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/T1_analysis/
cd $filepath
ls | grep -i sub- >$filepath/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the high or low cases
for sub in $(cat $filepath/subjList.txt); do
export SUBJECTS_DIR=/Users/w... |
0b790e77e378877bf29e7039562b46b5a97bf979ca6529795c25e5f02ae9039a | Shell | 728 | 23 | #!/usr/bin/env bash
# CI test gate: CPU-only, tracked-files-only subset of tests/torch.
# Exclusion baseline: ci/known_failures.txt (node IDs -> --deselect),
# ci/collect_ignores.txt (files -> --ignore). Policy: docs/ci.md.
set -euo pipefail
cd "$(dirname "$0")/.."
export CUDA_VISIBLE_DEVICES=""
args=(tests/torch -m ... |
d4603b36a59695b48b8e6ca841e4ced2ede730f31fb364e19c56546d6b939133 | Shell | 729 | 29 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
bd461816ca3a6847487ebeb2e113705ffc0add17eeb1f1f84150e4be7d21db79 | Shell | 734 | 20 | # affine transformation parameter for masking (for reg_aladin)
# -nac: initialize transformation with nifty header (default: centre of image)
# -cog: centor of mass/gravity of mask to initialize transformation (default: centre of image)
affine_param="" # e.g. -rigOnly -nac
# parameter for reg_resample
resamp_param=""
... |
8e2d1b49f67b4b0e83901b0bd89bc8770b40b164c89b1d7012e64e408eda3400 | Shell | 736 | 27 | #!/usr/bin/env bash
set -euo pipefail
artifact_dir="${1:-bazel-testlogs-artifact}"
testlogs_dir="$(bazel info bazel-testlogs 2>/dev/null || true)"
if [ -z "${testlogs_dir}" ] || [ ! -d "${testlogs_dir}" ]; then
echo "No Bazel testlogs directory found."
exit 0
fi
rm -rf "${artifact_dir}"
mkdir -p "${artifact_dir... |
06180dde292d5017e60994c3284561bbf820e3e7b0a526e17c4df03681272480 | Shell | 737 | 28 | #!/bin/bash
echo "------------------------------------------------------------------------------------"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR="${DIR}/../build"
mkdir -p ${DIR}
cd ${DIR}
mkdir -p ${DIR}/web
mkdir -p ${DIR}/wasm
mkdir -p ${DIR}/dist
WASMDIR=${DIR}/../various/wasm/
cp ${WASMDIR... |
74eac9f7a41c9bdd9ac04e5f179a6d761544eb4a534254e04925e8b8387fd8ee | Shell | 738 | 28 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH train --hla_class HLA_I \
--data_dir data/HLA_I_all_match/train_valid \
--model_dir ... |
9326e80acb27a0288fc19e110c0153d1bd094e5aa39eebe9158506096f24b4de | Shell | 740 | 28 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH train --hla_class HLA_I \
--data_dir data/HLA_I_full_mcpas/train_valid \
--model_... |
395cdbc995407371531408adae0b99e88e1d9af16eb7d696886a1d9ea8759d22 | Shell | 742 | 38 | #!/bin/bash
#SBATCH --time=0-03:00:00
#SBATCH --mem-per-cpu=4000
#SBATCH --array=0-14
#SBATCH --output=./slurm_logs/slurm-%A_%a.out
SUBJECTS_DIR=/scratch/n/tbi/mri_recons
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "SUBJECTS_DIR set as $SUBJECTS_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
ml purge
module load teflo... |
815fb297144c19cab11ea43e3c02b4a6478262bee9654ea53d5aa8bbd832f2e3 | Shell | 742 | 27 | #!/bin/bash
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
echo "_______________________________________________________________________"
echo "___ "
echo "___ Running smoke test"
echo "___ SRCDIR=${SRCDIR}, BDIR=${BDIR}"
echo "___"
... |
c95cfc5142264bf105ebcee7d4223df9f26ea8777b03024d9c12ee5b57fb0bb9 | Shell | 742 | 45 | #!/bin/bash
set -xe
source $(dirname "$0")/all-vars.sh
source $(dirname "$0")/all-utils.sh
source $(dirname "$0")/asserts.sh
bitrate=$1
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "${model_source}")
down... |
b72903b337e9381a4a1cfd23629bd01296e0a6334baff2bcbc45bb60b921d432 | Shell | 743 | 20 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
b920139fdfafb328197e5876d080b23c6a2961d90b2e2cc2ad13457dc2cf9a49 | Shell | 744 | 17 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
bd8bc43b700f15a0e58e8ce413fad4d31d82c40b077805247fdbd0e876ee6061 | Shell | 745 | 28 | #!/bin/bash
declare -i i=0
seed_file="ensemble_seeds_20.txt"
while IFS= read -r line
do
stringarray=($line)
rseed=${stringarray[0]}
np_seed=${stringarray[1]}
tf_seed=${stringarray[2]}
i+=1
DePTH train --hla_class HLA_II \
--data_dir data/HLA_II_all_match/train_valid \
--model... |
2c3e757c9eb0fc6579e373da0b6c6f62aacdda68affc5b1e328b29ed44c40c0e | Shell | 747 | 41 | #!/bin/bash
#SBATCH --time=0-01:30:00
#SBATCH --mem-per-cpu=10000
#SBATCH --array=0-73
#SBATCH --output=./slurm_logs/slurm-%A_%a.out
ml purge
module load teflon
ml anaconda3
conda init bash >/dev/null 2>&1
source ~/.bashrc
conda activate mne
TBI_DIR=/scratch/n/tbi-meg/v/processed/
CAMCAN_DIR=/scratch/n/restmeg/v/proc... |
2c520c2855ef89da14461123ebe2956bf9627afec4f621205ab933c8f559600a | Shell | 747 | 41 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
bitrate=$2
set_ldc_sample_filename "${bitrate}"
download_data
node --version
npm --version
NODE_ROOT="${DS_ROOT_TASK}/ds-test/"
NODE_CACHE="${DS_ROOT_TA... |
9e4a387d1a4f55144168067b9507a85ccad2d3b3f0740bfd674f86477058a4f3 | Shell | 748 | 19 | #!/bin/bash
#Run scripts for gut cell atlas analysis that is specific to 6mo_lmmp project
#Projections through the patterns learned in the 6month lmmp scRNA
R -e "rmarkdown::render('gut_atlas_projections.Rmd', output_file= 'gut_atlas_projections.html')"
#TODO: Projection_drivers based analysis - unfinished
R -e "r... |
fb2e83665df687fcba92917f3f9bb143e6f60f5589aa00d6b87a6da76e9ac3e2 | Shell | 748 | 34 | set -ex
MODEL='bicycle_gan'
# dataset details
CLASS='edges2shoes' # facades, day2night, edges2shoes, edges2handbags, maps
NZ=8
NO_FLIP='--no_flip'
DIRECTION='AtoB'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=1
NITER=30
NITER_DECAY=30
# training
GPU_ID=0
DISPLAY_ID=$((GPU_ID*10+1))
CHECKPOINTS_DIR=../checkpoint/${CLASS}/
NAM... |
30c9cdcb30fc18cd729477181ef27b1297900c1f7f4d7fbf1a1cf6e71acf423e | Shell | 749 | 21 | # this script will run FastSMC on a simulated data as described in the paper (in FILES/FASTSMC_EXAMPLE/)
# parameters can be changed if desired
cd ../FASTSMC_BUILD_DIR/ || exit
./FastSMC_exe --inFileRoot ../FILES/FASTSMC_EXAMPLE/example \
--outFileRoot ../cpp_example/FastSMC_output_example \
--decodingQuantFile .... |
c7ec9d300a8249bad297437fe4444196fdf26dde01f0328392111b99787555b9 | Shell | 749 | 38 | #!/bin/bash
ROOT="."
for AFFINE in $ROOT/mri2oct/affine*/affine.lta
do
AFFDIR=$(dirname $AFFINE)
echo $AFFDIR
nitorch reslice \
"$ROOT/mri/crop/mri.crop.mgz" \
-l $AFFINE \
-t "$ROOT/oct/oct.nii" \
-o "$AFFDIR/mri.crop.reslice.12um.mgz"
nitorch reslice \
"$ROOT/mri/crop/mri.crop.mgz" \
-l $AFFINE \
-t "$RO... |
f02572e93018f5173d96bfccc343f5f11fe9ccd10ab04e009d89597bd5794b09 | Shell | 749 | 34 | set -ex
MODEL='bicycle_gan'
# dataset details
CLASS='edges2shoes' # facades, day2night, edges2shoes, edges2handbags, maps
NZ=8
NO_FLIP='--no_flip'
DIRECTION='AtoB'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=1
NITER=30
NITER_DECAY=30
# training
GPU_ID=0
DISPLAY_ID=$((GPU_ID*10+1))
CHECKPOINTS_DIR=../checkpoints/${CLASS}/
NA... |
7263729d121148d98c688c63a34ff4ae17b7ddbb77b3f877aceaa0b568cdc289 | Shell | 751 | 42 | #! /usr/bin/env bash
set -eu
function run_tests() {
echo ""
echo "Running tests:"
for f in test_*.py simulate.py
do
if [[ -f "$f" ]]
then
echo "${usecase_dir}/$f: started."
python "$f" $1
echo "${usecase_dir}/$f: success."
fi
done
echo "All tests were successful."
}
if [[ $# ... |
385aeb2d30f28f0b686680c8a9906305e075c6f2ed7514f6a898045d8872c61e | Shell | 752 | 34 | set -ex
MODEL='bicycle_gan'
# dataset details
CLASS='opt2sar' # facades, day2night, edges2shoes, edges2handbags, maps
NZ=8
NO_FLIP='--no_flip'
DIRECTION='AtoB'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=3
NITER=30
NITER_DECAY=30
# training
GPU_ID=0
DISPLAY_ID=$((GPU_ID*10+1))
CHECKPOINTS_DIR=../checkpoint/${CLASS}/
NAME=${... |
bdef17dc2a9084799f69f44b63fb85908577599c1c9a901c8d8c908df907a1f7 | Shell | 752 | 20 | #!/bin/bash
# export CHECK_FOLDER='adversarial_examples/manifolds_dataset_jsinv3_word_audio_subsetREPTYPEcoch_RS0_l2_E1.000_I32_S0.100/'
# export CHECK_FOLDER='adversarial_examples/manifolds_dataset_jsinv3_word_audio_subsetREPTYPEcoch_RS0_l2_E0.300_I32_S0.100/'
export CHECK_FOLDER='metamers/400_16_class_imagenet_val_i... |
e3f22a94506788c158855f5de9f78ba99bfc67a5156773cf05578e89f846d798 | Shell | 753 | 34 | set -ex
MODEL='bicycle_gan'
# dataset details
CLASS='sar2opt' # facades, day2night, edges2shoes, edges2handbags, maps
NZ=8
NO_FLIP='--no_flip'
DIRECTION='AtoB'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=3
NITER=200
NITER_DECAY=200
# training
GPU_ID=1
DISPLAY_ID=$((GPU_ID*10+1))
CHECKPOINTS_DIR=./checkpoint/${CLASS}/
NAME=$... |
1e620c34489b66a394accac1d14e4c00aea5394afc793140f6dfa16d4ebcf5ff | Shell | 754 | 6 | /usr/share/fsl/5.0/bin/fslreorient2std /mnt/scans/HN-CHUM-001/image.nii.gz /mnt/output2/HN-CHUM-001_im.nii.gz
/usr/share/fsl/5.0/bin/fslreorient2std /mnt/scans/HN-CHUM-001/mask_GTV.nii.gz /mnt/output2/HN-CHUM-001_mask.nii.gz
/usr/share/fsl/5.0/bin/fslmaths /mnt/output2/HN-CHUM-001_im.nii.gz -mas /mnt/outputmasks/HN-CHU... |
fe7d97f723ef7a5b7bf5a72473edf33097ed227bc0611da50d72e095f83133dc | Shell | 756 | 25 | #!/bin/bash
echo "Copying binary builds back to build directory"
echo "------------------------------------------------------------------------------------"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR="${DIR}/../../build"
cd ${DIR}
WASMDIR=${DIR}/../various/wasm/
cp ${WASMDIR}/libbiswasm_wasm.js ${D... |
42a0f40214cad8e36da23d0440cf8114d434cd314260d9b746503c9eb850a2fa | Shell | 757 | 25 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-10
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/coembed
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/fimo_celltypes.txt`
input=${wd}/fimo/${celltype}_peak_seqs/da_peak_seqs.fa
outfh=${wd}/fimo/${celltype}_pea... |
ce28af922e9bc988ce99b0d7360bfb3fb151317ac2148fe35e38f0d528c620e6 | Shell | 757 | 36 | set -ex
MODEL='bicycle_gan'
# dataset details
CLASS='facades' # facades, day2night, edges2shoes, edges2handbags, maps
NZ=8
NO_FLIP=''
DIRECTION='BtoA'
LOAD_SIZE=256
CROP_SIZE=256
INPUT_NC=3
NITER=200
NITER_DECAY=200
SAVE_EPOCH=25
# training
GPU_ID=0
DISPLAY_ID=$((GPU_ID*10+1))
CHECKPOINTS_DIR=../checkpoints/${CLASS}/... |
74dace70c6568f9436cc6e57534315d06662a0f3a6666594924198c37e85caae | Shell | 758 | 33 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
set_ldc_sample_filename "${bitrate}"
download_data
virtualenv_activate "${pyalias}" "deepspeech"
if [ "$3" = "cuda" ]; then
deepspeech_pkg_url=$(get_pyth... |
06bd985f988e98e7d4b7b8f803f238b0692159c4a32d6129ef8a7b955777482d | Shell | 760 | 30 | #!/bin/bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd $DIR
if [ -d build ]
then
rm -r build
fi
JAVA_VER=$(java -version 2>&1 | sed 's/java version "\(.*\)\.\(.*\)\..*"/\1\2/; 1q')
if [[ "$JAVA_VER" < "17" ]]; then
echo "Java 7 or higher is required! Your version is..."
java -version
... |
becd69fe1a7c339c9ac5d9e2c48a3967a22ea5eec06063f2d8fd0698adba5c65 | Shell | 761 | 25 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-10
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/coembed
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/fimo_celltypes.txt`
input=${wd}/fimo/${celltype}_peak_seqs/all_peak_seqs.fa
outfh=${wd}/fimo/${celltype}_pe... |
0c1be5379f6598c1114dc207db7185be9eaad7b80466600a58a3782ebde24d42 | Shell | 762 | 19 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=6:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node094
module add openmind/min... |
a8c70cc6fd833929bfd72710615e776af445c75a0c25836ca6eada796e91510f | Shell | 765 | 24 | #!/bin/bash
#To run this for 1000 permutations execute:
# `sbatch --array=1-1000 permutations.slurm.bash`
#Slurm submission options
#LOOK AT THESE AND EDIT TO OVERRIDE FOR YOUR JOB
#!/bin/bash
#Slurm submission options
#SBATCH -o npointperm_%A_%a.out
#SBATCH --mail-type=END
export OMP_NUM_THREADS=1
#You shouldn't n... |
05d05003204952c5cb1881dc3dc4ff4fe28ee69f3c75eab028830875e0c7c33e | Shell | 766 | 26 | #!/bin/bash
dir=`pwd`
out_file=${dir}/../../out_midinvar/fixedeff_map_qc.csv
folder=/scratch.global/${USER}/analyses/fixedeff
background_mni=../ROI/MNI152NLin2009cAsym_res-02_desc-brain_T1w.nii.gz
# location nucleus accumbens
vox_x=44
vox_y=72
vox_z=37
min_thresh=0.5
max_thresh=5.0
for sub in `echo ${folder}/sub-* `... |
19495ee8be06995bb30f2fb45a2e1c10c434d7b774f29fec067c3cdb8fb5206e | Shell | 766 | 25 | #!/bin/bash
# ./scripts/test_historical_batch.sh "RepECN" 48 "repecn_t repecn_s repecn_b" "2 3 4"
# ./scripts/test_historical_batch.sh "ALAN" 48 "v1t v1s v1b" "2 3 4"
# ./scripts/test_historical_batch.sh "CARN DRRN EDSR-baseline LapSRN LatticeNet LBNet SwinIR" 48 "no" "2 3 4"
# ./scripts/test_historical_batch.sh "Shuf... |
55b406a88127420cb1094c5d9aae4afa9e97353260b653974a4c5fdc38483f0e | Shell | 767 | 25 | #!/bin/bash
# Usage: bash download_helixfold3_checkpoints.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c... |
d876fcd34d9c2cf3c3f1045f81752652636f045c32d3d7f171c0d1025ba0db00 | Shell | 767 | 36 | #!/bin/bash
#SBATCH --time=0-00:30:00
#SBATCH --mem-per-cpu=8000
#SBATCH --array=0-4
#SBATCH --output=./slurm_logs/slurm-%A_%a.out
SUBJECTS_DIR=/scratch/n/tbi/mri_recons
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "SUBJECTS_DIR set as $SUBJECTS_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
ml purge
module load teflon... |
e84406f4ce66701904f7674b2b75665b4e86a1bf5c0762b09259228ec17ef10d | Shell | 767 | 32 | #!/bin/bash
set -e
set -x
pytest \
--cov-report=xml \
--cov-report=term \
--cov=rpy2.rinterface_lib \
--cov=rpy2.rinterface \
--cov=rpy2.rlike \
./rpy2-rinterface/src/rpy2/rinterface/tests \
pytest \
--cov-append \
--cov-report=xml \
--cov-report=term \
--cov=rpy2.rinterface_li... |
c85312217dddd5a6204fd78c013317a03783a23496ff08b4e71586936fa3f08f | Shell | 768 | 24 | # 修改此处数据集路径
path='./datasets/SEN1-2/20%_train/ROIs1158_spring_20%_train'
# 修改此处
name='re-SEN1-2_20%_spring'
# 修改此处数据集样本数量
data_length=3898
# （弃用）10%: spring: 1948 summer: 1220 fall: 2028 winter: 1012
# 20%: spring: 3898 summer: 2440 fall: 4058 winter: 2025
# （弃用）50%: spring: 9746 summer: 6102 fall: 1... |
1d72756d3b9495bc798f5992752f2e9427697f658a3fcedd08047931047547ff | Shell | 770 | 26 | #!/bin/bash
# Usage: bash download_mgnify.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt insta... |
a9f7a3c9f4d961a376f76d408dc413876d22583f4c1c6e4f38e769aedbd88bb3 | Shell | 770 | 27 | #!/bin/bash
#SBATCH -n 1
##SBATCH --partition=pool1,gpu,pool3-bigmem
##SBATCH --time 8:00:00
#SBATCH --partition=pfen1
#SBATCH --exclude=compute-1-[39-40]
#SBATCH --job-name=permute
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
#SBATCH --error=logs/permut_sex_in_oud_degs_%A_%a.txt
#SBATCH --output=logs/permut_sex_in_oud_... |
0a688252968bef5c00ba3dc9f5b7278683111222b8126052920014b396f43eee | Shell | 772 | 15 | #! /bin/bash
set -xe
gtftools.py -l test.len Data/test.gtf && diff -q test.len Data/test.len
get_tpm_fpkm.py -c Data/test.count -g test.len && gunzip test_count_fpkm_tpm.tsv.gz && diff -q <(grep -v '#' test_count_fpkm_tpm.tsv) <(grep -v '#' Data/test_count_fpkm_tpm.tsv)
get_tpm_fpkm.py -c Data/test2.count -g test.le... |
aecc920012ed67868f246cc120675b3aa5ff389a6ae1382da4b64b3b64796ea4 | Shell | 773 | 25 | echo "------------------------------------------------------------------------------------"
export PATH=/usr/bin:${PATH}
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR="$( cd ${IDIR}/.. && pwd )"
echo "DIR=${DIR}"
EDIR=${DIR}/emsdk_portable/
source ${EDIR}/emsdk_env.sh
export PATH=${DIR}/js/bin:${DI... |
2f2ffc9f6841931e9adede9d43f2f4e58ab6788250fc16fd34d5c5773d3a8993 | Shell | 774 | 14 | #!/bin/bash
#SBATCH --cluster=beef # Don't change
#SBATCH --partition=long # Don't change
#SBATCH --account=researcher # Don't change
#SBATCH --job-name=aav5_sampling
#SBATCH --output=sampling_results_4.out
#SBATCH --gres=gpu:0 # Number of GPU(s) per node.
#SBATCH --cpus-per-task=8... |
53135312212f8addb978ffee0fc6a2f8196bc80a3a7e89f58a7e25d5174e2460 | Shell | 778 | 29 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSPEECH_PROD_MODE... |
927471f33124d47f0747a95680c73d875b1287a1a87b40f326e0c3fad80666d5 | Shell | 778 | 31 | set -ex
# models
RESULTS_DIR='./results/facades'
# dataset
CLASS='facades'
DIRECTION='BtoA' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 # gpu id
NUM_TEST=10 # number of input images d... |
2df7d4deac17eb7473a65cde19a7df614146a9929e7642a4ea1174c21bc277c6 | Shell | 779 | 26 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
audio_sample_rate=$1
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi;
# Force only... |
9cfb4183f75c25866813188ee56c7ed88965802ba3c1c10d35076f2eab970970 | Shell | 780 | 26 | #!/bin/bash
# Usage: bash download_mgnify.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt insta... |
05f1a70ade8cc0e42ae0a712f1753df753ce702418e9f0faee024f29fb028000 | Shell | 781 | 36 | #!/bin/bash
#Usage TODO
#Direcotry paths use global assigment
project_path=$1
image_folder=$2
cd ${project_path}
#Obtain patient list
mkdir -p DATA
find ${image_folder} -name "*.nii" | awk '{ print }' > DATA/patient_list.txt
# Create directory to store subject images
mkdir -p SUBJECTS
count=1
for i in $(cat ${pr... |
264983fa01d9f22b2f5ad62d848a173e598cc105e47a03e424d595afc9805f02 | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 2 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
83fcd7d90548b3e610c2da3a525da6678ebd2811e94612620491dd54cbc7eb75 | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 5 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
e4137e959cb50b3727ccabd64b640cd578ecf308cd04edf813cfdf13cd2bbe9c | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 4 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
e80c6be98d476a00d0d9eded88e3e9db7c33131698c843b5e1cccad8ba1c191d | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 1 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
e9a3918a82fbdb252b73ffe3b66f378382ba362015fa7a9ba7920f13ee5673d2 | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 6 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
eaa69c98fc8d76bdb392c2b15629194a5653392f14e0ce023b4ae2ebd07fb905 | Shell | 783 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 3 0 21
python run_AutX_pulses_true_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_IN... |
e077801bd8382185f5b815f780d3c9a7363267eafafbf1ca46b9d1d1b98c4dfa | Shell | 785 | 31 | set -ex
# models
RESULTS_DIR='results/combined_sar2opt'
# dataset
CLASS='combined_sar2opt'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 # gpu id
NUM_TEST=627 # number ... |
79b3b7d4ee5b5e91a3e75d924b6c707c7fcb709578fefb29be52fc50e6d97cf9 | Shell | 787 | 31 | set -ex
# models
RESULTS_DIR='./results/combined_sar2opt'
# dataset
CLASS='combined_sar2opt'
DIRECTION='BtoA' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 # gpu id
NUM_TEST=627 # numbe... |
ef1eb77a793b8b5bb9f24959363b2e08b6c1b3bdcd6138dd4192101cfd54c538 | Shell | 787 | 20 | #!/bin/bash
#SBATCH --job-name=met_cornet
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=4:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node093
#SBATCH --partition=normal
module add openmind/m... |
172337962071aaef134f962b5b70f9b60b472cb18b2a52f34ae49e86f023905a | Shell | 788 | 26 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/coembed
# celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
rds=$wd/data/rds/full_cocaine_dataset_with_naive_rn... |
f90be079729ce029384cf2e7f8fe3bfe16f27015fb3fa8353cb0f64b0dfd2f26 | Shell | 788 | 38 | #!/usr/bin/env bash
#
# declare default implementation for initializing a runtime environment
# Usage: initEnv <runtime-env-name>
#
function initEnv() {
if is_debug; then
# only when GP_DEBUG="true"
echo "initEnv(): initializing '$1' environment ..."
fi
}
#
# initialize the default, canonical ... |
3c9f85399b2cce18818d9112816e34306ecf05b4976d665f15062e07475703fb | Shell | 789 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=5:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node094
#SBATCH --partition=norm... |
5944cd311b9645dfa9389ac2bf14d7e92c8c2229c9120cb563b792477696c4e3 | Shell | 789 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=9:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=1-5
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node094
#SBATCH --partition=normal... |
642a8098ef80aeaf03dfd0ffaa5126145546e5aeda9ffacb7fb5305ee9d9998d | Shell | 789 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 5 0 21
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_... |
69d8847c007ab231d32f1ee3b35e66ed20037e09c18080d617a377eb23b5c300 | Shell | 789 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=6:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node094
#SBATCH --partition=norm... |
7a38027e83a4865c1734fc4be8c8cae88b8abbff2e743fef2340faa03416ba1e | Shell | 789 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=4:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node093
#SBATCH --partition=normal
module add openmind... |
867155907902abfe7e5b01ff3fc6c802d6f7dac1da332896e7ce5708d9508927 | Shell | 789 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=9:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint="high-capacity&11GB"
#SBATCH --exclude=node093,node040,node094
#SBATCH --partition=norm... |
f3ddb874d996d6d0cfa4f9c88a3c2e04a262fb4fcd1691e16f06901aecce1d47 | Shell | 789 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 3 0 21
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_... |
60c49cdef5988b57053ea6199494f1d91182e2a6d96409ccf8f2799de3cccb3a | Shell | 790 | 10 | #PBS -l walltime=23:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-1000
module load anaconda3/personal
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY_INDEX 6 0 21
python run_AutX_pulses_false_fully_connected_scale10E3_rfmix_gnomix_maxanc_onlyfemales.py $PBS_ARRAY... |
8ad6bd95140f4fabc2a17d2966c5ccfbf5d47ebb0aa99e0dc896e79983c0e4d5 | Shell | 790 | 14 | #!/bin/bash
#SBATCH --cluster=beef # Don't change
#SBATCH --partition=long # Don't change
#SBATCH --account=researcher # Don't change
#SBATCH --job-name=aav5_optimize
#SBATCH --output=opt_results_nuc_15.out
#SBATCH --gres=gpu:0 # Number of GPU(s) per node.
#SBATCH --cpus-per-task=8... |
aaf0cb626b1abcd84628389452e071e4c2b37820218bf7161da66a4d5a50edb2 | Shell | 790 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet101
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=6:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node093
#SBATCH --partition=normal
module add openmin... |
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