sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
00137019293b1e3d7a3f82c5a337234621600bcacfb31043da8ba01ba5e5a54f | Shell | 642 | 30 | #!/usr/bin/env bash
currentJob=0
dir=/export/a04/gkumar/kaldi-trunk/egs/fishcall_es/j-matt/exp/sgmm2x_6a_denlats
for f in $dir/.done.*; do
d=`echo ${f##*/} | awk 'BEGIN {FS="."} {print $3}'`
if [ $d -gt $currentJob ]; then
currentJob=$d
fi
done
currentJob=$((currentJob+1))
echo Currently proces... |
72e65cb0e5ebc58cc01835ec5b093f8878cf8bab800934cf712a3dcd51d72ef3 | Shell | 642 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/s7_%A.out
#SBATCH --job-name s7_msfi
#SBATCH --partition=long
module load LANG/P... |
b7e0776e0f181e738c29dba952770ea718d573c5960ca17eb15a54ebe4e1f98e | Shell | 642 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/s9_%A.out
#SBATCH --job-name s9_msfi
#SBATCH --partition=long
module load LANG/P... |
c774d3f5717ce8c9ef30397740ce741c88610dbdc5f82441e341588e07c085cd | Shell | 642 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/s6_%A.out
#SBATCH --job-name s6_msfi
#SBATCH --partition=long
module load LANG/P... |
df85c9b987617b66193ef7ed248942f0b4c2518e645bfaa125f2af10c27b6ccf | Shell | 642 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/s8_%A.out
#SBATCH --job-name s8_msfi
#SBATCH --partition=long
module load LANG/P... |
1399b7e5f1cd568b9a78ee6decd14acd547e3f2ff42b0a78478c64129b18927a | Shell | 643 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/acc_drop/s7_%A.out
#SBATCH --job-name s7_acc_drop
#SBATCH --partition=long
module load LA... |
cb470e483d55c91368843643b1e762b70a9c540fbd5811e6fcad78810ec9316f | Shell | 643 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/acc_drop/s9_%A.out
#SBATCH --job-name s9_acc_drop
#SBATCH --partition=long
module load LA... |
d2f7b9d18e88276516935eac6a0dc5b433b70f5b8436f6e57dc25d7dadd142e1 | Shell | 643 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/acc_drop/s8_%A.out
#SBATCH --job-name s8_acc_drop
#SBATCH --partition=long
module load LA... |
f77865af81d6aa76af11bdbe282f19583373d56885c926745df5f76fcda5bb2d | Shell | 643 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/acc_drop/s6_%A.out
#SBATCH --job-name s6_acc_drop
#SBATCH --partition=long
module load LA... |
12a394150e7176ebf76bca19e5b9a2b0b20293d4b121e13c1097d05ee2a3bc39 | Shell | 644 | 22 | #!/usr/bin/env bash
set -e
. ./cmd.sh
. ./path.sh
steps/get_prons.sh --cmd "$train_cmd" data/train data/lang exp/tri5a
utils/dict_dir_add_pronprobs.sh --max-normalize true \
data/local/dict exp/tri5a/pron_counts_nowb.txt \
exp/tri5a/sil_counts_nowb.txt exp/tri5a/pron_bigram_counts_nowb.txt data/local/dict_pp
u... |
9a215b6c22270e7d654262b843e4e9646f4e5d59178282a69ec8ce32ae4ac4b0 | Shell | 645 | 17 | #!/usr/bin/env bash
echoerr() { printf "%s\n" "$*" >&2; }
# Load the conda environment
if [ -z "$CONDA_DEFAULT_ENV" ]; then
echoerr "Load the conda environment ..."
source /opt/conda/bin/activate /gscmnt/gc7201/dinglab/medseq/lwang/conda_root/envs/gatk_wxs_cnv
fi
# Run snakemake via bsub
echoerr "Launch the L... |
ee9faad66e9b9edfac72b99445ee1999e6432bfb4e72afb796ee5863cdf201d7 | Shell | 645 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/s10_%A.out
#SBATCH --job-name s10_msfi
#SBATCH --partition=long
module load LANG... |
c5a88e2ca43a351a0076d00499caa277b4f3ae3e6588e359259e8be7a1752bc6 | Shell | 646 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/acc_drop/s10_%A.out
#SBATCH --job-name s10_acc_drop
#SBATCH --partition=long
module load ... |
1e22604b335ef2005e291b661213102e176a4df33fc0316d93b741c776cba4c3 | Shell | 647 | 12 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
export PYTHONPATH=$PYTHONPATH:$masif_source
PDB_ID=$(echo $1| cut -d"_" -f1)
CHAIN1=$(echo $1| cut -d"_" -f2)
CHAIN2=$(echo $1| cut -d"_" -f3)
# Load your environment here.
python $masif_source/data_preparation/00-pdb_download.py $1
python $... |
470d833b1d463d753d413c7b3b565ea58de3e458de39c76dc0b60937d22addee | Shell | 648 | 21 | #keyword search default
glmFile=conf/glm
duptime=0.5
case_insensitive=false
use_pitch=true
# Lexicon and Language Model parameters
oovSymbol="<unk>"
lexiconFlags="-oov <unk>"
boost_sil=1.5 # note from Dan: I expect 1.0 might be better (equivalent to not
# having the option)... should test.
cer=0
#Declar... |
c34d0b0eda12ff62dc34621c268fb17a403befa2e977bdce80048c48c2da5408 | Shell | 648 | 12 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
export PYTHONPATH=$PYTHONPATH:$masif_source
export masif_matlab
PDB_ID=$(echo $1| cut -d"_" -f1)
CHAIN1=$(echo $1| cut -d"_" -f2)
CHAIN2=$(echo $1| cut -d"_" -f3)
# Invoke your environment here.
python -W ignore $masif_source/data_preparation... |
cd1c3a9bed20f7c1c7a1ccb211bfd84ce38b56af674f0e1490f8c73d8b66961b | Shell | 648 | 22 | PDBID_CHAIN1_CHAIN2=$1
PDBID=$(echo $PDBID_CHAIN1_CHAIN2 | cut -d"_" -f1)
CHAIN1=$(echo $PDBID_CHAIN1_CHAIN2 | cut -d"_" -f2)
CHAIN2=$(echo $PDBID_CHAIN1_CHAIN2 | cut -d"_" -f3)
outdir=03-results/$PDBID_CHAIN1_CHAIN2/
cp uniCHARMM $outdir
cp create_lig $outdir
cp create.pl $outdir
# Copy evaluation script
cp eval_zd... |
d3453b04e8848050953c736c0205b1ddc8bd505c6b4c1bd2ed3217f82ddad5a0 | Shell | 650 | 22 | #!/usr/bin/env bash
# Copyright 2016 Alibaba Robotics Corp. (Author: Xingyu Na)
# Apache2.0
# This runs SGMM training.
. ./cmd.sh
. ./path.sh
steps/train_ubm.sh --cmd "$train_cmd" \
900 data/train data/lang exp/tri5a_ali exp/ubm5a || exit 1;
steps/train_sgmm2.sh --cmd "$train_cmd" \
14000 35000 data/train data/... |
18c94d4d8ebd75e4b21344d777f42bf6aa52e438aed134089d6a95fc86859ba8 | Shell | 651 | 20 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/seed/s8_%A.out
#SBATCH --job-name s8_MRNet
#SBATCH --partition=long
module load LANG/PYTH... |
620053be945a1d503db248fd5ef69739f5f2d6676b336e5034acad9f806489dc | Shell | 651 | 20 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/seed/s9_%A.out
#SBATCH --job-name s9_MRNet
#SBATCH --partition=long
module load LANG/PYTH... |
9481ce1331f69c0bdeed44272eea505a9f9bb685045168171a22a2a18c50f74e | Shell | 651 | 27 | #!/bin/bash
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
function run_fsl_std() {
# do some validation of the input folder
#create output for standard
stdfolder=$1"/std"
echo mkdir -p $stdfolder
mkdir -p $stdfolder
# run fsl reorient2std
for infile in $(find $1 -maxdepth 1 -mindepth 1 -name "mask_*");... |
9d0185823876ff935c26b8f734e124254c5a267ae9ad370c2a4ad49b9c2082ab | Shell | 651 | 20 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/seed/s7_%A.out
#SBATCH --job-name s7_MRNet
#SBATCH --partition=long
module load LANG/PYTH... |
19064f265d5ea494658e7bc40077c60e9a9576f67394a0222adaf41740ac8cb9 | Shell | 653 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
3722cb0c9ad5211ca60dc428b9e6f0623dc9491d06e0183ac55469ca22f16a0b | Shell | 654 | 20 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/seed/s10_%A.out
#SBATCH --job-name s10_MRNet
#SBATCH --partition=long
module load LANG/PY... |
6cdcb12f1bc256d24714eb97c16561b7be2257f11f0da60db751dadcf7707d8b | Shell | 655 | 15 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$PWD:$PATH
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/config/common_path.sh is not present -> Exit!" && exit 1
. $KA... |
2916d0a4226b93b48ebfb6ed002657261f4cacb8f9941d3118719e088f9f6ba2 | Shell | 656 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/msfi_log/shortcut_%A.out
#SBATCH --job-name shortcut_msfi
#SBATCH --partition=long
module... |
cccd602adcd5849ec12a216f6d63a49ab82718270e64cd9457fa9a60f7d14d05 | Shell | 656 | 9 | #!/bin/sh
wget -P ./arcface_model https://github.com/neuralchen/SimSwap/releases/download/1.0/arcface_checkpoint.tar
wget https://github.com/neuralchen/SimSwap/releases/download/1.0/checkpoints.zip
unzip ./checkpoints.zip -d ./checkpoints
rm checkpoints.zip
wget --no-check-certificate "https://sh23tw.dm.files.1drv.com... |
a9785cbd473b325f4fc5b7b3c24a95d1e1ada0826f7e2d44b92a516d805797fc | Shell | 658 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=300:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo Time is `date... |
f8f04ad15f70f59aa9ba438f971d2bf7ca7033edb30dd55a74c94b700c9581fa | Shell | 659 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
3519dd7b1ea8fe4d82a3a3881c9c1f6f4c2e4d82e47ef859e39ff40ba96a0c4f | Shell | 661 | 30 | #!/bin/bash
base=protein/other_protein_alignments
prank_out=$base/prank_out
#prank_input=$base/prank_input
mkdir -p $prank_out/aln_forCoevol
mkdir -p $prank_out/aln_forChecking
cd $base
ls prank_input | while read i;
#for i in $fasta_list
do
slurmpfx=$base/slurms/slurm_$i.%J
sbatch --error=$slurmpfx.err --outpu... |
63bb314634e9be48e7e5bfe00b9a9d5a8fd3c29f2454a65d9be4d6360769304b | Shell | 661 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
57ced53d31f76fb898702aff8a710584226aab3989c297cc46a00d78254eda6b | Shell | 662 | 13 | #!/usr/bin/env bash
# Copyright 2017 Johns Hopkins University (Author: Aswin Shanmugam Subramanian)
# Apache 2.0
wget http://bass-db.gforge.inria.fr/bss_eval/bss_eval_sources.m -O local/bss_eval_sources.m
wget https://github.com/JacobD10/SoundZone_Tools/raw/master/stoi.m -O local/stoi.m
wget https://github.com/JacobD1... |
089d7a5073e5ff32685aaba46be3d85567067d9aa3481d474bcd62cf19ff3652 | Shell | 665 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
9b5649db2ae0d6024072c571cfc0968b43278c90351ae5649eb92720749df69d | Shell | 665 | 24 | #!/bin/bash
# Job Parameters
#SBATCH --job-name=config
#SBATCH --array=0-21
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=21
#SBATCH --time=2-00:00:0
#SBATCH --mem=20G
#SBATCH --partition=cpu
#SBATCH --mail-type=END,FAIL # notifications for job done & fail
#SBATCH --mail-user=rancze@crick.ac.uk
#SBATCH --output=reports/%A... |
cf604ac4c5e7fa9922b25e864dd5fe4c9a9ce135c02aa23cd5d4fb266b072801 | Shell | 666 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
18ef6218c505fd41abc5a241d7bcfe9191c749cb81d071140d534bb8fce9256c | Shell | 667 | 18 | #!/bin/bash
#SBATCH --job-name=PCA_PLOT
#SBATCH --output=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/output/PCA_PLOT.out
#SBATCH --error=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/output/PCA_PLOT.out
#SBATCH --time=05:59:00
#SB... |
2d21df3a47912453ae9e2585b6f941d422631d6749b52a061bbf5d1150a560cc | Shell | 667 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=300:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo Time is `date... |
a713c598e7995ea61ea07f43d8cafaedeb758ac4122ff4fa175629fa59200465 | Shell | 667 | 26 | #!/bin/bash
#
# Wait for all of the filepaths given as arguments. This script exits successfully once all the paths exist.
# If any file takes longer than MAX_WAIT_SECS to appear, the script fails.
#
SLEEP_SECS="${SLEEP_SECS:-1}"
MAX_WAIT_SECS="${MAX_WAIT_SECS:-30}"
filelist=$@
for f in ${filelist}; do
echo "Che... |
caf5852a3f365f0923025d111d26bc1fff508780018e6380050f0b143319db5e | Shell | 667 | 25 | #!/bin/bash
# This script will take in Finnish Parliament Corpus utterance ID
# and play the corresponding segment from the original session
# video file using VLC.
if [ $# -ne 1 ]; then
echo "Usage: $0 <uttid>"
echo "e.g.: $0 01302-005-2020-00127494-00128438"
echo
echo "Given a Finnish Parliament Corpus utte... |
a3b73a561fed50b542d01e9a3c2dc6a44aefc5d9c972ffd87be8e7f8a3e1a1d3 | Shell | 668 | 24 | #!/bin/sh
mkdir -p charpragcap/resources/visual_genome_data
cd charpragcap/resources/visual_genome_data
wget https://cs.stanford.edu/people/rak248/VG_100K_2/images.zip
wget https://cs.stanford.edu/people/rak248/VG_100K_2/images2.zip
unzip images.zip
unzip images2.zip
#rm images.zip
#rm images2.zip
mv VG_100K_2/* VG_1... |
ebd63dbe59a1588708147f830676787e46ceb0ef4e6ef55c139a80a3386b0490 | Shell | 668 | 16 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
$DIR/../main.nf \
-dump-channels \
-with-tower "http://nextflow.int.janelia.org/api" \
--runtime_opts "--nv -B /nrs/scicompsoft/goinac -B /nrs/multifish" \
--lsf_opts "-P project" \
--workers "4" \
--worker_cores "4" \
... |
4031009ffdf0c77333a81bb6f5de15ae96bfc4fbf3761e92bd963daee696a98d | Shell | 669 | 9 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_matlab=$masif_root/source/matlab_libs/
masif_data=$masif_root/data/
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_site/
python $masif_source/masif_ppi_search/second_stage_alignment.py ../../../data/masif_ppi_search 100 20... |
d59e5d0bafc67b6f3abdaf1a7063ac345556ee1d4f8cfdd595fbc9e2c157cc8a | Shell | 671 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=300:00:00
#!PBS -l nodes=1:ppn=16,walltime=100:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
bf568df789f401569cb5d38fdd81cde8f3b5a99b597b85a4cc3212df5872f6dd | Shell | 672 | 26 | #!/bin/bash
#$ -l h_rt=8:00:00,h_data=32G,exclusive
#$ -cwd -V
#$ -N mm22stgi
#$ -j y
#$ -o gi.$JOB_ID.out
#$ -M videlock@mail
#$ -m bea
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/gencode.vM22.annotation.gtf.gz -O mm22.gtf.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/r... |
eca7534e34304c353e7036b651d9e9456abe08815c8c71e60df2590f93a614f7 | Shell | 673 | 13 | #!/usr/bin/env bash
BASEDIR=$(dirname "$0")
# (python $BASEDIR/define_nodes/define_nodes.py) && \
# (python $BASEDIR/flow/flow.py) && \
# (python $BASEDIR/walk_sort/generate_walks.py) && \
# (python $BASEDIR/walk_sort/walk_sort.py) && \
# (python $BASEDIR/graph_match/graph_match_grouped.py) && \
# (python $BASEDIR/reva... |
efc960a48981b6ef4ee727784eb166f83a844b410d1e4fd2ce3e173d53e9b4d6 | Shell | 674 | 22 | #!/usr/bin/env bash
# Make the features.
. ./cmd.sh
. ./path.sh
stage=1
set -e
. ./utils/parse_options.sh
mkdir -p exp/nnet2_online
if [ $stage -le 1 ]; then
# this shows how you can split across multiple file-systems. we'll split the
# MFCC dir across multiple locations. You might want to be careful here, if... |
17377825eeb91536d63307328bc19af30d3d42580a3b2a2548c122c7023d6289 | Shell | 679 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/s8_1119_mrnet_%A.out
#SBATCH --job-name s8_mrnet
#SBATCH --account=rrg-PIID
module load python/3.7
... |
19b1578ad6e0a0d65ec03b5673f82312e89e3923676636a74e0cd9f3949b8894 | Shell | 679 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/s7_1119_mrnet_%A.out
#SBATCH --job-name s7_mrnet
#SBATCH --account=rrg-PIID
module load python/3.7
... |
847d495c1212388b3fb588eb064e2dc4a2d89c88e714c1c0dba4b47aff9109f5 | Shell | 679 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/s6_1119_mrnet_%A.out
#SBATCH --job-name s6_mrnet
#SBATCH --account=rrg-PIID
module load python/3.7
... |
cb25afc38f7af4b7225e7898c615fc568c06c102beb1a73248fb05778f01c44b | Shell | 679 | 25 | #!/usr/bin/env bash
subject=$1
nprocs=$2
maxmem=15 # 400
rawdatadir="$(pwd)/../../../rawdata"
derivsdir="$(pwd)/../../../../test_fprep_upsampling/derivatives"
workdir="$(pwd)/../../../../fmriprep_wdir"
docker run -ti --rm \
--memory="$maxmem""g" \
-v "$rawdatadir":/data:ro \
-v "$derivsdir":/out \
-v "$workd... |
cfe85f7fbade4831dfc9245d49a014ec0962cb142667b7731f8a8a590eb9bc7d | Shell | 679 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/s9_1119_mrnet_%A.out
#SBATCH --job-name s9_mrnet
#SBATCH --account=rrg-PIID
module load python/3.7
... |
35ba6c048f075fb9ba29a7acb9c7067c5d6352fa72b8d1eba66049cdb41b2993 | Shell | 680 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/tumorsyn_gethm/s5_%A.out
#SBATCH --job-name s5_hm
#SBATCH --partition=long
FOLD=5
module load ... |
3b50236547699d79dc20c530e756d9f7f10219fa33253b031332cb191e75f767 | Shell | 680 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/tumorsyn_gethm/s3_%A.out
#SBATCH --job-name s3_hm
#SBATCH --partition=long
FOLD=3
module load ... |
67a369d99acab2cd76d8d9a6f5077b37edbac5b1fb14a1f5ef0d28e3567c1816 | Shell | 680 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/tumorsyn_gethm/s2_%A.out
#SBATCH --job-name s2_hm
#SBATCH --partition=long
FOLD=2
module load ... |
be4fbdd6b056a8926aa3a40f4f1c921614ff14692642446cdf2c5b3a5cafa727 | Shell | 680 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/tumorsyn_gethm/s4_%A.out
#SBATCH --job-name s4_hm
#SBATCH --partition=long
FOLD=4
module load ... |
de8c37f2ce6ce57c70e868b47cbd1b9be2a1a95246cc7f67f6414f318ea35805 | Shell | 680 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/tumorsyn_gethm/s1_%A.out
#SBATCH --job-name s1_hm
#SBATCH --partition=long
FOLD=1
module load ... |
7f3765bc014b1252bf16c0021f623e5d574f5163e53fe93e314c240fe6c9dd06 | Shell | 683 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/s10_1119_mrnet_%A.out
#SBATCH --job-name s10_mrnet
#SBATCH --account=rrg-PIID
module load python/3.... |
cb357bc61ca27df95b45a444d9730404ad7885fb7f3eaa7e24c194ae7c1c9350 | Shell | 683 | 30 | #!/usr/bin/env bash
# Copyright 2020-2021 Xiaomi Corporation (Author: Junbo Zhang, Yongqing Wang)
# Apache 2.0
if [ "$#" -ne 2 ]; then
echo "Usage: $0 <src-dir> <dst-dir>"
echo "e.g.: $0 /home/storage07/zhangjunbo/data/speechocean762/test data/test"
exit 1
fi
src=$1
dst=$2
[ ! -d $src ] && echo "$0: no such ... |
d1fecbf4577ce2cde0aa7fe399e1437bc4173a1e5b8b1152e52034e646a78c1b | Shell | 683 | 23 | #!/usr/bin/env bash
r1=$1
in=$2
numb_of_files=$3
r2=$4
echo "Decompress fastq.gz ..."
gunzip -c $r1 > $in/r1-unzip
cat $in/r1-unzip | paste - - - - | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > $in/r1.fa & pid1=$!
cat $in/r1-unzip | paste - - - - | LC_ALL=C sort --parallel=8 --temporary-directory=$HOME/tmp -k1,1 > $i... |
940ac3a6deff3984f8748a99c0cc1f85bfb60a62abd4429bd87ef33891ee35e8 | Shell | 684 | 16 | #!/usr/bin/bash
set -e
# Simple log helper functions
info() { echo -e "\033[1;34m[INFO ][MxStream] $1\033[1;37m" ; }
warn() { echo >&2 -e "\033[1;31m[WARN ][MxStream] $1\033[1;37m" ; }
export LD_LIBRARY_PATH=${MX_SDK_HOME}/lib:${MX_SDK_HOME}/opensource/lib:${MX_SDK_HOME}/opensource/lib64:/usr/local/Ascend/ascend-tool... |
6105bce2435b474153ff5a37253a74f720bad9b9f2a667179641b87711a4f6b8 | Shell | 686 | 22 | #!/bin/bash
#PBS -q himem
#PBS -l nodes=1:ppn=16
#PBS -l mem=240gb
#PBS -l walltime=100:00:00
#!PBS -l nodes=1:ppn=16,walltime=200:00:00
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
#! Record some useful job details in the output file
echo Running on host `hostname`
echo T... |
579ec930ca7c5cbd1b42f1ab39ec359475d736046ef7a85947c4b7881d454251 | Shell | 687 | 31 | #!/usr/bin/env bash
# Copyright 2014 Gaurav Kumar. Apache 2.0
currentJob=0
dir=/export/a04/gkumar/kaldi-trunk/egs/fishcall_es/j-matt/exp/sgmm2x_6a_denlats
for f in $dir/.done.*; do
d=`echo ${f##*/} | awk 'BEGIN {FS="."} {print $3}'`
if [ $d -gt $currentJob ]; then
currentJob=$d
fi
done
curren... |
59fab918c1762ed516f42090370ded94493e7f2ec83ff1dd411102913b2725bd | Shell | 687 | 15 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$PWD:$PATH
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/config/common_path.sh is not present -> Exit!" && exit 1
. $KA... |
731c73b19787a72b00a7865c42cf4b4b86fce3b5ada6d354665b83015bcec045 | Shell | 688 | 26 | mv ERR469 ERR4699947_1.fastq.gz
gunzip ERR4699947_1.fastq.gz
#!/bin/bash
START=4699947
END=4700000
# END=4700478
for (( c=$START; c<=$END; c++ ))
do
filenum="$c"
num1=${c:0:3}
num2=${c: -1}
filename="ERR${filenum}"
dir1="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR${num1}/00${num2}/${filename}/${filename}_1.fast... |
06cfc5f7fd7aa1c386b5a778c7bd225bb49293c7ceaee3c3ab50d8092d3c05ac | Shell | 689 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/gethm/s8_%A.out
#SBATCH --job-name s8_gethm
#SBATCH --partition=long
module load LANG/PYT... |
19b1a74cd754cd62e39f5b619f5634c0b6f108be26cbd95685107c4c124fc119 | Shell | 689 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/gethm/s7_%A.out
#SBATCH --job-name s7_gethm
#SBATCH --partition=long
module load LANG/PYT... |
94a3335373e05456a26e66eb87e578234578949aa70128aebc14cc4abc034397 | Shell | 689 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/gethm/s9_%A.out
#SBATCH --job-name s9_gethm
#SBATCH --partition=long
module load LANG/PYT... |
cc22731e5265133fa977d24e9ab9c6a1e86fe1732d014477adf4ea0b52884926 | Shell | 689 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/gethm/s6_%A.out
#SBATCH --job-name s6_gethm
#SBATCH --partition=long
module load LANG/PYT... |
dfe51edd25f7d2730357122b89eab1d68ab78730ddf2713382b902002770f4c5 | Shell | 691 | 23 | #!/bin/bash
#SBATCH --job-name=10x
#SBATCH -t 72:00:00
#SBATCH --mail-type=ALL,ARRAY_TASKS
#SBATCH --mail-user=alex.thiery@crick.ac.uk
## LOAD REQUIRED MODULES
ml purge
ml Nextflow/20.07.1
ml Singularity/3.4.2
ml Graphviz
export TERM=xterm
export NXF_VER=20.07.1
export NXF_SINGULARITY_CACHEDIR=/camp/home/thierya/work... |
ed7c8faa56efd68675663d33fbbe00517653f46d71b5a9a1d87e7638396fae81 | Shell | 691 | 29 | #!/usr/bin/env python
# Copyright 2014 Gaurav Kumar. Apache 2.0
# Gets the unique speakers from the file created by fsp_make_trans.pl
# Note that if a speaker appears multiple times, it is categorized as female
import os
import sys
tmpFileLocation = 'data/local/tmp/spk2gendertmp'
tmpFile = None
try:
tmpFil... |
b32021dee7aeeba5859a8f53368e1d2252192dd5772ef6a20f232f576eef825b | Shell | 692 | 22 | #!/usr/bin/env bash
# Installs pb_chime5
# miniconda should be installed in $HOME/miniconda3/
miniconda_dir=$HOME/miniconda3/
if [ ! -d $miniconda_dir ]; then
echo "$miniconda_dir does not exist. Please run 'tools/extras/install_miniconda.sh" && exit 1;
fi
git clone https://github.com/fgnt/pb_chime5.git
cd pb_... |
6d448c808594265060dd8db93c53009628d9791a0d219ab63d06ec285e9c00cd | Shell | 693 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/gethm/s10_%A.out
#SBATCH --job-name s10_gethm
#SBATCH --partition=long
module load LANG/P... |
443146050248407bb28ed0c99fd69e1ba4a0ec2747f998eedfa63d0a72d6b0bb | Shell | 695 | 23 | #!/bin/bash
# Example script to generate scripts to be run on a cluster. This script should not called directly as it only serves
# as a template; some values will be replaced by NMT during export. For more details see the NMT User Manual.
# NOTE: this example is specific for a SLURM queueing system.
#SBATCH -N {{ no... |
a77d1225ed1f5ec7f07751eef9d1b1908d262430703aa533bc107f2beea8a363 | Shell | 695 | 26 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=6-24:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/localscratch/authorid/log/train_model/s10_%A.out
#SBATCH --job-name s10
#SBATCH --partition=long
#SBATCH --nodelist=cs-venus-04
module l... |
42674ada1784ba98ba65c05e7c4d97ebbc21444f103addbd498340eb08468929 | Shell | 697 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/meniscus/m8_1119_mrnet_%A.out
#SBATCH --job-name m8_mrnet
#SBATCH --account=rrg-PIID
module load py... |
4eb136f0bf57e8f97d7d3fe2a8a48cb091868d95fc78de6cab75711f72e5b7d7 | Shell | 697 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/meniscus/m6_1119_mrnet_%A.out
#SBATCH --job-name m6_mrnet
#SBATCH --account=rrg-PIID
module load py... |
bfd810e2b5f9e7ecf8e368c795f2be66883e3acfabc300023279f457a6233c19 | Shell | 697 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/meniscus/m9_1119_mrnet_%A.out
#SBATCH --job-name m9_mrnet
#SBATCH --account=rrg-PIID
module load py... |
e06282d54e19961017d5290fc71080a1ccc4b74bda8ff591e1af05b10005bee0 | Shell | 697 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/meniscus/m7_1119_mrnet_%A.out
#SBATCH --job-name m7_mrnet
#SBATCH --account=rrg-PIID
module load py... |
9f4fbaafae943f01e0808448fe769b0ce2f0f892cd26bfb1d9469de3f2881b29 | Shell | 700 | 29 | #!/usr/bin/env python
# Copyright 2014 Gaurav Kumar. Apache 2.0
# Gets the unique speakers from the file created by fsp_make_trans.pl
# Note that if a speaker appears multiple times, it is categorized as female
import os
import sys
tmpFileLocation = 'data/local/tmp/callhome_spk2gendertmp'
tmpFile = None
try:
... |
1563079a167fa2b869b9217a3960eda226eb31550ebc04114634204abdf07ea7 | Shell | 701 | 23 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/meniscus/m10_1119_mrnet_%A.out
#SBATCH --job-name m10_mrnet
#SBATCH --account=rrg-PIID
module load ... |
43fcca6fdd4a0b270277dbfc3b786b259ffa38a433a2d443579642b49d1ceae9 | Shell | 701 | 23 | #!/bin/bash
# Example script to generate scripts to be run on a cluster. This script should not called directly as it only serves
# as a template; some values will be replaced by NMSAT during export. For more details see the NMSAT documentation.
# NOTE: this example is specific for a SLURM queueing system.
#SBATCH -N... |
173c5f90d96364c892daae1c44356dd5d38c842ff1fdd1e7804b344dc89eba1c | Shell | 711 | 27 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/brats_rerun/%x_%N_%j.out
#SBATCH --error=/scratch/authorid/brats_rerun/%x_%N_%j.err
#SBATCH -... |
32daf5acc5cb876882ae531318957125bac7c52d9a81b7d72f5c03772b5c03d9 | Shell | 711 | 27 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/brats_rerun/%x_%N_%j.out
#SBATCH --error=/scratch/authorid/brats_rerun/%x_%N_%j.err
#SBATCH -... |
45ba96274c3af5bb3c71284ffb7d5de253297a4deb423722ef4f8116f8781d7b | Shell | 711 | 27 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/brats_rerun/%x_%N_%j.out
#SBATCH --error=/scratch/authorid/brats_rerun/%x_%N_%j.err
#SBATCH -... |
49dc3d70a568adc67efc817f31c98853db64b3cc3dada2f816b5bd5fdbf86657 | Shell | 711 | 27 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/brats_rerun/%x_%N_%j.out
#SBATCH --error=/scratch/authorid/brats_rerun/%x_%N_%j.err
#SBATCH -... |
f2842b110bf010e7d60bb529e180a23a64008609dbfe33ca8284907c1d562057 | Shell | 711 | 27 | #!/bin/bash
#SBATCH --gres=gpu:2
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/brats_rerun/%x_%N_%j.out
#SBATCH --error=/scratch/authorid/brats_rerun/%x_%N_%j.err
#SBATCH -... |
1cbdf364803d8707fa3562763f0bff7158abb0d4fb0ffd8a1ef2690113ddb467 | Shell | 712 | 34 | echo "kernel name: " ` uname --kernel-name`
echo "network node hostname: " `uname --nodename`
echo "kernel release: " `uname --kernel-release`
echo "kernel version: " `uname --kernel-version`
echo "machine hardware name: " `uname --machine`
echo "processor type (non-portable): " `un... |
215ee28f71b3aab5b8f28cc3b1aa0e24482daf2defc113e46955148e494f86eb | Shell | 712 | 30 | #!/usr/bin/env bash
# Copyright 2014 Gaurav Kumar. Apache 2.0
data_dir=data
train_all=data/train_all
if [ $# -lt 1 ]; then
echo "Specify the location of the split files"
exit 1;
fi
splitFile=$1
# Train first
for split in train dev test dev2
do
cp -r $train_all $data_dir/$split
awk 'BEGIN {FS=" "}; ... |
76e0faed4768b7eac65c013d441f824e93bc3e55aab50667aab1eff0a2f48f12 | Shell | 713 | 22 | #!/usr/bin/env bash
# Copyright 2018 Zili Huang
# Apache 2.0.
#
# This script, called by ../run.sh, creates the DIHARD 2018 development data directory.
if [ $# != 2 ]; then
echo "Usage: $0 <path-to-dihard_2018_dev> <path-to-output>"
echo " e.g.: $0 /export/corpora/LDC/LDC2018E31 data/dihard_2018_dev"
fi
path_to... |
a1f4b842939ebe64f9e303805723fc794bf8d2551143a81e4839534a373b77b9 | Shell | 713 | 26 | #!/bin/bash
umask 0002
if [ -z "$SCRATCH_DIR" ] ; then
echo "SCRATCH_DIR not set, creating one using default TMPDIR"
export MCR_CACHE_ROOT=`mktemp -u -d`
else
export MCR_CACHE_ROOT=`mktemp -u -d -p "${SCRATCH_DIR}/mcr_cache_$$"`
fi
function cleanTemp {
if [ -n "$KEEP_MCR" ] ; then
echo "Keep $... |
80ab3ddbaacfd28146c44e5cda5625dd623e03fc405b6d1969f89255ff96ddbb | Shell | 714 | 26 | #!/bin/bash
if [ $# -ne 2 ]; then
echo "Usage: recipes/01_download_data.sh <start_session> <end_session>"
echo "e.g.: $0 1/2020 10/2020"
echo
echo "Downloads sessions in the given range."
echo
exit
fi
START=$1
END=$2
if [ ! -d corpus ]; then
echo "The directory 'corpus' (or a symbolic lin... |
1952681b8ca447578a97ff48298a71d97b6ad1f677fce0f74c89c4d7d3e15cfb | Shell | 716 | 22 | #!/usr/bin/env bash
# Copyright 2018 Zili Huang
# Apache 2.0.
#
# This script, called by ../run.sh, creates the DIHARD 2018 evaluation directory.
if [ $# != 2 ]; then
echo "Usage: $0 <path-to-dihard_2018_eval> <path-to-output>"
echo " e.g.: $0 /export/corpora/LDC/LDC2018E32v1.1 data/dihard_2018_eval"
fi
path_to... |
2f47fe57d672718153c19b897e4057f7e7fa12340ea6d167ce4109e748b166f0 | Shell | 718 | 19 | #!/bin/bash
#SBATCH --job-name=CIA_TEST0
#SBATCH --output=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-10-12-decon-optimzer/jobs/output/CIA_TEST0.out
#SBATCH --error=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-10-12-decon-optimzer/jobs/output/CIA_TEST0.out
#SBATCH --time=05:59:0... |
6f6de629315adc81b4d35d04c34c2ca5f530ec3b44eb4a37c263dc3f1bbdb301 | Shell | 723 | 30 | #!/bin/bash
# do some validation of the input folder
infile=$1
# create output folder
infolder=$(dirname $infile);
filename=$(basename $infile)
outfolder=$infolder"/pydeface"
echo ">> mkdir -p $outfolder"
mkdir -p $outfolder
# run pydeface
outfilename="defaced_"$filename
outfile=$outfolder"/"$outfilename
maskfile=$... |
450a4ffcc098d3428f679e7befadb6e3d6ceffe28e330673d435fd7a9ce45bcb | Shell | 724 | 25 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/weight_decay/0_%A.out
#SBATCH --job-name wt0
#SBATCH --account=rrg-PIID
module load python/3.7
module... |
4101a1bdecbbc509fad98cb02116739f8d22fa24c1b54c41ed2bdd6f62eddef7 | Shell | 725 | 34 | #!/bin/bash
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
function run_pydeface() {
# do some validation of the input folder
# create output folder
outfolder=$1"/pydeface"
echo mkdir -p $outfolder
mkdir -p $outfolder
# run fsl deface
infile=$1"/std/image_std.nii.gz"
outfile=$outfolder"/defaced.nii.gz"
... |
55287cc81dec00c538a3fc332741d34c4e4d61e756855c4d05fafd583ca57871 | Shell | 725 | 19 | #!/bin/bash
#SBATCH --job-name=CIA_TEST1
#SBATCH --output=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-10-12-decon-optimzer/jobs/output/CIA_TEST1.out
#SBATCH --error=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-10-12-decon-optimzer/jobs/output/CIA_TEST1.out
#SBATCH --time=05:59:0... |
f559efa99d7eb1fa17bb6afc0961c7a060d6e57ee956d5c9ec5110f680a07dff | Shell | 725 | 25 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/lr/1_%A.out
#SBATCH --job-name 1_lr
#SBATCH --account=rrg-PIID
module load python/3.7
module load ope... |
1837c1538b725ae19787454601ee3cd820833d9075ac37abae3b62eb8cfc739a | Shell | 728 | 25 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/lr/03_%A.out
#SBATCH --job-name 03_lr
#SBATCH --account=rrg-PIID
module load python/3.7
module load o... |
669f0f7c107e5d90f6e06c3e89490d9109a2251893ebd6436a31cd55896a09ed | Shell | 728 | 25 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/scratch/authorid/shortcut/log/MRNet/lr/01_%A.out
#SBATCH --job-name 01_lr
#SBATCH --account=rrg-PIID
module load python/3.7
module load o... |
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