sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4831a9d1d9356c3bbd17577a0283cce883b0ea683708bbc5e0fa044f5612bc2c | Shell | 277 | 2 | export NGPUS=8
python3 -m torch.distributed.launch --nproc_per_node=$NGPUS tools/train_net.py --config-file configs/e2e_faster_rcnn_DETNAS_COCO_FPN_300M_tong_1019_1x.yaml OUTPUT_DIR models/DETNAS_COCO_FPN_300M_tong_1019_1x_nosubmean_SyncBatchNorm_tong_FPNSYNCBN_BOXHEADSYNCBN
|
68f8a6e3c6d40527c02337583f9ffb6c24698dc9832fb3562be6c35694fa8639 | Shell | 277 | 7 | #!/bin/bash
DIR=/data/rkawaguc/data/190402_BICCN_sparse_mat/sm_from_snap/global_ng_list
FILE=global_bin_ng_1_3C.csv
FNAME="${FILE%.*}"
EXT="${FILE##*.}"
python Catactor.py column_annotation ${DIR}/${FILE}
Rscript annotation_metadata.R promoter ${DIR}/${FNAME}_with_bins.${EXT}
|
f4e0de560abc2ea9e2d41e50e0d0242813c64b05aa51ed85279e0ca8316af1fb | Shell | 277 | 12 | #!/bin/bash
# Download latest models from https://github.com/ultralytics/yolov5/releases
# Usage:
# $ bash weights/download_weights.sh
python - <<EOF
from utils.google_utils import attempt_download
for x in ['s', 'm', 'l', 'x']:
attempt_download(f'yolov5{x}.pt')
EOF
|
160f23664e8cba770f65285c502d393e310f0df13d1f6c2a744dfa72d074396b | Shell | 278 | 4 | KWSEval -e ecf.xml -r rttm -t keyword_outvocab.xml -s kwslist.xml -c -o -b -d -f ./kws/outvocab
KWSEval -e ecf.xml -r rttm -t keyword_invocab.xml -s kwslist.xml -c -o -b -d -f ./kws/invocab
KWSEval -e ecf.xml -r rttm -t kws.xml -s kwslist.xml -c -o -b -d -f ./kws/fullvocab
|
da215b4f668b3911af7542ed250ada01dd9d8eec58cb69ad04d6868ac5038090 | Shell | 281 | 19 | #! /bin/bash
# Copyright Johns Hopkins University
# 2019 Fei Wu
# Get duration of the utterance given data dir
set -eu
echo $0 $@
data_dir=$1
mkdir -p duration
./utils/data/get_utt2dur.sh $data_dir
echo "$data_dir"
python local/sum_duration.py $data_dir/utt2dur
echo ""
|
a44551c9961d7adda0e18bb562c2bf941fdbfecd8aaf0bd9c3fd8f604d72bd74 | Shell | 282 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o eval_SUBX.out
#SBATCH -e eval_SUBX.err
#SBATCH -J SUBX_stab
source activate GXAI
python3 eval_SG_accuracy.py --exp_method SUBX --model GIN --save_dir SUBX/SUBX_results/acc
|
2550e0cf90d72f4e49260d436ce2bfbdccb41e03b0d87077deaf9af9a720a32e | Shell | 283 | 17 | #!/bin/sh
scripts="$@"
if [ -z "$scripts" ]; then
scripts=*.script
fi
for script in $scripts; do
test=${script%.script}
echo -n "- $test... "
sh $script > $test.output
if cmp $test.output $test.ref >/dev/null; then
echo "OK"
else
echo "FAILED"
fi
done |
798c6fb89ec75b4b2e2d81b469b491ce496dd3a20d091c4275802e08dd4ddcd0 | Shell | 284 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu_quad
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o SUBX_cf0.out
#SBATCH -e SUBX_cf0.err
#SBATCH -J SUBX_cf0
source activate GXAI
python3 fair_mult_SG.py --save_dir SUBX_results --num_splits 4 --my_split 0 --ignore_group
|
64f36ffd55d5ebe716ec8764648deca0e2006131485206ae24088be630b6015b | Shell | 285 | 9 | # !/usr/bin/env sh
python -m torch.distributed.launch --nproc_per_node=8 ./tools/retrain.py \
./configs/fna_ssdlite_retrain.py \
--launcher pytorch \
--seed 1 \
--work_dir ./ \
--data_path ./coco/ \
--validate \
|
8cf957048d50aceb8705498a8c372a3932621007eb69c27dcdadd41cbce43312 | Shell | 289 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o eval_SUBX.out
#SBATCH -e eval_SUBX.err
#SBATCH -J SUBX_faith
source activate GXAI
python3 eval_SG_faithfulness.py --exp_method SUBX --model GIN --save_dir SUBX/SUBX_results/faith
|
607a886ae69550d82609a8d546aa140b4a7fa4df985d536b9c5a403d2d58ea04 | Shell | 291 | 13 | case "$USER" in
"ac1nmx")
# CHiME Challenge wav root (after unzipping)...
export WAV_ROOT="/data/ac1nmx/data/PCCdata16kHz"
# Used by the recogniser for storing data/ exp/ mfcc/ etc
export REC_ROOT="."
;;
*)
echo "Please define WAV_ROOT and REC_ROOT for user $USER"
;;
esac
|
f9a323152c9eef1a4a251fd1fa26f722c0cb757336998608f778304d9dd5c292 | Shell | 291 | 9 | # !/usr/bin/env sh
python -m torch.distributed.launch --nproc_per_node=8 ./tools/retrain.py \
./configs/fna_retinanet_fpn_retrain.py \
--launcher pytorch \
--seed 1 \
--work_dir ./ \
--data_path ./coco/ \
--validate \
|
71405eead052a9ef99911e529f695d5dc4fd442f9c4b6f1f92a34dd5d427807b | Shell | 292 | 28 | #!/bin/sh
set -e
clean_cache=false
# terminate script
die() {
echo "$1" >&2
echo
exit 1
}
clear_fscache() {
sync
echo 3 | tee /proc/sys/vm/drop_caches
}
# echo command before running it
run() {
echo "$1"
eval "$1"
if [ $clean_cache = true ]
then
clear_fscache
fi
return 0
}
|
8acc537d37aca2740312b6483321428acb6b461daff78f4daad0a8dce1da59f6 | Shell | 292 | 6 | masif_root=$(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_ppi_search/
python $masif_source/masif_ppi_search/masif_ppi_search_train.py $1
|
6005a81261dc72647a6cc9f4d7e6d22da320fbcd57b6705e9e3268358ce362aa | Shell | 293 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu_quad
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o SUBX_mutag.out
#SBATCH -e SUBX_mutag.err
#SBATCH -J SUBX_mutag
source activate GXAI
python3 graph_eval.py --exp_method SUBX --model GIN --dataset mutag --accuracy --faithfulness
|
a45fb68a4d81212170bd5bbc6ed37523705cbb685bee741e3e9f5b30b2c6034b | Shell | 293 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o fair_outs/CAM_fair.out
#SBATCH -e fair_outs/CAM_fair.err
#SBATCH -J CAM_fair
source activate GXAI
python3 eval_SG_fairness.py --exp_method CAM --model GIN --save_dir fairness_results
|
4080a985d8f2dff338676db2688e4552e3758c38722ef98032a38bffca578b12 | Shell | 294 | 6 | #!/bin/bash
echo "###Running legacy BLASTN with subject '$1' and query '$2'"
formatdb -p F -i $1 -n ROD
blastall -p blastn -d ROD -i $2 -o blastn.out -e 2e-11 -F F
echo "###Running blast_rod_finder.pl with query '$3' and minimum ROD size '$4'"
perl blast_rod_finder.pl -q $3 -r blastn.out -m $4 |
415dd3d5f22a3760e315aefd912a9143f4193c5abe8e81266e8ca169f70d432b | Shell | 294 | 11 | #!/bin/bash
# Get the results by ftp, then unarchive
cd "$HOME/hodgkin/Paramecium/Electrophysiology/Selection - AP model"
rm results_selection.tar.gz
# Download the results file
scp ganglion:/mnt/storage_s1/Paramecium/results_selection.tar.gz .
# Unarchive
tar xzvf results_selection.tar.gz
|
8db1f4b66e1068fd534fe129e1928e0ceac4357e66905ca51a5a1db47a14eb17 | Shell | 294 | 12 | #!/bin/bash
LOGFILE=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/start.txt
re='^[0-9]+$'
while IFS= read -r LINE; do
JOBID=$(echo $LINE | cut -f5 -d' ')
if [[ $JOBID =~ $re ]] ; then
echo "scancel $JOBID"
scancel $JOBID
fi
done < "$LOGFILE" |
b4a755797a8a5dc4938ba2d21e127e6f43dc4f4769e38381477a2e4a96630792 | Shell | 297 | 17 | #!/bin/bash
if [ $(($OMPI_COMM_WORLD_LOCAL_RANK%2)) -eq 0 ]
then
echo "even"
echo $OMPI_COMM_WORLD_LOCAL_RANK
export CUDA_VISIBLE_DEVICES=0
echo $CUDA_VISIBLE_DEVICES
else
echo "odd"
echo $OMPI_COMM_WORLD_LOCAL_RANK
export CUDA_VISIBLE_DEVICES=1
echo $CUDA_VISIBLE_DEVICES
fi
$@ |
2d1891f875403b1e975e1c88736248ca4d5894271c3bad0e2a1111d902e50187 | Shell | 299 | 12 | #!/bin/bash
# download modelName files from s3 do folder nspModelsPath
# params:
# modelName
# nspModelsPath
# example
# downloadModelFromS3 s3://nsp-project/models/genesis/
modelName=$1
nspModelsPath=$2
aws s3 sync s3://nsp-project/models/genesis/${modelName} $nspModelsPath
|
884b4714b92fa7ca296c7760a4fbf072de1adc3ab788b535ebcd1df809824cde | Shell | 300 | 11 | #!/bin/sh
# python manage.py flush --no-input
#python manage.py makemigrations
#python manage.py makemigrations microbiology
#python manage.py migrate
#python manage.py microbiology_createsu
#python manage.py microbiology_import_clwsql08
#python manage.py collectstatic --no-input --clear
exec "$@" |
9712f2fec744e9e17eb8a8e68da2bd8ec4330637d8f3d03a30cfdcc8740f9740 | Shell | 302 | 13 | #!/usr/bin/env bash
source ~/.bashrc
conda activate thingsmri_env
thingsmridir="$(pwd)/../../../../"
subject=$1
nprocs=50
docker run -it --rm --mount \
type=bind,source="${thingsmridir}",target=/thingsmri \
preproc \
python /thingsmri/bids/code/things/mri/reconall.py "${subject}" "${nprocs}"
|
81d08e2816cca66aa866c922a91ce6354682ff49df679d39387ddc3f13937789 | Shell | 304 | 14 | #!/bin/bash
set -e
cd /home/data/abcd/abcd-hispanic-via/code/log/3dTproject
rm -rf 3dErrors.txt
LIST=($(ls 3dTproject_*.err))
for file in ${LIST[@]}; do
echo "--- ${file}" >> 3dErrors.txt
err=$(echo "NO ERROR")
err=$(echo $(grep -s 'ERROR' ${file}))
echo "------------ ${err}" >> 3dErrors.txt
done |
2308be1a9a790b822c07f2c9e8a67433f14c2c09dd69b031cc28977550b7ad95 | Shell | 305 | 8 | #!/bin/bash
###################################
# This file needs to be sourced! #
###################################
#export directory of this script
export NMSAT_HOME="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
export PYTHONPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )":$PYTHONPATH |
0cceff410bf8e902d93d7e379407a67dba25b30203cd8b1f77b38084bfa58220 | Shell | 306 | 15 |
#for ppi_pair in 3F74_A_B 3HRD_E_H 1ERN_A_B 2B3Z_C_D 4KGG_C_A 2FE8_A_C 1SOT_A_C 2LBU_E_D 3PGA_1_4 3QWN_I_J 3TND_B_D 1XDT_T_R
i=1
while read ppi_pair;
do
echo "Starting $ppi_pair"
if !((i % 5)); then
./eval_one.sh $ppi_pair
else
./eval_one.sh $ppi_pair &
fi
((i++))
done < ../benchmark_list.txt
|
24e9f5cb4b6bc50a5b23915f1df3738fdb1dfcfcac64ac3d5f1ccb14661024bd | Shell | 306 | 11 | #!/bin/bash
#SBATCH --job-name=panexplorer
#SBATCH --cpus-per-task=18
#SBATCH --mem-per-cpu=20G
#SBATCH --partition=supermem
module load singularity/4.0.1
export PANEX_PATH=$PWD
singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s Snakemake_files/Snakefile_pggb_heatmap_upset
|
ace6c93415a509ac927df71f071e81d10055c364cee4d489d2b5f044d1a7014f | Shell | 307 | 6 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_data=$masif_root/data/
masif_matlab=$masif_root/source/matlab_libs/
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_ppi_search/
python3 $masif_source/masif_ppi_search/masif_ppi_search_cache_training_data.py $1
|
b138e437d2840cc4a72771ff9a75c40eb6d38bedf9a0e09dbd73b4bd85004a8a | Shell | 310 | 14 | #!/bin/bash
#SBATCH --time=2-00:00:00
#SBATCH --gres=gpu:2
#SBATCH --partition=gpu
#SBATCH -n 1
#SBATCH --mem=500000
#SBATCH -o train_%j.out
#SBATCH -e train_%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<EMAIL>
source activate selene-env
python -u ../../../selene_cli.py ./train_and_eval.yml --lr=0.01
|
00b7dee449551384dc255345a9b66315a32475f308dcd20074779dc6e77afc07 | Shell | 311 | 13 | #!/bin/sh
#author: Mahbub Ul Alam (mahbub@dsv.su.se)
#version: 1.0+
#copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
#license : MIT License
CUDA_VISIBLE_DEVICES=3 python3 batch_embeddings.py emily &>> emily_log.txt &
CUDA_VISIBLE_DEVICES=3 python3 batch_embeddings.py huang &>> huang_log.txt &
|
b23f1436a33984343f378236fd5c1fb1c07793b705ab04cbd709ad6b4013a657 | Shell | 313 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-12:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o SUBX_outs/SUBX1.out
#SBATCH -e SUBX_outs/SUBX1.err
#SBATCH -J SUBX1_stab
source activate GXAI
python3 stab_mult.py --exp_method SUBX --model GIN --save_dir SUBX_stab_results --num_splits 30 --my_split 0
|
739e5ef4556ee7ff362ee96f866b4876b76867db398c8fcaa557ef5bc0a727c0 | Shell | 315 | 6 | masif_root=$(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_ppi_search/
python $masif_source/gif_descriptors/eval_gif_descriptors.py nn_models.sc05.custom_params
|
dcfb10b60d7b306f5608de7533c876c65d8b91ec0241fe9b2a232967b774a058 | Shell | 317 | 18 | #! /bin/bash
# Sets the environment for other shell scripts.
set -e
# Directory containing these tool scripts.
CARLA_BUILD_TOOLS_FOLDER="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
function log {
echo "[`basename "$0"`]: $1"
}
function fatal_error {
echo -e >&2 "[`basename "$0"`]: ERROR: $1"
exit 2
}
|
76fa68ec67541f42eacfc52626973ae9366f8f9e6e175599fb63845d177cb7cf | Shell | 318 | 8 | #!/bin/bash
###################################
# This file needs to be sourced! #
###################################
#export directory of this script
export NETWORK_SIMULATION_HOME="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
export PYTHONPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )":$PYTHONPATH |
eab44bd9e0c47a69ce56aa2f56b4cd7b4d9591f3a5c7cd65dba4ff7a6802450b | Shell | 319 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o gcf_outs/SUBX_cNUM.out
#SBATCH -e gcf_outs/SUBX_cNUM.err
#SBATCH -J SUBX_cNUM
source activate GXAI
python3 gcf_saver.py --exp_method SUBX --model GIN --save_dir SUBX_results/gcf --num_splits 10 --my_split NUM
|
24e0ac37a13ff905b1188d3f18a327291b05403ce81c3819850096beaafbde19 | Shell | 321 | 11 | #!/bin/bash
# Transforms a HHblits psi file into a flat MA file containing in the first line
# the number of alignments and the sequences in the following lines
ff=`echo $1 | sed -e 's/\.psi/\.flatpsi/g'`
wc -l $1 |awk '{print $1}' > $ff
awk '{print $2}' $1 >> $ff
sed -i'' -e 's/-/./g' $ff
sed -i'' -e '2s/\.//g' $ff... |
34108681127acca672efa7062751b023f0a0f52332f3d98e528fb3c4ceca37de | Shell | 322 | 13 | #!/bin/bash
if [[ $@ = '--build-docker' ]]; then
echo "Building docker";
base/run_tests.sh --build-docker
sudo docker build --rm -f tests/docker/Dockerfile -t roots_test_docker ./
sudo docker image prune -f
else
DOCKER_IMAGE=roots_test_docker $(dirname ${BASH_SOURCE:-$0})/base/run_tests.sh $@
f... |
7b65285961e8d204c7c9adcd59000b346e1d199b12d3905d0704bd8965e6e834 | Shell | 324 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-12:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o mult_outs/SUBX_f49.out
#SBATCH -e mult_outs/SUBX_f49.err
#SBATCH -J SUBX_f49
source activate GXAI
python3 stability_saver.py --exp_method SUBX --model GIN --save_dir SUBX_results/stab --num_splits 50 --my_split... |
e53998f7e7767aff8447867d0990b514e36c6f5ae95e091d1c26af36983fe22c | Shell | 324 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-03:00
#SBATCH -p gpu_quad
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o ggf_outs/SUBX_fNUM.out
#SBATCH -e ggf_outs/SUBX_fNUM.err
#SBATCH -J SUBX_gNUM
source activate GXAI
python3 GGF_saver.py --exp_method SUBX --model GIN --save_dir SUBX_results/ggf --num_splits 50 --my_split ... |
fcfbda16ce5638d2af17fd685990c70cc8fba877346181f538acc221852dbe24 | Shell | 324 | 13 | #!/bin/bash
JOB_PREFIX=$1
LOGFILE=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-10-12-deconvolution_gav/jobs/$JOB_PREFIX/start.txt
re='^[0-9]+$'
while IFS= read -r LINE; do
JOBID=$(echo $LINE | cut -f5 -d' ')
if [[ $JOBID =~ $re ]] ; then
echo "scancel $JOBID"
scancel $JOBID
fi
done < "$LOGF... |
46b401abd5b7f7c9bef28bdd5fd2a013d55f74ad9d80c7cbdb8fb580615f006c | Shell | 328 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o mult_outs/SUBX_fNUM.out
#SBATCH -e mult_outs/SUBX_fNUM.err
#SBATCH -J SUBX_fNUM
source activate GXAI
python3 stability_saver.py --exp_method SUBX --model GIN --save_dir SUBX_results/stab --num_splits 50 --my_sp... |
b570be89baf86e84a78f19784edc08a45aa134471486ad8179322c608c41c1a0 | Shell | 328 | 7 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_ppi_search_source=$masif_root/source/masif_ppi_search
masif_data=$masif_root/data/
export masif_root
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_ppi_search_source
python $masif_source/masif_ppi_search/pdl1_benchmark/pdl1_benchmark... |
bbd9e5adf3b6c1c29edb75da34af857d7f9024ada7aba27c82c5d6e2d6e6f6ea | Shell | 329 | 15 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python synthesize.py \
--eval_batch 20 \
--num_workers 20 \
--seed 0 \
--stylegan_size 256 \
--dataset celebahq \
--ckpt exp/ckpt/stylegan2_celebahq_size_256_split_train/300000.pt \
--sentence2latent_ckpt exp/stylet2i/stylet2i_celebahq/ckpt/last.pt
... |
ebfe00b5f822ab4951c56f92aa7ea7822d328c65c18bc353f0a65c184aed71a2 | Shell | 332 | 17 | #!/bin/bash
# Run model fitting with multiple fitting scripts
# Use: fit directory fit_names
folder=$1
shift 1
cd $HOME/Paramecium-model-fitting
for arg in $@
do
echo "Fitting: $arg"
# Remove old yaml files
find "$folder/" -name "$arg.yaml" -delete
# Run fitting
python scripts/fitting/$arg.py "$f... |
b8d937698a12e0bf998556f707dc016c124de332e2a47d6b8eec20ff1244baba | Shell | 336 | 6 | masif_root=$(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 $masif_source/masif_ppi_search/second_stage_alignment.py ../../../data/masif_ppi_search_ub 100... |
a7e5649fa8b663f4e43f9c63df76c49a930dff62763198472cb612ee743ccee5 | Shell | 337 | 6 | export KALDI_ROOT=`pwd`/../../..
export PATH=$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
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
export PY... |
d1001b603f63d4829380178d07cf3f44836677ef5888521e7f3c8b807b724658 | Shell | 337 | 7 | #!/bin/bash
masif_root=$(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 -W ignore $masif_source/masif_site/masif_site_predict.py nn_models.all_feat_3l.cus... |
28220e0c8bf9d90e18c2fb07c1a0f1318dc546afc8f4ca0f2620318b11458be6 | Shell | 338 | 7 | export KALDI_ROOT=`pwd`/../../..
export PATH=$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
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
export P... |
ca5b570609044943b39689103326b7557d1e5f14ca9d065225aee3722415c1c3 | Shell | 338 | 6 | export KALDI_ROOT=$(pwd)/../../..
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
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
export P... |
2f1c8257d938dbfa96e709ebb9dec6eb543243f21f564eaf8d5de327de84a1e7 | Shell | 340 | 12 | #!/bin/bash
#SBATCH -c 1
#SBATCH -t 0-08:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=10G
#SBATCH -o fair_outs/GNNEX3_group.out
#SBATCH -e fair_outs/GNNEX3_group.err
#SBATCH -J GNNEX3_group
source activate GXAI
python3 fair_mult.py --exp_method GNNEX --model GIN --save_dir fairness_results --num_splits 4 --my_... |
0c9edf145a8e7a7cb758e9ef2a92ee0b020acc073cdb8725b19ab8f8fd4b788f | Shell | 342 | 11 | #!/bin/bash
# validateRealNUmber: chek if the argument agr1 is real number
echo "validateRealNumber: The arguments passed in are : $@"
ex='^[0-9]+([.][0-9]+)?$'
if [[ "$1" =~ $ex ]] ; then
echo 'validateRealNumber: parameter is Real number. OK'
else
echo 'validateRealNumber: You should enter an real!'... |
544a2112de3a99fd8d67ec71412ced565da54eaff23011b45ef28ccd0ea49536 | Shell | 343 | 7 | #!/bin/bash
masif_root=$(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 -W ignore $masif_source/masif_site/masif_site_label_surface.py nn_models.all_feat_... |
6429d3be889741411261d6c59e6c7d645393b40fc1e77a94822a07092c745f18 | Shell | 343 | 8 | #!/bin/bash
conda install -y pytorch=1.4.0 torchvision=0.5.0 -c pytorch
conda install -y numpy=1.18.1 scikit-image=0.16.2 tqdm
conda install -y -c anaconda ipython=7.13.0
pip install lmdb==0.98 opencv-python==4.2.0.34 munch==2.5.0
pip install -U scikit-image==0.15.0 scipy==1.2.1 matplotlib scikit-learn
pip install fla... |
3e1756b57bf2ec9f8c7de6bd65b1b99fce508d1c1a1bc2e58f2a7981100a685f | Shell | 345 | 6 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_data=$masif_root/data/
source /work/upcorreia/bin/load_masif_environment.sh
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_ppi_search/
python $masif_source/masif_ppi_search/masif_ppi_search_comp_desc.py nn_models.sc05.all_... |
96d3b68fdf6ed75d6a8e1a25c9eae7e6891075167a245c0b08bb679a51ba8572 | Shell | 347 | 11 | #!/bin/bash
mkdir ArrayExpress
unzip zipfiles/E-MTAB-7407.processed.1.zip -d ArrayExpress
unzip zipfiles/E-MTAB-7407.processed.2.zip -d ArrayExpress
unzip zipfiles/E-MTAB-7407.processed.3.zip -d ArrayExpress
unzip zipfiles/E-MTAB-7407.processed.4.zip -d ArrayExpress
cd ArrayExpress
for a in $(ls -1 *.tar.g... |
057f5b5db5bcd91c85b04aa8faf9c0c4b3d7b010b5bf0f9a778b0b826fb78b13 | Shell | 349 | 3 | # clang-format -style=google -dump-config > .clang-format
# find . \( -path './inst/include/ACTIONet/leiden/*' -o -path './src/ACTIONet/network_tools/leiden/*' -o -path './inst/include/ACTIONet/boost/*' \) -prune -o -type f -regex '.*\.\(cc\|c\|h\)' -exec clang-format -style=file -i {} \;
# Rscript -e "formatR::tidy_di... |
0c3595a22fd629f004f585b60cfbb29c6b9202153cf74e940a6bb405d54cf45a | Shell | 350 | 10 | #!/bin/bash
LOG_DIR_PATH="/var/log/jitsi/jibri"
LATEST_PJSUA_LOG_FILE="$LOG_DIR_PATH/pjsua.log"
AGGREGATED_PJSUA_LOG_FILE="$LOG_DIR_PATH/pjsua_all.log"
if [ -f "$LATEST_PJSUA_LOG_FILE" ]; then
echo "Appending pjsua logs from $LATEST_PJSUA_LOG_FILE, to $AGGREGATED_PJSUA_LOG_FILE"
cat "$LATEST_PJSUA_LOG_FILE" >> "$... |
2dd31cc0cfdae848f44e3b373d1beabe09dd8a709e97b38dfaeeff85f303f016 | Shell | 353 | 8 | SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
BASE_DIR=$SCRIPT_DIR/..
(cd $BASE_DIR/overleaf && git pull)
rsync -r --max-size=49m $BASE_DIR/results/figs $BASE_DIR/overleaf
rsync $BASE_DIR/results/glued_variables.txt $BASE_DIR/overleaf
(cd $BASE_DIR/overleaf && git add . && git commit... |
175f05538d058d4f0975efc2339d65e0079de15813f15b5b1c188b88d324a174 | Shell | 356 | 17 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python synthesize.py \
--eval_batch 20 \
--num_workers 40 \
--seed 0 \
--stylegan_size 256 \
--dataset celebahq \
--truncation 0.5 \
--ckpt exp/pretrained_stylegan2/stylegan2_ffhq.pt \
--latent_space wp \
--sentence2latent_ckpt exp/stylet2i/st... |
dc07c366655f3a015941162d34eff7cb69ae588420b33439851970e8b1b4645c | Shell | 357 | 20 | #!/usr/bin/env bash
# Copyright 2017 John Morgan
# Apache 2.0.
tmpdir=data/local/tmp
download_dir=$(pwd)
mkdir -p $download_dir
subs_src=$1
# download the subs corpus
if [ ! -f $download_dir/subs.zip ]; then
wget -O $download_dir/subs.zip $subs_src
(
cd $download_dir
unzip subs.zip
)
else
echo "$... |
b8fc98b87bfaba3b8c937fbb846c8a51224e0176aeb886198191b5f2fb7d3e4b | Shell | 359 | 10 | #!/bin/bash
RECORDINGS_DIR=$1
echo "This is a dummy finalize script" > /tmp/finalize.out
echo "The script was invoked with recordings directory $RECORDINGS_DIR." >> /tmp/finalize.out
echo "You should put any finalize logic (renaming, uploading to a service" >> /tmp/finalize.out
echo "or storage provider, etc.) in thi... |
e9fdf9f6aec6e7656e677020f57abb91607cd79d3e1d0eb205935ca205018175 | Shell | 359 | 17 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python synthesize.py \
--seed 0 \
--num_workers 20 \
--eval_batch 20 \
--stylegan_size 256 \
--dataset cub \
--truncation 0.5 \
--ckpt exp/ckpt/stylegan2_cub_size_256_split_train/last.pt \
--latent_space wp \
--sentence2latent_ckpt exp/stylet2... |
bfc8c62ad7a16b47bd88a961eee59581fd86cb8d7e34a998d34845c627bdcf7a | Shell | 360 | 13 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUBJ=(${@:2:1})
echo ${SUBJ}
#DATA_DIR=${HOME}/scratch/QC/MAGET_MNI_QC
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.2
itksnap -g $SUBJECTS_DIR/nii/sub-${SUBJ}_run-1_desc-preproc_T1w.nii -s $SUBJECTS_DIR/nii/sub-${SUBJ}_run-1_desc-masked_preproc_T1w_labels.nii.gz --... |
8f278f8a6689617228c086baf9ee86f38e8f670542ec6630e841e88c4e9f4a70 | Shell | 361 | 17 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python synthesize.py \
--seed 0 \
--num_workers 20 \
--eval_batch 20 \
--stylegan_size 256 \
--dataset nabirds \
--truncation 0.5 \
--ckpt exp/pretrained_stylegan2/stylegan2_nabirds.pt \
--latent_space wp \
--sentence2latent_ckpt exp/stylet2i/... |
33ffb0e94bd5135f14b820ca4a4e06774e3cd01d727bdac5f2ae93db4cd46485 | Shell | 362 | 14 | #!/bin/bash
# save statistics to the global file and
ststFile="$1"
dataFile="$2"
prefix="$3"
sts="${prefix}"
aws s3 cp s3://nsp-project/experiments/globalStatistics.nsp $ststFile
for i in `tail -n 24 ${dataFile}`; do
sts="${sts} ${i}";
done;
echo "${sts}" >> $ststFile
aws s3 cp $ststFile s3://nsp-pr... |
f78cb91fa40ebefc96f0335552edade004c738c870b5e7d2ddd1423a2d8e0d1b | Shell | 364 | 5 | infile=/data/interesting_side_projects/SSAML/github_fork/test_skewed_distribution/datasets/simulated_dataset_classfication_skewed.csv
outfolder=/data/interesting_side_projects/SSAML/github_fork/test_skewed_distribution/result_skewed
# run mode 1 and mode 2 with datatype=0 (custom)
./runner_power.sh 1 0 $infile $outfold... |
f593170df244065a8213d1bb1ad31bf2d82dbb0c95348bbdb0864158ba445078 | Shell | 366 | 19 | #!/bin/bash
# run with sudo
#author: Mahbub Ul Alam (mahbub@dsv.su.se)
#version: 1.0+
#copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
#license : MIT License
apt -y install python3-pip
pip3 install --upgrade torch==1.8.1
pip3 install --upgrade wandb
pip3 install pandas
pip3 install gpiozero
apt-get -y ins... |
928a4ed08b9762606ab57df818d8c03bf54c009cb4679237378ca4697ff6925e | Shell | 368 | 13 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUBJ=(${@:2:1})
echo ${SUBJ}
#DATA_DIR=${HOME}/scratch/QC/MAGET_MNI_QC
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.2
itksnap -g $SUBJECTS_DIR/nii/sub-${SUBJ}_run-1_desc-preproc_T1w.nii -s $SUBJECTS_DIR/nii/iw_Lobules-SUIT_u_a_sub-${SUBJ}_run-1_desc-preproc_T1w_seg... |
03f0e53f1650601f8f89a54f849e22e2b04153c3e413621c147711e9eb3c37f8 | Shell | 369 | 6 | export KALDI_ROOT=`pwd`/../../..
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/sph2pipe_v2.5:$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
. $KALDI_ROOT/tools/config/common_p... |
965f5dc3cf3e76bf2e826b2a6ad2b72b6759724d7978d19d0a24c6db2020c15c | Shell | 372 | 23 | #!/bin/sh
pull_data=${1:-false}
dirlist=$(ls -d */ | grep -v Dadi_values | grep -v all_plots | grep -v tables)
if $pull_data
then
for j in $dirlist
do
echo ' '
echo ${j}
scp tyoeasley@128.252.185.7:/scratch/janine.bijsterbosch/WAPIAW_2/figure_plotting/${j}plotting* ${j}
done
fi
for j in $dirlist
do
echo... |
9462bb20a9284cbf909d5a2aef34eb54afb20dd812ed0b99b2c9f91a804d0916 | Shell | 373 | 6 | masif_root=$(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_ppi_search/
python -W ignore $masif_source/masif_ppi_search/masif_ppi_search_comp_desc.py nn_models.sc05.al... |
cff7fa1d36734ca32b7f483d172586d9e427c8903d2f0ea3a131045dc2a5e4be | Shell | 373 | 7 |
ml Python
python make_go_matrices.py 2020-03-27-eigenvector-genes.txt 2020-03-25-uniprot_ensembl_map.txt.gz &
python make_hpo_matrix.py 2020-03-27-eigenvector-genes.txt 2020-03-25-ncbi-to-ensembl.txt.gz &
python make_kegg_matrix.py 2020-03-27-eigenvector-genes.txt 7.0 2020-03-25-ncbi-to-ensembl.txt.gz &
python make_r... |
bdcf3d5208d24b6bd26c14618575dd228f2881b7788162f941ae301512c3ce8e | Shell | 376 | 13 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:4
#SBATCH --mem=32G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0129_plain_BRATSIDH.out
#SBATCH --job-name 0129_plain_BRATSIDH
pyth... |
76b13f30ecc33a6fea0aacff707c77e6358616c3f4bb01e7b16a4ce960675842 | Shell | 378 | 7 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
$DIR/../main-spots-extraction.nf \
-with-tower "http://nextflow.int.janelia.org/api" \
--runtime_opts "-B /nrs/scicompsoft/goinac/multifish" \
--stitchdir "/nrs/scicompsoft/goinac/multifish/ex1/LHA3_R3_subset/stitching/export.n5" \
--outdir "/nrs/scicompsoft... |
8a78d763694db2e0fb6bc311736ab336d7b12742202bacaed69a09340225d3a7 | Shell | 378 | 7 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_matlab=$masif_root/source/matlab_libs/
masif_data=$masif_root/data/
source /work/upcorreia/bin/load_masif_environment.sh
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_site/
python -W ignore $masif_source/masif_site/masif_... |
c61c0737e1ee75b2de1f3999a02a0d19caa1a18e6a3f2d4d0914da11527fc60d | Shell | 378 | 6 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_data=$masif_root/data/
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_ppi_search/:$masif_data/masif_ppi_search/transformation_training_data/
masif_root=$(git rev-parse --show-toplevel)
python $masif_source/masif_ppi_search... |
c76315cbc91ecdfad771cd48f22c126e277f73c43595dcc02fc1b89dddd5217b | Shell | 380 | 3 | NCCL_IB_HCA=$(pushd /sys/class/infiniband/ > /dev/null; for i in mlx*; do cat $i/ports/1/gid_attrs/types/* 2>/dev/null | grep v >/dev/null && echo $i ; done; popd > /dev/null)
export NCCL_IB_HCA
python3 distributed_arch_search/test_server.py --config-file configs/e2e_faster_rcnn_DETNAS_COCO_FPN_300M_search.yaml MODEL.W... |
f56a3c15d54c451f4dd8c4766957b6b389282edb358986cc38997010c2882946 | Shell | 380 | 7 | masif_root=$(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/
# Activate your environment here.
python -W ignore $masif_source/masif_ppi_search/second_stage_alignm... |
36607e0004712b423440410eede1873679a1c2ab2fe98edd503a03360aae73c8 | Shell | 382 | 7 | export KALDI_ROOT=`pwd`/../../..
export PATH=$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
. $KALDI_ROOT/tools/config/common_path.sh
export PATH=$KALDI_ROOT/t... |
81b64e912075c945611fdd39f6ed7eded059841403082872e41790d8408c058d | Shell | 383 | 7 | 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/src/path.sh is not present -> Exit!" && exit 1
. $KALDI_ROOT/tools/c... |
b47db2e3c1d1b590fa3819f2bb380696868130bf61f1fcabedba45581e153fe1 | Shell | 383 | 7 | masif_root=$(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/
# Activate your environment here.
python -W ignore $masif_source/masif_ppi_search/second_stage_alignm... |
068b0954c027885d7b97dd112136bb91d6737ed51877c0e94eae2d414a98c9d8 | Shell | 384 | 17 | if [ $# -ne 1 ]; then
echo >&2 "Usage: ./setup_experiment.sh <expname>"
echo >&2 ""
echo >&2 "Sets up an experiment to be run in the babel directory with the "
echo >&2 "provided name."
exit 1;
fi
expname=$1
cd ..
mkdir ${expname}
cd ${expname}
cp ../asr1/{cmd,path,run,recog_wav}.sh .
cp -P ../asr1/steps .
c... |
0efeac84ad605547791d0600050702b1b5dcbd84c70aa3387b87deb4ef9d7707 | Shell | 385 | 13 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:4
#SBATCH --mem=32G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0201_plain_BRATSIDH.out
#SBATCH --job-name 0201_plain_BRATSIDH
pyth... |
b4c434fca440f463c82804f30a8b0a573f9ec8a6406dfbc4274b63a035a47850 | Shell | 386 | 13 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:4
#SBATCH --mem=32G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0203_plain3_BRATSIDH.out
#SBATCH --job-name 0203_plain_BRATSIDH
pyt... |
2a55758d512fe41c5d408bf191700fee42340897f15f4a3ec5f87effc1e534c7 | Shell | 389 | 26 | #!/bin/bash
#
# Runs the configure script if the bin directory does not exist.
# Runs make in the bin directory.
#
if [[ -z "$1" ]]; then
BIN_DIR="bin"
else
BIN_DIR=$1
fi
if [[ ! -d ${BIN_DIR} || ! -f ${BIN_DIR}/Makefile ]]; then
bash build/configure.sh ${BIN_DIR}
fi
pushd ${BIN_DIR} > /dev/null
make ITKJP2
# S... |
4a4966165cacac00284c239669d26418bc050e9018641b7491fd0b80f4a4cc12 | Shell | 389 | 6 | sbatch masif_site_train.slurm nn_models.all_feat_1l.custom_params
sbatch masif_site_train.slurm nn_models.hbond_only.custom_params
sbatch masif_site_train.slurm nn_models.pb_only.custom_params
sbatch masif_site_train.slurm nn_models.hphob_only.custom_params
sbatch masif_site_train.slurm nn_models.shape_only.custom_para... |
c7d165a4f0ff668f2629c7adf04a1276f4dff3f0262b86044b9ea042984bc11f | Shell | 389 | 16 | #
rm -r inst/include/autodiff
mkdir tmp
cd tmp
git clone https://github.com/autodiff/autodiff.git
mkdir ../inst/include/autodiff/
cp -r autodiff/autodiff/common ../inst/include/autodiff
cp -r autodiff/autodiff/forward ../inst/include/autodiff
cp -r autodiff/autodiff/reverse ../inst/include/autodiff
cd ..
rm -rf tmp/
... |
6475a873cb29dec4252ff2319ee09c779bcff1a6a46a4c6de27fed46384bea68 | Shell | 392 | 7 | export KALDI_ROOT=$(pwd)/../../..
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/kaldi_lm:$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
. $KALDI_ROOT/tools/config/common_path.... |
ba4ed353a318ac3d403b084e51e3acaab931567d3e7a1273e6f767bf1fe78896 | Shell | 393 | 5 | # This file downloads and unzips GTEx expression data and metadata
curl https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz > data/gtex_tpm.gct.gz
gunzip data/gtex_tpm.gct.gz
curl https://storage.googleapis.com/gtex_analysis_v8/annotations/GTEx_Analysi... |
d52e8cf764644b5e0b99150267b49fd415ad77a1a1165c75ee7200888189bdbc | Shell | 394 | 14 | #!/bin/bash
# validateRange: chek if the argument agr1 is between <ag2,agr3>
echo "validateRange: The arguments passed in are : $@"
if [ "$1" -eq "$1" 2> /dev/null ]; then
if [ ! "$1" -ge $2 ] || [ ! "$1" -le $3 ]; then
echo "validateRange: parameter $1 outside the range <$2,$3>!"
exit 2
fi
else
... |
2c53a06d11d82932c61f9592f386a73ee962552661717aa7a309fc5c546a0da7 | Shell | 395 | 7 | export KALDI_ROOT=`pwd`/../../..
export PATH=$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
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
export LD... |
bf53689a2c3463010fec1eca43dd4d31c6782982e744acb3909c6ba0668bdb9a | Shell | 396 | 6 | export KALDI_ROOT=`pwd`/../../..
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/sph2pipe_v2.5:$KALDI_ROOT/tools/sctk/bin:$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
. $KALDI... |
1e76148f62ddb299e9db4def956b2dcfdbaaa3015f0c337d0813316e1f7b1b93 | Shell | 397 | 16 | #!/bin/sh
GROUP=${2:-owlery}
USER=${1:-owlery}
# Adding desired system group
if ! getent group $GROUP > /dev/null 2>&1 ; then
echo "Creating system group: $GROUP"
addgroup --system $GROUP
fi
# Adding desired system user
if ! id -u $USER > /dev/null 2>&1; then
echo "Creating user $USER in group $GROUP"
... |
56ee09f7c806730b6ef3ffa4f05b8707e1fb853262575b77cf07c14f22f90d88 | Shell | 398 | 11 | #!/usr/bin/env bash
set -euo pipefail
ALPAMAYO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
MODEL_ENV="${ALPAMAYO2_MODEL_ENV:-${ALPAMAYO_ROOT}/.venv-model}"
export CUDA_VISIBLE_DEVICES="${ALPAMAYO2_CUDA_DEVICES:-1,2,3}"
export PYTORCH_CUDA_ALLOC_CONF="${PYTORCH_CUDA_ALLOC_CONF:-expandable_segments:True}"
ex... |
5fd9e7e2a502693852e3ee1f753d74d2e72cd9b4ca51e10b26e031d737979109 | Shell | 399 | 7 | 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... |
17e35ec169ee3c80646f971b2486a35e05ea263c4914945163be52f114e6c91a | Shell | 400 | 8 | 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... |
2689ac4b929b0f1b45410539994220ee0a11bed9ed71cf547efcb36e9802f81b | Shell | 400 | 15 | #!/bin/bash
#
# Author: Mario Juez-Gil <mariojg@ubu.es>
# Spark master node init script.
#
# source: https://github.com/big-data-europe/docker-spark/blob/master/worker/worker.sh
export SPARK_HOME=/usr/local/spark
mkdir -p $LOGS
ln -sf /dev/stdout $LOGS/stdout.log
$SPARK_HOME/bin/spark-class org.apache.spark.deploy.... |
b4bebc784da83496eec166533a70c8d06f18824f6ae54520dfc9b8ab83874e20 | Shell | 401 | 15 | #!/bin/bash
if [ $# -lt 1 ]; then
echo "Error: At least one argument is required."
exit 1
fi
export AFQ_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )/.." && pwd )"
sed "s|PLACEHOLDER_FOR_PACKAGE_PATH|${AFQ_PATH}|g" ${AFQ_PATH}/gpu_docker/cuda_track_template.def > ${AFQ_PATH}/gpu_docker/_temp.def
apptainer b... |
62ae2856fe22effbc43160edc016a094b9fda8d8a35ead61b154edc684006e5e | Shell | 402 | 7 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_matlab=$masif_root/source/matlab_libs/
masif_data=$masif_root/data/
# Compute geometric invariant descriptors, as implemented in Yin et al. PNAS 2009
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_ppi_search_ub/
python $ma... |
9fee4df5d973686c0beac413fcb62459944451ed35b3cc983a14af9dabe6e15f | Shell | 402 | 14 | #!/bin/bash
export TIMESTAMP=$(date +%Y%m%d%H%M%S)
docker-compose rm -f
echo "Spawning Runner... TIMESTAMP=${TIMESTAMP}"
mkdir -p logs
docker-compose config >> "logs/${TIMESTAMP}.log"
docker-compose up --force-recreate
docker-compose logs >> "logs/${TIMESTAMP}.log"
echo "Logs saved in logs/${TIMESTAMP}.log"
echo "Cle... |
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