sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
77ab245952cb74cf3de6f7d75c710472a3bf7377e5dbc8ac424ade3a229cbff5 | Shell | 509 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Macaca_nemestrina.%J.err
#SBATCH --output=Macaca_nemestrina.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Macaca_nemestrina /data/share/htp/TRNP1/TRNP1_exo... |
2a9269661bf088b710831342d910c6c105ab587a555e57fe304d0c491f2a0fde | Shell | 510 | 11 | # Compute the descriptors of a pdbid_chain or those of a list
# Usage:
# ./compute_descriptors.sh -l lists/training.txt
# or:
# ./compute_descriptors.sh {PDBID_CHAIN}
# where {PDBID_CHAIN} is something like 4ZQK_A
masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_data=$masif_root/da... |
37bec3ec5ea132319e9f592cd4cf8d86a13ce188baf2ad16d21d87a6ce0c3247 | Shell | 510 | 21 | #!/bin/sh
# All the data files needed for both training/evaluation and _in silico_
# mutagenesis.
wget https://zenodo.org/record/2214130/files/data.tar.gz
tar -xzvf data.tar.gz
# Outputs from training (e.g. log files, test performance, figures)
wget https://zenodo.org/record/2214130/files/training_outputs.tar.gz
... |
45655e2dd3a5ddb80e57a4011bddb62106c3ae48a49804cb267fa31237a9f8bb | Shell | 510 | 15 | #!/bin/bash
# check whether bs4 and lxml is installed
if ! python3 -c "import bs4" 2>/dev/null; then
echo "$0: BeautifulSoup4 not installed, you can install it by 'pip install beautifulsoup4' if you prefer to use python to process xml file"
exit 1;
fi
if ! python3 -c "import lxml" 2>/dev/null; then
echo "$0: l... |
964bc8cad8cb78c400a28560e324353aa01d048a32250014a3222ffeb392e8d2 | Shell | 510 | 19 | data_dir=datasets/stamatak
results_dir=results/stamatak
datasets=`find $data_dir -name "*.phy" -o -name "*.fas" | sort`
n_datasets=`echo $datasets | wc -w`
echo "found ${n_datasets} datasets"
echo
for ((idx=1;idx<=${n_datasets};idx++)); do
msa_file=`echo ${datasets} | cut -d' ' -f${idx}`
tree_file=${data_dir}/d... |
73d27253c5735fd6443fb0266d8d651fe87a93fea12443569f6f0274268aee58 | Shell | 512 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Castor_canadensis.%J.err
#SBATCH --output=Castor_canadensis.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Castor_canadensis /data/share/htp/TRNP1/TRNP1_exo... |
221e5b86ff4ec3eb04fe0751ad60099474126b290aaa3f471fcaa0efaf50e581 | Shell | 513 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Erythrocebus_patas.%J.err
#SBATCH --output=Erythrocebus_patas.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Erythrocebus_patas /data/share/htp/TRNP1/TRNP1_... |
593c6bb7bc2339e16ee29c623a5870585420ec51252fd8b8f63c9f96e0a2edee | Shell | 515 | 22 | #!/usr/bin/env bash
data_dir=/export/corpora/LDC/LDC2011T11/
arabic_giga_dir=Arabic_giga/
[ ! -d $arabic_giga_dir ] && mkdir $arabic_giga_dir
#for x in `find $data_dir -name "*.gz"`; do
# echo $x
# dest_file=`basename $x .gz`
# gunzip -c $x > ${arabic_giga_dir}/${dest_file}.orig
#done
#for x in $arabic_giga_dir/... |
c23b2d4002dd81f65701fbd1901cb7ddbaddf5701e79e1c2bfd46ca4b7aa1764 | Shell | 515 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Theropithecus_gelada.%J.err
#SBATCH --output=Theropithecus_gelada.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Theropithecus_gelada /data/share/htp/TRNP1/... |
97f236fe962cd83da4b686a9bcc88458b7d757f41063dd75565f6cf0e80b4171 | Shell | 516 | 19 | mkdir -p datasets/coco
ln -s /path/to/coco/annotations datasets/coco/annotations
ln -s /path/to/coco/train2014 datasets/coco/train2014
ln -s /path/to/coco/val2014 datasets/coco/val2014
mkdir ImageNet-Pretrain-models/
git clone https://github.com/cocodataset/cocoapi.git
cd cocoapi/PythonAPI
python3 setup.py build_ext ... |
d870230f45e68e567b968f2e3d81a0e4e1a5c0ce8e55ece88de8fbea021b0356 | Shell | 516 | 11 | #!/bin/bash
# Copyright 2020 Audio, Speech and Language Processing Group (ASLP@NPU), Northwestern Polytechnical University (Authors: Zhuoyuan Yao, Xiong Wang, Jingyong Hou, Lei Xie)
# 2020 AIShell-Foundation (Author: Bengu WU)
# 2020 Beijing Shell Shell Tech. Co. Ltd. (Author: Hui BU)
# Apache 2.... |
679604e1fe704386a2be1eedef5a3c775cb01a05ca9e69ecb4abe22ddb148d54 | Shell | 517 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Callithrix_jacchus.%J.err
#SBATCH --output=Callithrix_jacchus.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Callithrix_jacchus /data/share/htp/TRNP1/TRNP1_... |
3bc8e5233f817a1b8b981f83e4c97f6e6f8fffb1938104fd0dbe3409fd60b5c1 | Shell | 519 | 16 | #!/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/s5_tumorsyn_%A.out
#SBATCH --job-name s5_tumorsyn
#SBATCH --partition=long
module loa... |
4d1d4f641abcbc786a5ad5058d29bfae2dae85e9ef469a1f91cab585a6949536 | Shell | 519 | 16 | #!/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/s2_tumorsyn_%A.out
#SBATCH --job-name s2_tumorsyn
#SBATCH --partition=long
module loa... |
5e7e72af99fd54ddace20d4183c3ef6cadff265b724dc44c7a98712d12cacfbd | Shell | 519 | 16 | #!/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/s3_tumorsyn_%A.out
#SBATCH --job-name s3_tumorsyn
#SBATCH --partition=long
module loa... |
61754e2e5839a4f5abcca1220cfcf0dc4dd4387d0624bc992de403e198781f92 | Shell | 519 | 16 | #!/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/s4_tumorsyn_%A.out
#SBATCH --job-name s4_tumorsyn
#SBATCH --partition=long
module loa... |
c31ce290e2e7f1e8ae93588789dd0c360a8f4a9cb8d5f7835f68613498410cad | Shell | 519 | 16 | #!/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/s1_tumorsyn_%A.out
#SBATCH --job-name s1_tumorsyn
#SBATCH --partition=long
module loa... |
36e3a2d7d84ea2d8ad02dac8fb123662a25903f21530b691751a1b29e8b27525 | Shell | 520 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Lipotes_vexillifer.%J.err
#SBATCH --output=Lipotes_vexillifer.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Lipotes_vexillifer /data/share/htp/TRNP1/TRNP1_... |
65d7e15d1ae7043416980f7e914d0a89c8d600a59b5ab705c823b0e280be1386 | Shell | 520 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Elephantulus_edwardii.%J.err
#SBATCH --output=Elephantulus_edwardii.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Elephantulus_edwardii /data/share/htp/TRN... |
02bca7357fbcb89900912c384bc25bd56ae8f1a54b2f440afed6777528275b70 | Shell | 522 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Delphinapterus_leucas.%J.err
#SBATCH --output=Delphinapterus_leucas.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Delphinapterus_leucas /data/share/htp/TRN... |
d85264fba3a5b80a7082eabbea23e3592169427fb20071580b39cfd16d67f41f | Shell | 523 | 14 | #!/bin/sh
echo "Loading OWLERY"
# Set defaults if environment variables are not set
OWLURL=${OWLURL:-"http://www.virtualflybrain.org/owl/vfb.owl"}
LOGLEVEL=${LOGLEVEL:-"INFO"}
sed -i "s|http://www.virtualflybrain.org/owl/vfb.owl|${OWLURL}|g" /srv/conf/application.conf
sed -i "s|INFO|${LOGLEVEL}|g" /srv/conf/applicat... |
391c8dc401e32709fa4d7d97c0b2f5d13bcc963dfaefc84f7bfa94faae61411c | Shell | 525 | 19 | #!/bin/bash
JOBS_DIR=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/
LOGFILE=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/start.txt
JOB_PREFIX=$1
START=$2
END=$3
echo $(date) > $LOGFILE
for I in $(seq $START $END); do
JOBNAME="$... |
65a2ba0aa0513ca0a69699bbf0304bd884ce2301f87155252813b5d2766b7f96 | Shell | 526 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Odocoileus_virginianus.%J.err
#SBATCH --output=Odocoileus_virginianus.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Odocoileus_virginianus /data/share/htp/... |
ac22de17da681dca3419e4f50530e9220275a12bed1032ed89ed24a165f60673 | Shell | 528 | 30 |
#!/bin/bash
# script that stop NSP container
# Set default values for parameters
# Process command line arguments
while [[ $# -gt 0 ]]
do
key="$1"
case $key in
-h|--help)
echo "Usage: ./deleteNspImages.sh "
echo "Delete all NSP images"
echo " -h, --help: show this help message"
... |
12359fca821412c8dd21ea86b2a6b689c283e145a2e7a46f22a6e20ac5ef94d7 | Shell | 529 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Propithecus_coquereli.%J.err
#SBATCH --output=Propithecus_coquereli.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Propithecus_coquereli /data/share/htp/TRN... |
52aa15519d5e38166c178f75542689fff7be3e0539a50153bc38e879c394bce2 | Shell | 529 | 20 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=mafft_adjust_direction.%J.err
#SBATCH --output=mafft_adjust_direction.%J.out
#SBATCH --workdir=regulation/scripts/MPRA/slurms
declare -a arr=("intron" "upstream3" "upstream2" "upstream1" "exon2" "downstream" "exon1")
## now loop through the above array
for i in "${arr[@]}"
d... |
5d72cc859c7112cd02010cccc2368e2c928fc9d516850fa58fadd7a4a65e77a8 | Shell | 529 | 15 | #!/bin/sh
# This script builds and installs your Maven project to the given Imagej2/Fiji directory
# - *without* running the unit tests
# It will delete all duplicate .jars which may break your ImageJ installation!
# It's recommended to use this script only on a clean copy of ImageJ which you don't
# use in your daily ... |
af238914550a7a462c1c9908d32d9d1ddc3640d8312c9db2bf0f7d326b5fe542 | Shell | 529 | 23 | #!/bin/bash
#PBS -l select=1:ncpus=1:mem=7G
#PBS -N flexibility_simulation
#PBS -j oe
echo "working directory: " $PBS_O_WORKDIR
echo "omp thread num: " $OMP_NUM_THREADS
echo "ncpus: " $NCPUS
echo "cuda visible devices: " $CUDA_VISIBLE_DEVICES
date +"%Y/%m/%d %p %I:%M:%S"
start_time=`date +%s`
cd $PBS_O_WORKDIR
/home... |
f6e8204b5b7923e41dfdc2e8991c9b7c61c62b23c97f18890c14c7501f0585a1 | Shell | 529 | 16 | #!/bin/bash
#TODO : better error checking, exit with proper error message and state save
#Todo : use curl as a failsafe
test -e hdf5-1.10.4.tar.gz && rm hdf5-1.10.4.tar.gz
test -d hdf5 && rm -r hdf5
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.gz || exit 1
tar -xzf hdf... |
2a25e2f8700d0b22bd5cd9c4748ef78519f7d6ce2e4f84a6554512ad7720e179 | Shell | 530 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Zalophus_californianus.%J.err
#SBATCH --output=Zalophus_californianus.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Zalophus_californianus /data/share/htp/... |
d4c051850ae77f4bc07ee56c4ac16bd0c2e94efdca9b16b94585d81f820e7729 | Shell | 531 | 9 | dataDir="./Boix_data"
mkdir -p $dataDir
wget --directory-prefix $dataDir https://personal.broadinstitute.org/cboix/epimap/metadata/main_metadata_table.tsv
wget --directory-prefix $dataDir --execute="robots = off" --mirror --no-parent -nd --wait=5 -A "FINAL*.bigWig" https://epigenome.wustl.edu/epimap/data/observed/
#p... |
f1352d6fe69888e29e215c683c11c29325078e02c2552c686231f9953f44e447 | Shell | 531 | 14 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:4
#SBATCH --mem=32G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --array=1-5
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0210_miccai_eval_get_trained_model_5foldcv_BRAT... |
ca98500a21ca6e68a49c3d8ee14c35af5f8b28e9642e8f9c5de7a64ee8d9cad6 | Shell | 532 | 13 | if [ -z $KALDI_ROOT ]; then
export KALDI_ROOT=`pwd`/../../..
fi
export PATH=$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/comm... |
132f3599882d459cf87fecbea0b6d5a28c0ff4a08a6a553facb44fa689e97b58 | Shell | 534 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Macaca_fascicularis.%J.err
#SBATCH --output=Macaca_fascicularis.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Macaca_fascicularis /data/share/htp/TRNP1/TRN... |
7cec88d2d768f20b9908a6afc0c059aed8f0eb1012b6d351661da67fbe970f9b | Shell | 536 | 23 | #!/bin/bash
docker_image=$1
model_dir=$2
if [ -z "${docker_image}" ]; then
echo "please input docker_image"
exit 1
fi
if [ ! -d "${model_dir}" ]; then
echo "please input model_dir"
exit 1
fi
docker run -it \
--device=/dev/davinci0 \
--device=/dev/davinci_manager \
--d... |
cdd146f7335ea278d43e8b11bdae5375d9ea4b810f6521399e865a1fc9217c64 | Shell | 536 | 20 | SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
BASE_DIR=$SCRIPT_DIR/..
while getopts 'r' opt; do
case $opt in
r)
export RERUN_SIMS=true
export RESAVE_DATA=true
echo "[make_project.sh] Set to rerun simulations and resaving data"
... |
41eb98f1b61bfca30299910e5872043ee83ca81c3a57152987a07d78738e6b2e | Shell | 537 | 24 | #!/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/s30_%A.out
#SBATCH --job-name s30
#SBATCH --partition=long
#SBATCH --nodelist=cs-venus-04
module l... |
9491d60b26da8778b07485cc4e02297b92cf14582bc812aa89d50193645fb97e | Shell | 537 | 24 | #!/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/s40_%A.out
#SBATCH --job-name s40
#SBATCH --partition=long
#SBATCH --nodelist=cs-venus-04
module l... |
58ff3b641f3554c633ce4024e8972e8b00dce0752a77a12d24bc321d0c34ed3b | Shell | 538 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Piliocolobus_tephrosceles.%J.err
#SBATCH --output=Piliocolobus_tephrosceles.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Piliocolobus_tephrosceles /data/s... |
0a35f8c05fc2a91adaa6260e45e9edc79ce3bc99be803d19db07f55fd934afc2 | Shell | 539 | 14 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --gres=gpu:4
#SBATCH --mem=32G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --array=1-5
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0208_miccai_eval_get_trained_model_5foldcv_BRAT... |
a61250983ce402a358f209c6e6b7139a4ebfcdc21062fcaf9d0c89007fb09ce0 | Shell | 540 | 13 | #!/bin/bash
#SBATCH --gres=gpu:2
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --array=1-5%1
#SBATCH --time=5-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --error=../out/0303_%A_error_%a.out
#SBATCH --output=../out/0303_%A_get_hm_5foldcv_BRATS_IDH_cc_%a... |
19cf3594c8e26dad07e9a582db1cfd89617105446e4ee0b9e271dfef70b13c87 | Shell | 541 | 16 | #!/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/s2_1118_mrnet_%A.out
#SBATCH --job-name s2_mrnet
#SBATCH --partition=long
module load LA... |
1ab8a72e4319adccf1d9582b172204b88609529cb9348a30033c4bb6c3129183 | Shell | 541 | 16 | #!/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/s1_1118_mrnet_%A.out
#SBATCH --job-name s1_mrnet
#SBATCH --partition=long
module load LA... |
51dd5091020aa5d5c2dcbf41f90612dd549c36ca53acb40656266317f5366854 | Shell | 541 | 16 | #!/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/s3_1118_mrnet_%A.out
#SBATCH --job-name s3_mrnet
#SBATCH --partition=long
module load LA... |
7c3e5b934e69543c6e039e91c4ea37a1e6ff7222abf7de561b8e669b7bf29857 | Shell | 541 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_brain_mass_GI_3.%J.err
#SBATCH --output=body_mass_brain_mass_GI_3.%J.out
#SBATCH --time=4-00:00:00
srun coevol -d /data/share/htp/TRNP1/paper_data/protein/fastas/prank_output/prank_TRNP1_coding_30species_forCoevol_longer.best.nuc.phy -t /data/share/htp/TRNP1/pa... |
a7d5e807e5b57b64daf51967c07f69e883e12354bc03ee0a9a96004c21905824 | Shell | 541 | 16 | #!/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/s4_1118_mrnet_%A.out
#SBATCH --job-name s4_mrnet
#SBATCH --partition=long
module load LA... |
e058bc82624f07d32b0bc12714a6bc2abd7768bb600c13911f3ebc1cbb0c0f15 | Shell | 541 | 16 | #!/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/s5_1118_mrnet_%A.out
#SBATCH --job-name s5_mrnet
#SBATCH --partition=long
module load LA... |
f6f6d3001033a2fb300fa4e82afe828c24922dc90ba6e6576b150dafb4e6bdc3 | Shell | 541 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_brain_mass_GI_2.%J.err
#SBATCH --output=body_mass_brain_mass_GI_2.%J.out
#SBATCH --time=4-00:00:00
srun coevol -d /data/share/htp/TRNP1/paper_data/protein/fastas/prank_output/prank_TRNP1_coding_30species_forCoevol_longer.best.nuc.phy -t /data/share/htp/TRNP1/pa... |
fb6421b318a475a2d027026237b544805fbdafa21676173f312acdf3c5537cd7 | Shell | 541 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_brain_mass_GI_1.%J.err
#SBATCH --output=body_mass_brain_mass_GI_1.%J.out
#SBATCH --time=4-00:00:00
srun coevol -d /data/share/htp/TRNP1/paper_data/protein/fastas/prank_output/prank_TRNP1_coding_30species_forCoevol_longer.best.nuc.phy -t /data/share/htp/TRNP1/pa... |
8dd8269cc9a2247d0cee9240e2bce449aa1f91cddde0a116c60233bdb214ef59 | Shell | 544 | 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/1118_tumorsyn_%A.out
#SBATCH --job-name save_tumorsyn
#SBATCH --partition=long
#SBATCH --nodeli... |
cc2823a3585fe33e39a0d5711a7be0ffa003ff19340e5b8c8dada772f96bd85f | Shell | 546 | 17 | #!/bin/bash
#SBATCH --gres=gpu:4
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=3-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/BRATS_IDH/log/0423_%A_BRATS_HGG_fold1.out
#SBATCH --job-name 0423_BRATS_HGG_cc
#SBATCH --partition=long
#SBA... |
8b3f94426f33410ba67dfdc6bcd42b32901d59dd2ad738987d32230703377c84 | Shell | 548 | 19 | #!/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/master/master.sh
export SPARK_MASTER_HOST=$(hostname)
export SPARK_HOME=/usr/local/spark
# configuring and loading spark environment.
#. $SPARK_HOME/sbin/sta... |
bdde4b94e3340af40c56bc44245d2b90e9467d5d53b5faa99a975a012610fd45 | Shell | 548 | 12 | #!/usr/bin/env bash
# Generate a docker container that supports FreeSurfer and FSL
neurodocker generate docker --base=debian:stretch --pkg-manager=apt \
--fsl version=6.0.3 method=binaries \
--freesurfer version=6.0.0 method=binaries --copy license.txt /opt/freesurfer-6.0.0/ \
--install gcc g++ graphviz tree nan... |
fc4694f1cab1a00fb0c247a370e5ddec72cb0fdd7ab922068d0362b26b19933c | Shell | 558 | 32 | #!/bin/bash
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
echo ">> Example"
echo ">> process_subject.sh /m/cs/scratch/faceai/rawdata/OAR_GTV/1/1_T2.nii.gz /m/cs/scratch/faceai/projects/faceai_testingdefacing/results/"
echo
indir=$(dirname $1)
infile=$(basename $1)
subjID=$(basename $indir)
outdir=$2/$subjID/
... |
ad3336a5a4937fbfd370745f56ecc32433a79721531079237dcd28055f7fca0e | Shell | 561 | 6 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
. /export/babel/data/software/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/sph2pipe_v2.5/:$KALDI_ROOT/src/bin:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/src/fstbin/:$KALDI_ROOT/src/gmmbin/:$KALDI_ROOT/src/featbin/:$KALDI_R... |
2d7ce7ee1b8900da08b7de4918f3da4ce11e83e667d4ec030cbc6e5c63c88216 | Shell | 562 | 18 | #!/bin/bash
#SBATCH -A slurm
#SBATCH --partition=all
#SBATCH --job-name=crg2
#SBATCH --time=100:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4G
#SBATCH --output=%x-%j.out
SF="/srv/shared/pipelines/crg2/Snakefile"
CP="/srv/shared/conda_envs/crg2-conda/"
SLURM="/srv/shared/pipelines/crg2/slurm_profile/"
CONFIG="confi... |
6dfd5a99ae1b937bb4998fcf0cbf2f2570c540f9d59982dfbeb35df502b11ee8 | Shell | 562 | 21 | SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
BASE_DIR=$SCRIPT_DIR/..
build=false
while getopts 'b' opt; do
case $opt in
b) build=true ;;
esac
done
shift $((OPTIND -1))
export DISPLAY_FIGS=False
jupytext --to notebook --output $BASE_DIR/docs/$1.ipynb $BASE_DIR/scri... |
6e048371188b50cfb855e1de17fd8dd92d78ecbf1699a55c208c10b4e14cbd00 | Shell | 562 | 8 | #!/bin/bash
cd data/training_srfs/
outid=$(echo $1| sed -e 's/.srf//g')
pdbid=$(echo $1 | cut -d"_" -f1)
chain=$(echo $1 | cut -d"_" -f2)
pdbid_chain=$pdbid\_$chain
../../probis/probis -results -z_score -1000 -noprune -longnames -ncpu 64 -surfdb -local -sfile training_srfs.txt -f1 ../../data/testing_srfs/$1 -c1 $chain ... |
c5e9cf8dfb5c78329558d247f90e3b9e94930ef7babb0280f6c1784d645509e7 | Shell | 562 | 6 | python3 graph_eval.py --exp_method GCAM --dataset mutag --model GIN --accuracy --faithfulness
python3 graph_eval.py --exp_method GBP --dataset mutag --model GIN --accuracy --faithfulness
python3 graph_eval.py --exp_method RAND --dataset mutag --model GIN --accuracy --faithfulness
python3 graph_eval.py --exp_method GRAD... |
39290b8debe88a174e69686233257f9c3b713cdfac7e60e21df07d731846e5f2 | Shell | 564 | 14 | curl http://images.cocodataset.org/annotations/annotations_trainval2014.zip -o "./data/preprocess/annotations_trainval2014.zip"
curl http://images.cocodataset.org/zips/val2014.zip -o "./data/preprocess/val2014.zip"
unzip ./data/preprocess/annotations_trainval2014.zip -d ./data/preprocess
unzip ./data/preprocess/val201... |
9eacd27206170743a84b3790fa16c7df55e38eeaa5e5c2d98fc4f6e486c2c8bf | Shell | 564 | 14 | 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... |
8ea805db873bfb2f0ae4d0da8671db1054c2a7b156be5cbbb60de4b0748f5a9e | Shell | 568 | 14 | # Compute neurite lengths for each cell id in data/soma_ids
# -> data/pyr_dist_to_leaves.csv
# -> data/inh_dist_to_leaves.csv
python scripts/compute_dist_to_leaf.py
# Compute total path length covered by each compartment label
# -> data/pyr_compartment_lengths.csv
# -> data/inh_compartment_lengths.csv
python scripts/c... |
ad913583e6aea72eea4e7fa66973fbd0a1f309a20b9a75d36b82bc890d1732b4 | Shell | 573 | 16 | #!/bin/bash
x=`samtools idxstats $1 | grep "X"`;
y=`samtools idxstats $1 | grep "Y"`;
xcov=`echo $x | awk '{ printf("%0.5f", $3/$2); }'`;
ycov=`echo $y | awk '{ printf("%0.5f", $3/$2); }'`;
# xcov=$(echo "scale=4; $(samtools idxstats $1 | grep "X" | cut -f 3)/$(samtools idxstats $1 | grep "X" | cut -f 2)" | bc)
# yco... |
2550b4f9c9608618d0694420121f0378a51402fd0f06f6b034a6d45d6a79e551 | Shell | 574 | 17 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=3-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/BRATS_IDH/log/0428_%A_hm_BRATS_HGG_fold1.out
#SBATCH --job-name 0428_hm_BRATS_HGG_cc
#SBATCH --partition=lon... |
148e64511d8c9d4caac129331c2996e49b449d246e4fb3822b90d6a2d3efd039 | Shell | 576 | 16 | # File is already sorted
cut -f 1-3 33545_peaks.bed > GATA1_proery_bm.bed
sed -i "s/$/\tProery_BM|GATA1/" GATA1_proery_bm.bed
bgzip -c GATA1_proery_bm.bed > GATA1_proery_bm.bed.gz
tabix -p bed GATA1_proery_bm.bed.gz
python get_test_regions.py GATA1_proery_bm.bed \
GRCh38_no_alt_analysis_s... |
1e18cadfebaebe2527577cdaa6c95cfa403100da4903c4b5aa853b8342db40bb | Shell | 578 | 18 | #!/bin/bash
family=$1
multiqc=`echo $family/qc/multiqc/multiqc_data/multiqc_picard_dups.txt`
dups=(`cat $multiqc | awk -F '\t' '{print $10}'`)
samples=(`cat $multiqc | awk -F '\t' '{print $1}'`)
num_of_samples=$((`echo ${#samples[@]}`-1))
for i in `seq 1 $num_of_samples`
do
dup_rate=`awk "BEGIN {print ${dups[i]}*100}... |
511d5bbd61baf398bc4a0dfc8f43cff107cd999066b32994f4c3e8d69c386280 | Shell | 579 | 20 | #!/usr/bin/env bash
# Copyright 2015 Johns Hopkins University (Author: Jan Trmal <jtrmal@gmail.com>)
# 2021 Xiaomi Corporation (Author: Junbo Zhang)
# Apache 2.0
[ -f ./path.sh ] && . ./path.sh
command -v python3 >&/dev/null \
|| { echo >&2 "python3 not found on PATH. You will have to install Python3,... |
212ab9a4fdf831145a60c0468a70cb76630e62b36e3d49b547b1ee7a22ac2df9 | Shell | 582 | 25 | #!/bin/bash
set -e
KB="/Users/matentzn/ws/kb2_data/data/databases/graph.db"
NEODIR="/Users/matentzn/Library/Application Support/com.Neo4j.Relate/Data/dbmss/dbms-b824802f-99fc-48bc-af0d-34b011b9b7f7/"
NEO4J2OWLDIR="/Users/matentzn/vfb/neo4j2owl"
PLUGIN="$NEO4J2OWLDIR/target/neo4j2owl-1.0.jar"
cd $NEO4J2OWLDIR
#mvn ... |
c42609573b62349fab4ca4c9a3577f3fcbde7c30904aa16beab25eb96150c77f | Shell | 582 | 7 | curl -Lo classifier128.pth https://dl.fbaipublicfiles.com/FaderNetworks/classifier128.pth
curl -Lo classifier256.pth https://dl.fbaipublicfiles.com/FaderNetworks/classifier256.pth
curl -Lo eyeglasses.pth https://dl.fbaipublicfiles.com/FaderNetworks/eyeglasses.pth
curl -Lo male.pth https://dl.fbaipublicfiles.com/FaderNe... |
5c2109501c742d6a206dd04af53ccf1f56d728c6bd6a12ba65080ce6023aa586 | Shell | 596 | 24 | #!/bin/bash
# set absolute paths for all model files required by Brewery
# SS3
echo 3 > models/modelv7_ss3
ls models/SS3/*v7 >> models/modelv7_ss3
echo 3 > models/modelv8_ss3
ls models/SS3/*v8 >> models/modelv8_ss3
echo 1 > models/modelv78_ss3
ls models/SS3/*v78 >> models/modelv78_ss3
# SS8
echo 3 > models/modelv7_s... |
a6461c200504fd07492a860f56ca87c5b167ebcae3fbe658971246206674451a | Shell | 597 | 16 | #!/bin/bash
# Atualizando as informações do git
git config --global user.email "gfsilveira@gmail.com"
git config --global user.user "Guilherme F Silveira"
# Instalando o programa tree, para obtenção da estrutura de diretórios e atualizando a estrutura
sudo apt-get update
sudo apt-get install -y tree
tree > directory_... |
e2be263b8694681f763f519f07995d341dbe0af080f4553ba150074f24eb5106 | Shell | 597 | 23 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUB_list=(${@:2:1})
#DATA_DIR=${HOME}/scratch/ET_fmriprep_anat_20.2.0/freesurfer-6.0.1/
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.6
#-v $SUBJECTS_DIR/sub-$SUBJ/mri/T2.mgz
#-v $SUBJECTS_DIR/sub-$SUBJ/mri/aparc.DKTatlas+aseg.mgz:colormap=lut:opacity=0.4
n_sub=$(wc... |
f337d8fb541102d1b66b9c29269c9a155f1ad7add9664bcb977ad4a87791ec81 | Shell | 597 | 26 | #!/bin/bash
route=$1
file=$2
name=$3
mkdir tmp
cp $route/$file tmp
cd tmp
tar -xaf $file
r="./home/paciente/Descargas"
for i in $(ls $r)
do
echo "file '"$r"/"$i"'" >> mylist.txt
done
ffmpeg -f concat -safe 0 -i mylist.txt -c copy output.webm 2>/dev/null >> /dev/null
ffmpeg -i output.webm -filter:v fps=fps=15 $n... |
3773471d00a6bf596240b45041c3143aa9d7012da6861b820eec548d935881fb | Shell | 601 | 26 | #!/usr/bin/env bash
# Copyright 2017 Hossein Hadian
# 2017 Babak Rekabdar
# 2017 Chun Chieh Chang
# 2017 Ashish Arora
# This script prepares the dictionary.
set -e
dir=data/local/dict
. ./utils/parse_options.sh || exit 1;
mkdir -p $dir
local/prepare_lexicon.py ... |
a767a94d2aa7a80df4a7940ea9c5f16030dd7d12230ab2d0128f2fcd69fa8446 | Shell | 601 | 22 | #!/bin/bash
giga_dir=$1
source_dir=/export/corpora5/LDC/LDC2011T11/arb_gw_5
num=2000000
suffix="2000k"
[ ! -d $source_dir ] && echo "source Arabic Gigaword does not exist." && exit 1;
[ -f $giga_dir/text ] && mv $giga_dir/text $giga_dir/text.bkp
mkdir -p $giga_dir/
find $source_dir/data/ -name "*.gz" | while read ... |
0ada45de196d366184cfb7b8ff6611e4d8a5a4a77251fc9fb1b458236e87dfd3 | Shell | 606 | 6 | for i in {1..421}
do
sed s/NUMBER1/${i}/ /projects/lu-lab/BenStuff/research/projects/oldhome/scripts/networks/rset/rsetlists/rsetlist_template.r | sed s/NUMBER1/${i}/ > /projects/lu-lab/BenStuff/research/projects/oldhome/scripts/networks/rset/rsetlists/files/makersetlist${i}
sed s/INDEXNUMBER/${i}/ /projects/lu-lab/Be... |
2fa0c7683493b4fa08ad4e1ebf1f891e4204445806bae8ef4c9d19a25fb6c12f | Shell | 606 | 26 |
ml Python/2.7.12-foss-2015b
# $1 : input plink file
liftoverutils=/groups/umcg-biogen/tmp03/tools/liftover/liftOverUtils.py
liftovertool=/groups/umcg-biogen/tmp03/tools/liftover/liftOver
buildout=hg38
chainfile=/groups/umcg-biogen/tmp03/tools/liftover/hg19ToHg38.over.chain.gz
python $liftoverutils --mode gwastobed ... |
31f8f81323186fc9cd8e62fe52df6bb90942621f52750663a45f66e51fcca239 | Shell | 606 | 31 |
#!/bin/bash
# Show running and stopped NSP containers
# Set default values for parameters
# Process command line arguments
while [[ $# -gt 0 ]]
do
key="$1"
case $key in
-h|--help)
echo "Usage: ./showNspContainers.sh"
echo "Show running and stopped NSP containers."
echo " -h, --he... |
f179dd00901fe1b4215ee25ebabbfc83a730fd40b97e8fe9d06cbbfebf4b4a19 | Shell | 609 | 13 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
[ ! -f /export/babel/data/software/env.sh ] && echo >&2 "The file /export/babel/data/software/env.sh is not present -> Exit!" && exit 1
. /export/babel/data/software/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/... |
87a8623a317c18cff5646b44dff13df79bb63b498c0a6db7ce29ea095d19736a | Shell | 612 | 18 | #!/bin/bash
if [ $# -ne 2 ]; then
echo "Usage: recipes/04_postprocess_ctms.sh <segments_list> <recipe>"
echo "e.g.: $0 segments.list /path/to/recipe_file"
echo
echo "Postprocess CTMs in <segments_list> (generated in the previous step)."
echo "In postprocessing, the CTM is matched to the original tr... |
8c41e6b19c5227108ec0b92b0b52a0992b41fa6c784de3ee5eae85152a5649a5 | Shell | 614 | 16 | #!/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/tumorsyn_xai/log/tumorsyn/gethm_fold_7/0531_tumorsyn_%A.out
#SBATCH --job-name 0531_xai_svs
#SBATCH --partit... |
dc1dfb68cb4b31b47dfb4f7eb407ac35e8a892b29719b5539e2773d2fef97e20 | Shell | 616 | 13 | # Adapted from https://stackoverflow.com/questions/59111396/loop-through-the-directories-to-get-the-image-files
# Usage
# chmod 755 compress_images.bash
# bash compress_images.sh ./_static/images
find "$1" \( -iname \*.png \) -print0 | while read -r -d $'\0' file; do
# base="${file##*/}" $base is the file name wit... |
2f5cf149775a97ba3068e3f4d8ba70109b3a530771249bac53b04ac9bc76b4dc | Shell | 619 | 28 | #!/usr/bin/env bash
# Copyright 2010-2011 Microsoft Corporation
if [ -f ./path.sh ]; then . ./path.sh; fi
if [ $# -ne 2 ]; then
echo "Usage: scripts/score_text.sh <decode-dir> <data-dir>"
exit 1;
fi
dir=$1
data=$2
if [ ! -f $data/text ]; then
echo Could not find transcriptions in $data/text
exit 1
fi
ca... |
bcc19b9d4ada2ffd36927d188268c7283a1fcfa2dafc666846ca427aafcacbd2 | Shell | 620 | 22 | #!/bin/bash
#SBATCH --gres=gpu:2
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=3-07:00:00
#SBATCH --account=rrg-PIID
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=../out/0421_%A_BRATS_HGG_fold1.out
#SBATCH --job-name 0421_BRATS_HGG_cc
module load python/3.7
module load ope... |
0a62414e97040ec4ae0078be199522490dea5edf74d44cfcc6edf2103a70ac02 | Shell | 624 | 30 | #!/bin/bash
#
# Runs the configure script if the bin directory does not exist.
# Runs make in the bin directory.
#
set -o errexit
if [[ -z "$1" ]]; then
BIN_DIR="bin"
else
BIN_DIR=$1
fi
# Build ITK JP2 library
ITK_JP2_SRC=../../lib/ITKJP2Lib
ITK_JP2_BIN=${ITK_JP2_SRC}/bin
bash build/build_itkjp2.sh ${ITK_JP2_SRC} ... |
6d190696d4eb8d36f78eb0af3ea0595ad56cfc775e85b2eae871d97def6ff139 | Shell | 624 | 15 | # For the first of the two proteins, write a list of the residues that are to be blocked: those that are not in the target site. The target
# site, which would be the 'center of the interface' is the patch with the highest shape complementarity to the target.
# utils/compute_blocked_res_list.py
# Now run ZDock's c... |
cd20b5a5c5b0e07274aeb57932e6ae192b7d540215414389841937199f450fad | Shell | 628 | 15 | #!/bin/bash
if [ $# -lt 3 ]
then
echo "Error: not enough arguments given."
echo "Required arguments:"
echo "--------------------"
echo "Argument 1: name of the conda environment to use, e.g. \`blptl\`"
echo "Argument 2: path to the directory that contains the images to segment, e.g. \`./data/images\`"
echo ... |
074b98ec0562eade2c1946dc7004776136955cec71e1b01fc24bd9b44de54119 | Shell | 629 | 22 | #!/bin/bash
# first check that the venv is active
if [ -z $VIRTUAL_ENV ]; then
echo "Virtual environment is not active, you might want to run:"
echo "source external/deface/bin/activate"
return
fi
currenv=$(echo $VIRTUAL_ENV|awk -F "/" '{print $NF}');
if [ $currenv != "deface" ]; then
echo "Your act... |
02ffeca8dd0e9aed0672266f8bda86f1b95dec03e196530ca578ead1ce8e7c4a | Shell | 630 | 9 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
$DIR/../main-spots-intensities.nf \
-with-tower "http://nextflow.int.janelia.org/api" \
--runtime_opts "-B /nrs/scicompsoft/goinac/multifish" \
--labels "/nrs/scicompsoft/goinac/multifish/ex1/LHA3_R3_subset/segmentation/LHA3_R3_subset-c2.tif" \
--warped_imag... |
6d5c5a95b97602616fdfc42b050ba82ecd3005de87f8bcdb1d8999d9cd9041d3 | Shell | 631 | 21 | 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 $outdir
# Copy evaluation script
cp eval_zd... |
396b8148b2669aae871bf735f7d58f6f7359e6191466af1a264e0d154f3e5cb6 | Shell | 633 | 17 | #!/bin/bash
set -e
# Run all jupyter notebooks in the tutorial directory
# Download data/models
rm -rf data
drugex download
# Run each notebook (order matters so let's do it manually)
jupyter nbconvert --to notebook --execute Sequence-RNN.ipynb
jupyter nbconvert --to notebook --execute Graph-Transformer.ipynb
jupyt... |
9033b6af0a7ab78cbca3284a4b51b13c3d2075181f72aad473ce8f271567c78e | Shell | 633 | 8 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source/
masif_matlab=$masif_root/source/matlab_libs/
masif_data=$masif_root/data/
source /home/gainza/lpdi_fs/masif/tensorflow-1.12_on_cpu/bin/activate
export PYTHONPATH=$PYTHONPATH:$masif_source:$masif_data/masif_ppi_search/:$masif_data/masif_ppi_sea... |
04650e0d2c86716a448c1ffc3dcebc036ae732a9b7fc40184780a706ce413419 | Shell | 636 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/mi_log/s7_%A.out
#SBATCH --job-name s7_mi
#SBATCH --partition=long
module load LANG/PYTHO... |
2dc75a4e52b7d2ab7c4fd56236eb35d3e01b477ed645d015ddd4c8f3f2c2ca45 | Shell | 636 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/mi_log/s6_%A.out
#SBATCH --job-name s6_mi
#SBATCH --partition=long
module load LANG/PYTHO... |
5744929569afe0299225cc7ee3a6593814e4f5f6f403fa8a169f7af2d5285863 | Shell | 636 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/mi_log/s9_%A.out
#SBATCH --job-name s9_mi
#SBATCH --partition=long
module load LANG/PYTHO... |
6a48030e434420289ce877623761ebf48c7f5fe371d30e5a442b0004f49b725f | Shell | 636 | 18 | #!/bin/bash
#SBATCH --gres=gpu:1
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=5-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/shortcut/log/MRNet/mi_log/s8_%A.out
#SBATCH --job-name s8_mi
#SBATCH --partition=long
module load LANG/PYTHO... |
9c9dff33a784cbd0e6796b5e0f96cd46dd1b618ecb2b1cc4aac18df29ec4efdb | Shell | 638 | 19 | #!/usr/bin/env bash
BASEDIR=$(dirname "$0")
(python $BASEDIR/plot_clustered_adjacency/plot_clustered_adjacency.py) && \
(python $BASEDIR/plot_bar_dendrogram/plot_bar_dendrogram.py) && \
(python $BASEDIR/plot_blockmodel/plot_blockmodel.py) && \
(python $BASEDIR/flow_row/flow_row.py)
# adjacency matrix (2D)
# ffwd/feed... |
c7cdc281d0bf1673920970a22f47e42f6c5062d2a996743b70510fc9839df8b0 | Shell | 638 | 19 | #!/usr/bin/env sh
# export directory where cromwell and wdltool locate to JARS
set -e
WDL=workflows/fungal_variant_calling_gatk3.wdl
printf "##########\nBegin test\n##########\n"
java -jar ${JARS}/wdltool-0.14.jar validate $WDL
printf "##########\nSyntax test done. \n##########\n"
java -jar ${JARS}/cromwell-30.1.j... |
2b23a11eded801faf069b68ad69a43df18e44a446ea6439ae6e9899bedad4132 | Shell | 639 | 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/mi_log/s10_%A.out
#SBATCH --job-name s10_mi
#SBATCH --partition=long
module load LANG/PYT... |
161ce260e3db3b5148e54ae8d895c28789b4cc4fc646bdb764efb9cf1d31bfc2 | Shell | 641 | 15 | #!/bin/bash
if [ $# -lt 3 ]
then
echo "Error: not enough arguments given."
echo "Required arguments:"
echo "--------------------"
echo "Argument 1: name of the conda environment to use, e.g. \`blptl\`"
echo "Argument 2: path to the directory that contains the images to segment, e.g. \`./data/images\`"
echo ... |
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