sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2948f79a8ea5bc838a110bed5501085a22fdde6d47c805f25bea5855067f4fe4 | Shell | 403 | 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/
python $masif... |
34ce2dc6e39a6e5667935878cf196225c9d4822c8e4e326e6a4b2d630609b2b4 | Shell | 406 | 10 | for perc in 5
do
infile=/data/interesting_side_projects/SSAML/github_fork/test_outlier/datasets/simulated_dataset_classfication_outlier_perc$perc.csv
outfolder=/data/interesting_side_projects/SSAML/github_fork/test_outlier/result_outlier_perc$perc
# run mode 1 and mode 2 with datatype=0 (custom)
./runn... |
b5aed1563697a64b1f80d03bd7aa3c6be3e1a7809d698fe2aa74acb26a58b8d5 | Shell | 406 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Sus_scrofa.%J.err
#SBATCH --output=Sus_scrofa.%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 Sus_scrofa /data/share/ngs/genomes/UCSC/Sus_scrofa susScr3.fa /... |
83cc7b997ce3e088148152531d4b16bc1add40ffdb3c7cf5e52edf4b67594a6c | Shell | 407 | 14 | #!/bin/bash
# validatePositiveInteger: chek if the argument i and positive Integer
echo "validatePositiveInteger: The arguments passed in are : $@"
if [ "$1" -eq "$1" 2> /dev/null ]; then
if [ ! "$1" -gt 0 ]; then
echo 'validatePositiveInteger: You should enter a positive Integer! '
exit 2
fi
else... |
f5b14b76da88ac228bebcd1f93192614f734dafe9a51720772de35a8ae55f38c | Shell | 408 | 13 | #!/bin/bash
set -e
BASEDIR=$(cd "$(dirname "$0")"; pwd)
NEXTFLOW_SPARK_GITURL=https://github.com/JaneliaSciComp/nextflow-spark
NEXTFLOW_SPARK_VERSION=1.4.0
# Download Nextflow Spark module
mkdir -p ${BASEDIR}/external-modules/spark
curl -skL ${NEXTFLOW_SPARK_GITURL}/archive/${NEXTFLOW_SPARK_VERSION}.tar.gz \
| t... |
30c51dc5cb57fd47577d1c087222e99dfd58002f88889f72ffc0438ba705bef1 | Shell | 409 | 9 | #!/bin/bash
DOCUMENT_ID="1mzNxCyrUTBF7-lQGPLYT0HuUODvVvtsb"
FINAL_DOWNLOADED_FILENAME="val.zip"
curl -c /tmp/cookies "https://drive.google.com/uc?export=download&id=$DOCUMENT_ID" > /tmp/intermezzo.html
curl -L -b /tmp/cookies "https://drive.google.com$(cat /tmp/intermezzo.html | grep -Po 'uc-download-link" [^>]* href=... |
5b23d6c028121ca90e79701300795aedaf78d95622cbfef8df7bea568fa64315 | Shell | 411 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Mus_musculus.%J.err
#SBATCH --output=Mus_musculus.%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 Mus_musculus /data/share/ngs/genomes/UCSC/Mus_musculus mm10... |
ce4fd1f5005569c6c0f5afa2ec79473de02193684ab4f6b20b59d04e53a2f985 | Shell | 413 | 13 | #keyword search default
glmFile=conf/glm
duptime=0.5
case_insensitive=false
# 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
[ -f ./path.sh ] && . ... |
18dd2a0ce79c333748f1afd71729c8ffa5511e8bd41ec145c2c0caea1509df47 | Shell | 414 | 15 | #!/bin/bash
aws configure set aws_access_key_id $nsp_aws_access_key_id
aws configure set aws_secret_access_key $nsp_aws_secret_access_key
aws configure set region $nsp_region
if [ -n "$1" ]; then
aws configure set aws_access_key_id $1
aws configure set aws_secret_access_key $2
aws configure set... |
691841586d20988ed066d2ecf35185a2993a9bb686d04de67770a18752b10cbc | Shell | 414 | 18 | #!/bin/bash
GenotypeHarmonizerDir=`dirname $0`
cd ${GenotypeHarmonizerDir}
sh GenotypeHarmonizer.sh \
--inputType PLINK_BED \
--input ./exampleData/hapmap3CeuChr20B37Mb6RandomStrand \
--update-id \
--outputType PLINK_BED \
--output ./exampleOutput/binaryPlinkExampleOut \
--refType VCF \
--ref ./exampleData/10... |
011ecf8d5f8199a1ae46d12430891055a7f592afd28d5051a386551858f631db | Shell | 420 | 18 | #!/bin/bash
data=$1
output=$2
nfolds=$3
start=$4
end=$5
gpu=$6
if [[ -n "$data" ]] && [[ -n "$start" ]] && [[ -n "$end" ]] && [[ -n "$gpu" ]]; then
for i in $(eval echo {$start..$end})
do
CUDA_VISIBLE_DEVICES=$gpu python train.py --data_dir=$data --output_dir=$output --n_folds=$nfolds --pretrain_epochs... |
f4da2484a480543831f23185b1fcf1f1288fd5509dc99b28a6932b9cd1468d31 | Shell | 420 | 15 | #!/bin/csh
#$ -M vmannam@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N gans_config9433 # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_THR... |
2e573bed017cbb40b3415297d8023c9af6254783a65f94f56271ccbd02a11b03 | Shell | 422 | 23 | mkdir vcf
mv vcf
# Generate vcf_ftp_list.txt
python download_vcf.sh
while IFS='' read -r LINE || [ -n "${LINE}" ]; do
filename="ftp://ftp.sra.ebi.ac.uk/${LINE}"
echo $filename
wget -r $filename
done < vcf_ftp_list.txt
while IFS='' read -r LINE || [ -n "${LINE}" ]; do
filename="ftp.sra.ebi.ac.uk/${LINE}"
c... |
beaa1ee547842a5924bb636703cb28686dba003cf5cf4ab345e03f6633b06f90 | Shell | 422 | 15 | #!/bin/bash
#usage: sh get_dependency.sh
#generate this once; write a rule to copy the output file
#output=dependencies_<DATE>; run this from crg2 repo path
d=`date +%m-%d-%Y`;
if [ -z $2 ]; then
out="programs.${d}.txt";
else
out=$2;
fi;
for i in `find $1 -name "environment.yaml"`; do grep "==" $i | awk '{ split(... |
dc2e332110ddcbceb41befb734c95d0f48d34b2aa079beb137e26d53a671315b | Shell | 423 | 16 | #!/usr/bin/env python
import sys
text = sys.argv[1]
output = sys.argv[2]
with open(text, 'r') as text:
with open(output, 'w') as output:
for line in text.readlines():
sentence = list()
line_list = line.split()
line_list.reverse()
for word in line_list:
... |
6d5e67d266a5233cdb7e6617fbfd47c0aa51218780b5432bbf7bfb73f4a4a9d1 | Shell | 426 | 19 | #!/bin/bash
GenotypeHarmonizerDir=`dirname $0`
cd ${GenotypeHarmonizerDir}
sh GenotypeHarmonizer.sh \
--inputType SHAPEIT2 \
--input ./exampleData/hapmap3CeuChr20B37Mb6RandomStrand \
--update-id \
--outputType SHAPEIT2 \
--output ./exampleOutput/shapeit2ExampleOut \
--refType VCF \
--ref ./exampleData/1000gCe... |
905f8f058d30d7f72e8a32f77ba9eaa4307e5185b1b4f648a3d8c6f52444b2e6 | Shell | 426 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Papio_hamadryas.%J.err
#SBATCH --output=Papio_hamadryas.%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 Papio_hamadryas /data/share/ngs/genomes/UCSC/Papio_ha... |
788c402e3246a8175ccaf1296b04c9c4da802f08c3e72880983f748bfa963aca | Shell | 429 | 7 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/irstlm/bin/:$PWD:$PATH
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/config/common_path.sh is not pre... |
f84d2182c092fe901c81fa047a9711fd400aa8595d6b1e6e8bc20bcc5d6786c5 | Shell | 429 | 9 | export KALDI_ROOT=`pwd`/../../..
export PATH=$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
. $KALDI_ROOT/tools/config/common_path.sh
export LC_ALL=C
export PY... |
0fc4a4402e081f32b5780bc1f0bc6b4453b2fe62be8718c4324ec7a0f513603e | Shell | 430 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Rattus_norvegicus.%J.err
#SBATCH --output=Rattus_norvegicus.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Rattus_norvegicus /data/share/ngs/genomes/UCSC/Ra... |
c49fdbfbe5849ae9af16b8486ef17f2a18c1fd2377fc6c706a39c4cd0eb4a4c8 | Shell | 430 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Macaca_mulatta.%J.err
#SBATCH --output=Macaca_mulatta.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Macaca_mulatta /data/share/ngs/genomes/UCSC/Macaca_mula... |
fbdc7d40c3787a083bf6238a859b318ae127ad9bfccc120f5973488b5fc8ca04 | Shell | 430 | 17 | #!/bin/bash
BASE_DIR=$(realpath `dirname "$BASH_SOURCE"`)
export DENO_DIR=$BASE_DIR/.deno
export DENO_PATH=$DENO_DIR/deno
export PATH=$DENO_DIR:$PATH
if ! [ -e $DENO_PATH ];
then
echo "Downloading deno..."
wget https://github.com/denoland/deno/releases/download/v1.30.0/deno-x86_64-unknown-linux-gnu.zip -O... |
a485901f92170b328e64dcb1d5ae4ff45ed9b0da7e1ac747ac68a8ccd750f7fa | Shell | 431 | 20 | #!/bin/bash
infile=$1
infolder=$(dirname $1)
filename=$(basename $1)
# create output folder
outfolder=$infolder"/fsl_deface"
echo ">> mkdir -p $outfolder"
mkdir -p $outfolder
# run fsl deface
outmask=$outfolder"/mask"
outfile=$outfolder"/defaced_"$filename
if [ -f $outmask".nii.gz" ]; then
echo $outmask exists... |
22666f3091625d821cf7dac0eaa0d64f79157293bfba0c27fba353840122321d | Shell | 432 | 20 | python run_summarization.py \
--mode=train \
--data_path=./data/small.bin \
--vocab_path=./data/vocab \
--log_root=logroot \
--exp_name=test-experiment \
--max_dec_steps=210 \
--max_enc_steps=2500 \
--num_sections=5 \
--max_section_len=500 \
--batch_size=4 \
--vocab_size=50000 \
--use_do=True \
--optimizer=adagrad \
--... |
88ceef1bdb8b921cb1f4b029bb2f924c16b0e85251cc02f84fce279f4d12562f | Shell | 434 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Procavia_capensis.%J.err
#SBATCH --output=Procavia_capensis.%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 Procavia_capensis /data/share/ngs/genomes/UCSC/Pr... |
2350d65225b15326a7e4073f775888eba6b2cfeead4927a554d1eac136de5f93 | Shell | 438 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Chlorocebus_sabeus.%J.err
#SBATCH --output=Chlorocebus_sabeus.%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 Chlorocebus_sabeus /data/share/ngs/genomes/UCSC... |
3a451116fb8d00f4b1881931854d4a42127c83443c212c232b227fb108459ba1 | Shell | 438 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Otolemur_garnettii.%J.err
#SBATCH --output=Otolemur_garnettii.%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 Otolemur_garnettii /data/share/ngs/genomes/UCSC... |
5bff4fb57f4d28f5e7022aafe4985b5fcf8e2a454c45c75d22b81dfc46e5985a | Shell | 446 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Microcebus_murinus.%J.err
#SBATCH --output=Microcebus_murinus.%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 Microcebus_murinus /data/share/ngs/genomes/UCSC... |
a57efb736920541b450b0137ff95cd2fdf9fd1163db41a735213c0ffe92c1abb | Shell | 446 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Dasypus_novemcinctus.%J.err
#SBATCH --output=Dasypus_novemcinctus.%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 Dasypus_novemcinctus /data/share/ngs/genome... |
4b8e0e51c61ec7fa9873a6a1a9728be8a09045f80281adb167d8e1d0e8700677 | Shell | 447 | 13 | #!/bin/bash
# script that execute simulations symulations from the file simulationsToRun.txt
# script generate history of executed simulations
# input:
writeOutput.sh "Running NSP simulation manager."
writeOutput.sh "Load simulations into remote queue, or locally using a new PowerShell session."
while [ 1 -gt ... |
543edd49b1e2652719f9174e2fff64ddcffb5003af3ac0bfff8d476c8e3d5ffc | Shell | 448 | 15 | #!/bin/csh
#$ -M vmannam@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N vm711_lr1 # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_THREADS 4 ... |
797cabfba16b8e8b4593aa719fde5d5b0162002e624dbd13497f71f5b6f163e1 | Shell | 449 | 11 | mkdir data
wget http://msvocds.blob.core.windows.net/annotations-1-0-3/captions_train-val2014.zip -P ./data/
wget http://images.cocodataset.org/zips/train2014.zip -P ./data/
wget http://images.cocodataset.org/zips/val2014.zip -P ./data/
unzip ./data/captions_train-val2014.zip -d ./data/
rm ./data/captions_train-val201... |
2d51ec569fdaa36200b3f2ec6725983bdc7fd3169fd7633722fd6b188652a78a | Shell | 450 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Heterocephalus_glaber.%J.err
#SBATCH --output=Heterocephalus_glaber.%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 Heterocephalus_glaber /data/share/ngs/gen... |
68ae4abac3c34917f52dc2dd05243fc79ccd6e7e7921cad17c1668597dbffe41 | Shell | 453 | 19 | # do some validation of the input folder
#create output for standard
stdfolder=$2"/std"
echo ">> mkdir -p $stdfolder"
mkdir -p $stdfolder
# run fsl reorient2std
for infile in $(find $1 -maxdepth 1 -mindepth 1 -name "*.nii*"); do
stdfile=$(basename $infile)
echo ">> fslreorient2std $infile $stdfolder/$stdfile"
if ... |
7b981bde1074de9b9d4c9133eb685c98adb5a8c02c4172099c42ffddb973e128 | Shell | 456 | 18 | #!/bin/bash
{
CUDA_VISIBLE_DEVICES=0 PYTHONPATH=.:$PYTHONPATH python train.py \
--batch 40 \
--num_workers 14 \
--seed 0 \
--dataset celebahq \
--ckpt_clip_for_train exp/ft_clip_text/ft_clip_ViT-B_32_celebahq_train/ckpt.pth \
--ckpt exp/ckpt/stylegan2_celebahq_size_256_split_train/300000.pt \
... |
2d940f570cc3a0a7c3f5db6ac23935a5adeb653386b6895e23d78f9766c2214a | Shell | 457 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=GI_1.%J.err
#SBATCH --output=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/paper_data/protein/trees/tree_TRNP1_coding_3... |
5994c5f37604b57b4f6eaf9c4e9813709f7bb4ef2db021632c28b2e7535c7260 | Shell | 457 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=GI_2.%J.err
#SBATCH --output=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/paper_data/protein/trees/tree_TRNP1_coding_3... |
837a0689cffedf5ccb9382dd33b0f03933e8c5f2df6a9867f9adf9833b1e626c | Shell | 457 | 7 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/irstlm/bin/:$KALDI_ROOT/tools/kaldi_lm/:$PWD:$PATH
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/conf... |
e914261e7d93d43ba855aa282aeb08baebce31e90c8d20afd5d830744768e16b | Shell | 457 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=GI_3.%J.err
#SBATCH --output=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/paper_data/protein/trees/tree_TRNP1_coding_3... |
8683ba31e6fbef90030cd0bc08a1afb01fab69f36a63107ba667c8f92aaae4ec | Shell | 458 | 7 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$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 $KALDI_ROOT/tools/con... |
31f0c3a5fdcbc18c4cde4d2a94df4221d9aceb2b1708e201e23a553a456d2230 | Shell | 459 | 12 | #!/bin/bash
# This script is used to initialize the environment in a Google Colab notebook and pull tutorial data automatically.
# Just run it with `!bash colab.sh` in a Colab notebook.
# Download and install dependencies
wget https://raw.githubusercontent.com/CDDLeiden/DrugEx/master/tutorial/utils.py
wget https://ra... |
7e247cec9cb78bbc51beb868e6c4923e1507a98b5b0d9fd63cf05b830dec3736 | Shell | 460 | 15 | #!/bin/csh
#$ -M vmannam@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N vm6142 # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_THREADS 4 ... |
2d1d47d1cdd1d12f8d4d9e0d39110607049bd1529a0575da64cea573e184305e | Shell | 461 | 16 | #!/bin/csh
#$ -M vmannam@nd.edu # Email address for job notification
#$ -m abe # Send mail when job begins, ends and aborts
#$ -q gpu # Specify queue
#$ -l gpu_card=1
#$ -N gans_DEd_config63 # Specify job name
#$ -pe smp 4 # Specify parallel environment and legal core size
setenv OMP_NUM_TH... |
f2ca4ba4843d33aed4ddaadb6a49131df160c842524b57c565568ccaa28fb28f | Shell | 463 | 20 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python train.py \
--batch 40 \
--num_workers 26 \
--seed 0 \
--stylegan_size 256 \
--dataset ffhq \
--truncation 0.5 \
--ckpt_clip_for_train exp/ft_clip_text/ft_clip_ViT-B_32_celebahq_train/ckpt.pth \
--ckpt exp/pretrained_stylegan2/stylegan2_ffhq... |
6389bcd2c3d2e96c2b14e1ae41e6ddde182fe14837a486ba3369f1effec9172c | Shell | 469 | 14 | #!/bin/sh
# This script builds and installs your Maven project to the given Imagej2/Fiji directory
# 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 work
#
# author: Richard Domander (Ro... |
0fa6241f65f17ecdc6f33d48e447d22b55032ee23cb9cb5e91bd09dc9f85c63a | Shell | 470 | 14 | # "queue.pl" uses qsub. The options to it are
# options to qsub. If you have GridEngine installed,
# change this to a queue you have access to.
# Otherwise, use "run.pl", which will run jobs locally
# (make sure your --num-jobs options are no more than
# the number of cpus on your machine.
#a) JHU cluster options
ex... |
3afb9bb04f796c922526b0e8b6a89ef285c6145a140c7038f994ed0aff8adc8d | Shell | 475 | 8 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/extras/env.sh ] && . $KALDI_ROOT/tools/extras/env.sh
[ -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 $KAL... |
784710a17add20bb0302a497ec7e3833c5025b3dc982c82eda2835efe6864b5d | Shell | 475 | 8 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
$DIR/../main-registration.nf \
-with-tower "http://nextflow.int.janelia.org/api" \
--runtime_opts "-B /nrs/scicompsoft/goinac/multifish -B /nrs/scicompsoft/rokicki" \
--fixed "/nrs/scicompsoft/goinac/multifish/ex1/LHA3_R3_subset/stitching/export.n5" \
--movi... |
6ecb27f79625e29198766397a9d0d9ac0d8b6905569e825339020e46b711caa7 | Shell | 476 | 15 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUBJ=(${@:2:1})
echo ${SUBJ}
#DATA_DIR=${HOME}/scratch/ET_fmriprep_anat_20.2.0/freesurfer-6.0.1/
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.6
freeview -v $SUBJECTS_DIR/sub-$SUBJ/mri/T1.mgz -v $SUBJECTS_DIR/sub-$SUBJ/mri/aparc.a2009s+aseg.mgz:colormap=lut:opacity=0... |
448c3828f724b0b9ea5599fa444b87cbe8468c12266deab1d667ce7478ebcb13 | Shell | 477 | 13 | #!/bin/bash
wget https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface_linux
wget https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/talairach_mixed_with_skull.gca.gz
wget https://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/face.gca.gz
gunzip talairach_mixed_with_skull.gca.gz
gunzip face.gca.gz
mkdi... |
fd3fdd8d0a9cd15ddc403136063d99202ecc395305d912684bb14751e3655e43 | Shell | 477 | 11 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source
export PYTHONPATH=$PYTHONPATH:$masif_source
export masif_seed_root
export masif_source
PDB_ID=$(echo $1| cut -d"_" -f1)
CHAIN1=$(echo $1| cut -d"_" -f2)
CHAIN2=$(echo $1| cut -d"_" -f3)
source ~/lpdi_fs/masif/tensorflow-1.12_on_cpu/bin/activate... |
9fb60cd9d691edc5817094646a10c89aff20618ab4407b8c698e138ad800bab6 | Shell | 478 | 16 | #!/bin/bash
#SBATCH --mem=128G
#SBATCH --cpus-per-task=8
#SBATCH --time=3-07:00:00
#SBATCH --mail-user=email@email.com
#SBATCH --mail-type=ALL
#SBATCH --output=/project/labname-lab/authorid/BRATS_IDH/log/0508_video_%A_BRATS_HGG_fold1.out
#SBATCH --job-name 0508_video
#SBATCH --partition=long
#SBATCH --nodelist=cs-venu... |
82acbc060b4e9182ce3ceb6a5f5769376e50eebad1fa2d36865831a15f2dbbd5 | Shell | 480 | 20 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUB_list=(${@:2:1})
#DATA_DIR=${HOME}/scratch/QC/MAGET_MNI_QC
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.5
n_sub=$(wc -l < $SUB_list)
echo $n_sub
for (( i_sub=1; i_sub<=${n_sub}; i_sub++ ))
do
echo $i_sub
SUB_STR=$(sed -n "${i_sub}p" ${SUB_list})
echo ${SUB_STR}
... |
fe9114b302e4dbc7383db82501f0f0eba20b32a449d47a604c591c92a55d6451 | Shell | 480 | 8 | export KALDI_ROOT=../../..
export PATH=$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_path.sh... |
258785c34dbb4ae93d8ac0b60b6ba032946e3608b54c2b167a0d3c84cc1f4a81 | Shell | 481 | 16 | #!/bin/bash
VERSION=latest
nvidia-smi > /dev/null 2>&1;
if [[ $? -gt 0 ]]; then
docker run --rm -it -v $(pwd):/share ucsdtnel/autolfads:${VERSION} \
--data /share/data \
--checkpoint /share/container_output \
--config-file /share/data/config.yaml
else
docker run --rm --runtime=nvidia --gpus='"device=0"' -it... |
b5ea121ec142a3e51a73ebf8768b2eeab92a91de1eed2e4e5f25f9ea16774f3f | Shell | 481 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Mus_caroli.%J.err
#SBATCH --output=Mus_caroli.%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 Mus_caroli /data/share/htp/TRNP1/TRNP1_exon_promoter_resequenci... |
ec79ea953bcafc676e6949da8111a952b0a3476e5c6e09cca3d1ec02113f20a2 | Shell | 481 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Mus_pahari.%J.err
#SBATCH --output=Mus_pahari.%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 Mus_pahari /data/share/htp/TRNP1/TRNP1_exon_promoter_resequenci... |
f315dfe4d99bf05da5ef55be6199d7e8993f20950f3580476bf4dcf531d72319 | Shell | 481 | 11 | masif_root=$(git rev-parse --show-toplevel)
masif_source=$masif_root/source
export PYTHONPATH=$PYTHONPATH:$masif_source
export masif_seed_root
export masif_source
PDB_ID=$(echo $1| cut -d"_" -f1)
CHAIN1=$(echo $1| cut -d"_" -f2)
CHAIN2=$(echo $1| cut -d"_" -f3)
source ~/lpdi_fs/masif/tensorflow-1.12_on_cpu/bin/activate... |
63329524e0057d14fded3d2d79a57d8e35a4aaf544451d56d6df45612c09668a | Shell | 483 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Orcinus_orca.%J.err
#SBATCH --output=Orcinus_orca.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Orcinus_orca /data/share/htp/TRNP1/TRNP1_exon_promoter_rese... |
fab62546efe1271621d5569d1111c097f62eaad07fec0c409a476293e967f613 | Shell | 483 | 19 | #!/bin/bash
set -e -x
# Install a system package required by our library
yum install -y atlas-devel
yum install -y zlib-devel
yum install -y bzip2-devel
yum install -y xz-devel
# Compile wheels
for PYBIN in /opt/python/cp3[567]*/bin; do
"${PYBIN}/pip" install -r /io/dev-requirements.txt
"${PYBIN}/pip" wheel /... |
fccbd1ad20b6ed76fc71e04cd283913d8f68a9567c16bd8687ebc7b566b09ee5 | Shell | 483 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Mus_spretus.%J.err
#SBATCH --output=Mus_spretus.%J.out
#SBATCH --nodelist=gorilla1
#SBATCH -p high
Rscript /data/share/htp/TRNP1/paper_data/protein/scripts/collect_coding_seqs2_extended/collect_coding_seqs2_function.R Mus_spretus /data/share/htp/TRNP1/TRNP1_exon_promoter_reseque... |
73a742f0836e34cd256e9f5291d6316c3552981391d67ec6b40d63da0a1e718c | Shell | 484 | 21 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python train.py \
--iter 80001 \
--batch 40 \
--num_workers 26 \
--stylegan_size 256 \
--dataset cub \
--truncation 0.5 \
--ckpt_clip_for_train exp/ft_clip_text/ft_clip_ViT-B_32_cub_train/ckpt.pth \
--ckpt exp/ckpt/stylegan2_cub_size_256_split_tra... |
8d043be541251653a30d31befcd2a7003776fd6ca11080f3d52c55fad14c467c | Shell | 484 | 21 | #!/bin/bash
{
PYTHONPATH=.:$PYTHONPATH python train.py \
--iter 80001 \
--batch 40 \
--num_workers 26 \
--stylegan_size 256 \
--dataset nabirds \
--truncation 0.5 \
--ckpt_clip_for_train exp/ft_clip_text/ft_clip_ViT-B_32_cub_train/ckpt.pth \
--ckpt exp/pretrained_stylegan2/stylegan2_na... |
04cd3d47f375f0f12e19d60a67b8d2c2f75bc77ed588b18710e52e787d240dae | Shell | 485 | 18 | #!bin/bash
for K in $(seq 2 1 8)
do
for p in $(seq 0.01 0.01 0.1)
do
for alpha in $(seq 0.1 0.1 0.9)
do
cd src
/path/to/Rscript spaCI_preprocess.R "../dataset/example_data/st_expression.csv" "../dataset/example_data/st_meta.csv" ${K} ${p} 'spaCI_database.RDS' '../datase... |
072a797b2afd216d5283f4f1c996364f6d4de916535fc29737fff810e9f7992e | Shell | 485 | 25 | #!/bin/sh
RAXMLBINARY=raxmlHPC-SSE3
INPUTALIGN=$1
OUTPUTFILE=$2
RANDOMSEED=$3
EXECNAME=mtTemp
OUTRAXML=RAxML_bestTree.${EXECNAME}
if [ -z "${RANDOMSEED}" ]; then
RANDOMSEED=12345
fi
rm RAxML*.${EXECNAME} 2> /dev/null
${RAXMLBINARY} -s ${INPUTALIGN} -p $RANDOMSEED -m GTRGAMMA -n ${EXECNAME} 2>&1 > /dev/null
if [ ... |
16d1f7ef5040ce7a7fbd6be0d0679159546f3636481a903308214082333b132e | Shell | 485 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_2.%J.err
#SBATCH --output=body_mass_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/paper_data/protein/trees/tree_... |
976b2335adbc88c5c9c294dbcbf056b74e8e2a5a6d59d78b7559cf1abcee0e3b | Shell | 485 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_1.%J.err
#SBATCH --output=body_mass_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/paper_data/protein/trees/tree_... |
dcd4166e87fb3658920187477c9936a9f1b1c050dcd2c52af88db66d792a070e | Shell | 485 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=body_mass_3.%J.err
#SBATCH --output=body_mass_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/paper_data/protein/trees/tree_... |
06b16c6e7ae34da45720f8fc91540aea3af3772ff27145cd2ae72076cb1e39fb | Shell | 486 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Felis_catus.%J.err
#SBATCH --output=Felis_catus.%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 Felis_catus /data/share/htp/TRNP1/TRNP1_exon_promoter_reseque... |
b32f87267b003d7fa3dd886f86f65f265001667f9803ae4361c08c04535c877d | Shell | 486 | 20 | set -e
# Ensure www-data (apache user) has access to website files
chown -R www-data:www-data /var/www/
# Start fuseki in background,
# Data is stored in /OntologyData,
# "/NeuroMLOntology" is the name of the fuseki database
# Starts on port 3030
echo 'Starting fuseki server...'
/fuseki/fuseki start
curl http://local... |
ed1c576d1746d6c95175580be350e9f32c8f6987c0f5ff49a3bf8ccd39a2d830 | Shell | 486 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Pongo_abelii.%J.err
#SBATCH --output=Pongo_abelii.%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 Pongo_abelii /data/share/htp/TRNP1/TRNP1_exon_promoter_rese... |
49be9f7fd842cfd01ed37081168adbb272258de0a77c2eb5a176b54f00539bb4 | Shell | 488 | 20 | #!/bin/bash
DATA_DIR=(${@:1:1})
SUB_list=(${@:2:1})
#DATA_DIR=${HOME}/scratch/QC/MAGET_MNI_QC
OLD_SUBJECTS_DIR=$SUBJECTS_DIR;
SUBJECTS_DIR=$DATA_DIR
OPACITY=0.5
n_sub=$(wc -l < $SUB_list)
echo $n_sub
for (( i_sub=1; i_sub<=${n_sub}; i_sub++ ))
do
echo $i_sub
SUB_STR=$(sed -n "${i_sub}p" ${SUB_list})
echo ${SUB_STR}
... |
520af2386f33b0e280fee6fd4661ad5ef1ac2fb2847921e3977393271ff5b441 | Shell | 488 | 17 | #!/bin/bash
ENVNAME=lab
pythonversion=3.8
nglviewversion=2.7.7
labversion=2.1.5
ipywidgetsversion=7.5.1
conda create -n $ENVNAME python=$pythonversion -y
source activate $ENVNAME
conda install ipywidgets==$ipywidgetsversion -c conda-forge -y
conda install nglview==$nglviewversion -c conda-forge -y
conda install jup... |
461bb7b86261c7e7356dbf65964757827a41edde66a304ebe62a5d9eca3b29f9 | Shell | 489 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=brain_mass_1.%J.err
#SBATCH --output=brain_mass_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/paper_data/protein/trees/tre... |
4d4deb999ce5fc8efabbc08a6498b11e499127355cd25461002c4f385ed1630e | Shell | 489 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=brain_mass_3.%J.err
#SBATCH --output=brain_mass_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/paper_data/protein/trees/tre... |
d5cfcfb344755adf6da44ef5936f8f60a49c5fe290797eedd7095ce1d36ef42a | Shell | 489 | 6 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=brain_mass_2.%J.err
#SBATCH --output=brain_mass_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/paper_data/protein/trees/tre... |
c219726831b9476f2aa40228d208186e12f9c0f00e12f4c59100f0dc2f48ee1a | Shell | 490 | 23 | #!/usr/bin/env bash
set -e
COMMIT_ID=`git log -1 --pretty=short --abbrev-commit`
MSG="Adding docs to gh-pages for $COMMIT_ID"
BASE_DIR="`pwd`"
HTML_DIR="$BASE_DIR/_build/html/"
TMPREPO=/tmp/docs/$USER/DrugEx/
rm -rf $TMPREPO
mkdir -p -m 0755 $TMPREPO
git clone --single-branch --branch gh-pages `git config --get rem... |
0e05b2f02aa5dab224c0a35ebc9a06fcfaef641bf3df8fb77b79badb1e16aa60 | Shell | 491 | 9 | #! /usr/bin/env bash
input=$1
output=$2
cat $input |
awk -F'\t' '{ if ( $4 == "-" ) {$2=$2-1;$3=$3-1;print $0} else {print $0} }'| #correct for the bedtools/bamfile mismatch on negative strands end location
tr ' ' '\t' |
grep -v "_" | sed -e 's/chrX/chr23/g' | sed -e 's/chrY/chr24/g' | awk '{if($4=="+"){... |
fc5af1ba688a6598977fc6e59c88792722fdd3f574d84ee516d79b5f13298e1d | Shell | 492 | 25 | #!/bin/sh
RAXMLBINARY=raxmlHPC-SSE3
INPUTALIGN=$1
OUTPUTFILE=$2
RANDOMSEED=$3
EXECNAME=mtTemp
OUTRAXML=RAxML_bestTree.${EXECNAME}
if [ -z "${RANDOMSEED}" ]; then
RANDOMSEED=12345
fi
rm RAxML*.${EXECNAME} 2> /dev/null
${RAXMLBINARY} -s ${INPUTALIGN} -p $RANDOMSEED -m GTRGAMMA --JC69 -n ${EXECNAME} 2>&1 > /dev/null... |
169630f4a615ccfe95632f781a75c6b475601a3fb6b157f9660bb3427dbaadbd | Shell | 493 | 25 | #!/bin/sh
RAXMLBINARY=raxmlHPC-SSE3
INPUTALIGN=$1
OUTPUTFILE=$2
RANDOMSEED=$3
EXECNAME=mtTemp
OUTRAXML=RAxML_parsimonyTree.${EXECNAME}
if [ -z "${RANDOMSEED}" ]; then
RANDOMSEED=12345
fi
rm RAxML*.${EXECNAME} 2> /dev/null
${RAXMLBINARY} -s ${INPUTALIGN} -y -p $RANDOMSEED -m GTRGAMMA -n ${EXECNAME} 2>&1 > /dev/nul... |
fd06d2f38adee196b68f15beebec6f945dc94f97147fc5d4f9011b5127079836 | Shell | 493 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Gorilla_gorilla.%J.err
#SBATCH --output=Gorilla_gorilla.%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 Gorilla_gorilla /data/share/htp/TRNP1/TRNP1_exon_prom... |
1c9c3de96f885f0bdb4abad7fcf6645c7ab6eec0a1bc5a38d4bd449aebb23ba5 | Shell | 494 | 15 | #! /bin/sh
PROCPATH=../../data/processed
MODPATH=../../data/models
for celltype in 5HT mPFC GABA; do
python ./run_benchmarks.py \
$PROCPATH/${celltype}_fastnoise/${celltype}_goodcells.ldat \
$MODPATH/${celltype}/${celltype}_GIFs.lmod \
$MODPATH/${celltype}/${celltype}_AugmentedGIFs.lmod \
... |
acea3c715d1b1cc23edea759643dac1aa2e76ae782a4c6218084765b3c28cf94 | Shell | 495 | 8 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
$DIR/../main-assign-spots.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_spots "/n... |
d1e5f7eef0a80037e2f7adecbd5941226287bd2e4ab03050dc478311c4f70430 | Shell | 496 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Phoca_vitulina.%J.err
#SBATCH --output=Phoca_vitulina.%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 Phoca_vitulina /data/share/htp/TRNP1/TRNP1_exon_promote... |
e2cd4e8676f2b9da1ddff71c121bc3f68c16f2871eca5bfc324b548417052382 | Shell | 497 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Tursiops_truncatus.%J.err
#SBATCH --output=Tursiops_truncatus.%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 Tursiops_truncatus /data/share/htp/TRNP1/TRNP1_... |
a815af62f0cb3dc17085ae4fa790c5e22f87cdb2b0beb88bfb75ee3215c4bb25 | Shell | 498 | 20 | #!/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... |
ea0fc0477b5367747ce66108cd01feaced5f999fda9e628e8be67c3b342a6678 | Shell | 498 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Pan_troglodytes.%J.err
#SBATCH --output=Pan_troglodytes.%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 Pan_troglodytes /data/share/htp/TRNP1/TRNP1_exon_prom... |
02aac99ef6eb2cfb4bf36480069434cb22bb691fe1a62c2e2363599596c25788 | Shell | 499 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Cercocebus_atys.%J.err
#SBATCH --output=Cercocebus_atys.%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 Cercocebus_atys /data/share/htp/TRNP1/TRNP1_exon_prom... |
7f9b3c92b0f39c69c664f8f3d3feff938634c7d4539f34165fda4fd6e5cbdb26 | Shell | 499 | 5 | export KALDI_ROOT=`pwd`/../../..
. /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/:$KALDI_ROOT/src/lmbin/:$KALDI_ROOT/src/sgmmbin/:$KALDI_ROOT/src/sgmm2b... |
92d548b1a4b545022832051f4913a79b48cd3ef9ef1fa71dddf5f3fdc138f17e | Shell | 499 | 18 | #!/bin/bash
#SBATCH --job-name=crg2
#SBATCH --time=100:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4G
#SBATCH --output=%x-%j.out
SF=~/crg2/Snakefile
CP="/hpf/largeprojects/ccm_dccforge/dccdipg/Common/snakemake"
SLURM=~/crg2/slurm_profile/
CONFIG=config_hpf.yaml
module purge
source /hpf/largeprojects/ccm_dccforge... |
185a3c9b46021ac5adc63350b83492726907b41b51dac9312c390fd897b9877a | Shell | 500 | 17 | #!/bin/bash
set -e
NEO4J2OWLDIR="/Users/matentzn/vfb/neo4j2owl"
PLUGIN="$NEO4J2OWLDIR/target/neo4j2owl-1.0.jar"
PLUGIN_OWL2CSV="$NEO4J2OWLDIR/target/owl2neo4jcsv.jar"
KB="/Users/matentzn/vfb/docker-neo4j-knowledgebase/neo4j2owl.jar"
PROD="/Users/matentzn/vfb/vfb-prod/neo4j2owl.jar"
DUMPS="/Users/matentzn/vfb/vfb-pipe... |
3c4dbe76ce31a450a65aeb787a3405a12e0213c1aa7e791a1caa37f28963b50f | Shell | 500 | 20 | #!/usr/bin/env bash
oracle_dir=exp/sgmm2x_6a_mmi_b0.2/decode_dev_it1/oracle
split=dev
data_dir=data/dev
lang_dir=data/lang
for i in {5..20}; do
mkdir -p $oracle_dir/score_$i
cp $oracle_dir/$split.ctm $oracle_dir/score_$i/
done
. /export/babel/data/software/env.sh
# Start scoring
/export/a11/guoguo/babel/103... |
f7d6561dcb8531c24fb82ccbf147ebbfbba1122b592a94885fc9704a8e7c5acc | Shell | 500 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Panthera_pardus.%J.err
#SBATCH --output=Panthera_pardus.%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 Panthera_pardus /data/share/htp/TRNP1/TRNP1_exon_prom... |
7e96bd5a3b2b64ed0ffce4f62696cf9a87f927a1c665eec52141a85c35f51a3b | Shell | 502 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Physeter_catodon.%J.err
#SBATCH --output=Physeter_catodon.%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 Physeter_catodon /data/share/htp/TRNP1/TRNP1_exon_p... |
16402c7363cce8aa4fafeee88c61935a81c6c6016c64835ec1290b01a65a017b | Shell | 503 | 8 | #!/bin/bash
DRUGEX_ENV=drugex
INPUT_FILE='chembl_30_100000.smi'
qsub -v BATCH_SIZE=512,MODEL=rnn,CONDA_ENV=$DRUGEX_ENV,INPUT_FILE=$INPUT_FILE,EXPERIMENT_ID=`git rev-parse --short HEAD`,WORKDIR=`pwd` qsub.sh
qsub -v BATCH_SIZE=256,MODEL=seq_trans,CONDA_ENV=$DRUGEX_ENV,INPUT_FILE=$INPUT_FILE,EXPERIMENT_ID=`git rev-pars... |
793c0aa7723aa8fbd5fc41bc5796689f681f9a68feec54580378d9b676070fdb | Shell | 503 | 10 | export KALDI_ROOT=`pwd`/../../..
[ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh
export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/sctk/bin:$PWD:$PATH
export PATH=$PWD/dscore:$PATH
export PYTHONPATH="${PYTHONPATH}:$PWD/dscore"
[ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo ... |
8eb0488596b1324f9083f470c2dedeea70e4b6f763f1383e1ea05fc25ca2a6f5 | Shell | 504 | 9 | #!/bin/bash
# Create an archive with model fitting results
# Use: make_archive fit_name
# (Make the script executable with chmod 755 and put it in the path, eg /usr/local/bin)
rm /mnt/storage_s1/Paramecium/results_selection.tar.gz
rsync -a --progress --include="*$1.yaml" --include='*/' --exclude='*' '/mnt/storage_s1/P... |
a20bf5d50c9731f2e12563c23b10166187b8a3ed024f46cccf3a2d06d18227d4 | Shell | 504 | 14 |
#!/bin/bash
read -r -a l <<< $@;
a=($(echo ${l[4]} | awk '{ split($1,x,""); print x[1],x[2],x[3],x[4];}'));
callers=();
sum=$(IFS=+; echo "$((${a[*]}))")
if [[ ${a[0]} == 1 ]]; then callers+=("gatk-haplotype"); fi;
if [[ ${a[1]} == 1 ]]; then callers+=("samtools"); fi;
if [[ ${a[2]} == 1 ]]; then callers+=("free... |
efd2fd3c6cbeae1ae8d4a6e9591eaa149490b942293af6142cfd50f81ca9cd74 | Shell | 504 | 26 | #!/bin/bash
#where my PAML outputs are located with 2 folders called NS7 and NS8
workdir=/data/share/htp/TRNP1/paper_data/protein/PAML
declare -a arr=("NS7" "NS8")
prot=TRNP1
for i in "${arr[@]}"
do
lnL=$(cat $workdir/$i/"$i"_model_output.txt | grep '^lnL')
if [ $i == "NS8" ]; then
p0=$(cat $workdir/$i/"$i"_mod... |
21010830a5cbf1d81a8f8a7cfb75668aa5bbb577b5438435cd77f6773a32fbbb | Shell | 509 | 7 | #!/bin/bash
#SBATCH -n 1
#SBATCH --error=Cebus_capucinus.%J.err
#SBATCH --output=Cebus_capucinus.%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 Cebus_capucinus /data/share/htp/TRNP1/TRNP1_exon_prom... |
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