sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0e292710070dcdc1fd5b5041c36fb0452feb126f53d40f90a43fe94f1d53a1ab | Shell | 97 | 3 | #!/bin/bash
rm -Rf test ./*~ .objects .bin .results ./*.ll ./*.bc ./*.vfcwrapper* ./*.log ./*.o
|
47f52a257d1f2e4ae3535af928af82d8075afe0771d48fc8077ce007a38bd737 | Shell | 97 | 6 | #!/bin/sh
in="$1"
out="$2"
Rscript `dirname $0`/pvalue_correction_scoreCount.r "$in" "$out" -1
|
55ef0478ed01b9d30e261284ccda0824c6cdda869b46fbd7346a9a315759ad55 | Shell | 97 | 6 | #!/bin/sh
in="$1"
out="$2"
Rscript `dirname $0`/pvalue_correction_scoreCount.r "$in" "$out" 10
|
254c372bbedcfce5e60a3e716d4b41642708d90b62b99ed3a716ffad775894e1 | Shell | 98 | 1 | python launcher_scripts/run_from_config.py configs/iceberg/msg_all/dag_train_msg_all_iceberg.yaml
|
07e5553ddeaed37fecafd0647083dd9ce6877a01ec988159c2fc492a441b02c6 | Shell | 99 | 3 | #!/bin/bash
rm -Rf *~ *.so* rr_mode_* test.log run_parallel check_status.py *.ll .vfcwrapper* *.o
|
1755a08cfc253b18e4d3ed05eaaebd4be30ebd016f928de45ed3ef4ebeeafcfb | Shell | 99 | 6 | if [ ! -e hsa ]
then
wget http://ouyanglab.jax.org/hsa/HSA.zip
unzip HSA.zip
rm HSA.zip
fi
|
26988b9e6602bbe23ee51caee545708f49c004ce2459b9cc2fa5ba4fd8809616 | Shell | 99 | 3 | #!/bin/bash
rm -Rf *~ test test.log *.o *.ll *.prof baseline.txt replay-*.txt .vfcwrapper* .test*
|
c4fc541cdfa7ab3d6b0f1249132e5b705617111c3589d5780ff3e0409e3bd3e2 | Shell | 99 | 4 | if [ ! -e Chromosome3D ]
then
git clone https://github.com/multicom-toolbox/Chromosome3D.git
fi
|
cc6b4c60214c8519c8be57da173f735e3b6dbf0155521f249d7baf1b9d929004 | Shell | 100 | 3 | #!/bin/bash
rm -Rf *~ test sizes test.log out.txt sizes-O*.txt *.o *.ll *.prof .vfcwrapper* .test*
|
020c2744bbb40e45ba1acfa5366f606f7439c09aebfe7006df304b467b8bc812 | Shell | 101 | 1 | python launcher_scripts/run_from_config.py configs/iceberg/msg_all/dag_inten_train_msg_known_ce.yaml
|
e43e9a199e77373a102722d370df2101ba1de65792d52d69285d18a31b49cfdf | Shell | 101 | 3 | #!/bin/bash
rm -Rf *~ log_run* out_run* test.log test_openmp_* test_pthread_* *.ll *.o .vfcwrapper*
|
50c08ca487874d4f2efd0e64ebd70e6d440c570aea8b217e1935ace0c1e2fc49 | Shell | 102 | 4 | f=$1
PREFIX=${f%.tsv}
cat $f | awk 'NF == 4 && $2 != "nan" {print "C\t"$2"\t"$3"\t"$4}' > $PREFIX.xyz |
ccca9330d1973d7520467aacf47dc8b09578c57f158e92766504cd76bb80477c | Shell | 102 | 6 | #!/bin/sh
in="$1"
out="$2"
Rscript `dirname $0`/bayesFactor_correction_scoreCount.r "$in" "$out" 10
|
cd9347397901d1d48df3b604a41abe165071b965bd87971dfcf643f88fdee5c7 | Shell | 102 | 6 | #!/bin/sh
in="$1"
out="$2"
Rscript `dirname $0`/bayesFactor_correction_scoreCount.r "$in" "$out" -1
|
248f48127f75dad9663f605e08084fd37800abe4929fc5621c36d75646fc5f35 | Shell | 103 | 3 | oat posifilt kalman pos flt -c test.toml posifilt-kalman &
sleep 1
time oat posigen rand2D pos -n 1000
|
4e917074b3e54281bf679d233553412838cf124a329da8e384a2b0458dd6ef64 | Shell | 104 | 1 | python launcher_scripts/run_from_config.py configs/iceberg/msg_simulation/dag_train_msg_simulation.yaml
|
eeca58801ea47f2a13b8a5ed39b58b977460ea38b803a97dd45b7301112c93a3 | Shell | 104 | 1 | wget -r -np -nH --cut-dirs=2 --reject="index.html*" http://nlp.uoregon.edu/download/okapi-eval/datasets
|
f45f3dd2184ffdf1b3ed9742b2bfc7287e98b68a6ee9fc1ca80cc2c02ee81f28 | Shell | 105 | 3 | #!/bin/bash
mamba create --force -n sra bioconda::entrez-direct bioconda::sra-tools conda-forge::csvkit
|
887e54dab913c5002b417524fa19fdea6300f696fec6877ef99bf872b90291e1 | Shell | 106 | 4 | #!/bin/bash
python -m torch.distributed.launch --nproc_per_node=2 amp_master_params.py
python compare.py
|
988552107165b840a245aa960573532068d8be8dd3963543e74863967fd93a61 | Shell | 106 | 3 | module --force purge
module load UCX-CUDA/1.14.1-GCCcore-12.3.0-CUDA-12.1.1 Python/3.11.3-GCCcore-12.3.0
|
f415581d97b7792ced0eaaa5fdc656b71892c24fee97426f016b6fafd6f49b64 | Shell | 106 | 3 | #!/bin/bash
rm -Rf *~ binary32-* binary64-* sr-binary32 sr-binary64 logs/ *.o *.ll .vfcwrapper* test.log
|
3c6ea77ac1aff89332e3003728058fd487007d76093a0b8f706a141d45547e9c | Shell | 107 | 7 | #!/bin/bash
# Starts cluster
set -eou pipefail
pushd cluster
docker compose pull
docker compose up -d
popd
|
b2eb88912e2289cfdee22a20f5ec2791b3ae29ac837d44274200ad9fc7acb536 | Shell | 108 | 3 | #!/bin/bash
rm -Rf *~ log* *.o *.ll .vfcwrapper* test_{float,double} test.log check_status.py run_parallel
|
3c199176de1171002cd07cc0869a551bd0d76a557ce9e2134ea0173c39086802 | Shell | 111 | 8 | #!/bin/bash
for i in `seq 1 100` ;
do
valgrind --tool=verrou --rounding-mode=$1 ./a.out || exit 42
done
|
86a1b08cabf5d1afd19f8c27425ab59d31ebffd71bccf4ed3a1c9b753dfa8529 | Shell | 111 | 7 | #!/bin/bash
set -e
set -o pipefail
# Generate subpopulation barplots
Rscript 01-subpopulation_distribution.R
|
0c4d6fe6fe9afaee8be3d999e4374723d9bfe7da7014e99a30f5943f46371168 | Shell | 116 | 3 | #!/bin/bash
rm -Rf *~ test.log unst_branch unst_branch.*.*.gcda unst_branch.*.*.gcno *.gcov* *.ll .vfcwrapper* *.o
|
7dc3fd4928ee2f2b0774507d24a44a6a5259d707615af2376b8be0663e6a1922 | Shell | 117 | 4 | #!/bin/bash
DIR=$1
valgrind --tool=verrou --rounding-mode=downward trace_verrou_task.py ./Muller.py > $DIR/res.dat
|
156131284bcdc106827255966c9f79923818c616d7c82adfd1a434bd33a2d4c3 | Shell | 118 | 8 | #!/bin/bash
cd $1
module load bedtools
for i in *;do
echo $i
bedtools map -a $i -b $2 -c 4 -o mean > DNase_$i
done
|
613a1f01fc8e8c51384ea006f7f44221f8bd088ca7800471cd09ef5f6cfb96a0 | Shell | 119 | 5 | #!/bin/bash
# Change X Server display resolution for CalliCog touchscreens.
xrandr --output HDMI-1 --mode "1280x720"
|
63794927cb96f7938a476a7fae159c4ac059c15fc4cb965d563aaa32e4e135bb | Shell | 119 | 3 | #!/bin/bash
rm -Rf *~ log test_{float,double} tmp.* test.log out_* run_parallel check_status.py *.ll .vfcwrapper* *.o
|
9100c3739bb772e7ba8841b2de1729dd37fcf62e5d91cffe97b7cdd26b74e13d | Shell | 119 | 3 | #!/bin/bash
CUDA_VISIBLE_DEVICES=0,1 python -m torch.distributed.launch --nproc_per_node=2 ddp_race_condition_test.py
|
ad42f829f40bab2e472f0f0939d3662a6d3870dd85042f79549ec7af9f2bb285 | Shell | 119 | 5 | #!/bin/bash
# Clean up test files
rm -f test*.c test*.cpp test*.f90 test*.o test*.so test*.a
rm -rf "path with spaces" |
b2ce973d62c924143e09b4e085c47c6ef789223f2b7e3fb4849d262ab462633f | Shell | 119 | 3 | oat framefilt mask raw flt -c test.toml framefilt-mask &
osleep 1
time oat frameserve test raw -f $1 -c test.toml test
|
7c3e11e93ae512d2e419213c3155ea0af0d13eaed2d32a87666fb79cb555ddc1 | Shell | 121 | 3 | #!/bin/bash
set -o pipefail
snakemake -s rnaseq.rules --profile .sequana/profile_local 2>&1 | tee .sequana/snakemake.log
|
d60971bfc59bd9dcdda13b38964d61b0a409df6d13357ba5893d56455fe66af3 | Shell | 121 | 6 | #!/bin/bash
conda activate idelucs
find fastas/ -name '*.fasta' | parallel --bar -j 20 -I {} python 3_make_cgr.py {}
|
d96fdfb81661b4a3e0a47426af491aec1f846649363c7a5a40558209827ba67e | Shell | 122 | 2 | . run_scripts/autoregr_baseline/01_run_autoregr_train.sh
python run_scripts/autoregr_baseline/02_sweep_autoregr_thresh.py
|
8cff5302de417744544982c451dc8e9cd204395a22b09a915da570e4632e5e13 | Shell | 123 | 5 | #!/bin/bash
OUTDIR=$1
valgrind --tool=verrou --backend=vprec --vprec-preset=fp24 \
./unitTestInteger >${OUTDIR}/res.dat
|
261ccf9746f034990461d764235235e92e577285494629bfad2b2a1117f957c0 | Shell | 126 | 3 | #!/bin/bash
rm -Rf *~ .vfcwrapper* *.o *.err test.log run_parallel test_{additive,generative}_{float,double} check_status.py
|
14a9d7f3cff5cc6dbf983302fa071bbed874b58d3bbf39c9282733535b2c2e7e | Shell | 127 | 6 | #!/bin/bash
export FLASK_APP=flask_app
export FLASK_ENV=development
export FLASK_DEBUG=1
flask run --host=0.0.0.0 --port=5000
|
20bf9ee5579f96172cf4d72f6cf37efcb677fea5d027ec61d6e3fc46acacd665 | Shell | 127 | 6 | #!/bin/sh
cat NC_009444.1.gff | sed "s/CDS/exon/" > genes.gff
echo "##FASTA" >> genes.gff
cat NC_009444.1.fna >> genes.gff
|
38a897ebd03ca03d4cb33ae44d969b5b6940aec2902e4b4190607b6f3fdbbfb2 | Shell | 127 | 6 | #!/bin/sh
cat NC_008463.1.gff | sed "s/CDS/exon/" > genes.gff
echo "##FASTA" >> genes.gff
cat NC_008463.1.fna >> genes.gff
|
3feb1c462d27d7ff2daa45f8bf30af4f2be3754a21981ef3594311464ff5d338 | Shell | 127 | 6 | #!/bin/sh
cat NC_002516.2.gff | sed "s/CDS/exon/" > genes.gff
echo "##FASTA" >> genes.gff
cat NC_002516.2.fna >> genes.gff
|
68a9a941267d5cc62e888c2a01c2fb08a01b06c901e82a0fef3631cf977a1d56 | Shell | 127 | 3 | #!/bin/bash
rm -Rf *~ config.txt output.txt test test.log test_exponent test_mantissa test_range *.o *.ll .vfcwrapper* .test*
|
8d792a962e785410399b77cb513b5066cea2ff1044d20c05f5adc577f19b585f | Shell | 127 | 6 | #!/bin/sh
cat NC_012660.1.gff | sed "s/CDS/exon/" > genes.gff
echo "##FASTA" >> genes.gff
cat NC_012660.1.fna >> genes.gff
|
243986cc6626767ed2ac14d1f014c00cfe192a9dae48971dcc60d8db76932229 | Shell | 128 | 3 | oat framefilt undistort raw flt -c test.toml framefilt-undistort &
sleep 1
time oat frameserve test raw -f $1 -c test.toml test
|
c78d010c990a9bd609967ae6e9cee4920105d3463165280190e3d42b2100451f | Shell | 132 | 5 | source ../paths.sh
GCC=${GCC_PATH}
${GCC} compute_mpfr_rounding.c -lmpfr -Wall -Wextra -o compute_mpfr_rounding -O3 -march=native
|
abb04187d2778fc86f89ffc8e1735ff5fa8b64ba0ba3d4e9e5d2bed563c2a433 | Shell | 136 | 8 | #!/bin/bash
pkexec apt remove python3-venv python3-tk
rm -r ~/IJOQ-venv
rm ~/.local/share/applications/IJOQ.desktop
echo Setup done!
|
07f0165f7f2ec4898fabb0bce4d59defe408d666af4dc5fcb7bf0856e2ec309b | Shell | 137 | 4 | mkdir third-party
git submodule add https://github.com/pybind/pybind11.git third-party/pybind11
git submodule update --init --recursive
|
f8c029892e96b1c81be7501d0db4a157e68f5d5a844dfe0cbb90530437e324aa | Shell | 137 | 9 | #!/bin/bash
set -e
set -o pipefail
# generate demo clin summary stat tables
Rscript -e "rmarkdown::render('01-demo-clin-stats.Rmd')"
|
176f4427c81e9e992a2d0909650bcac61269de98cddaeda79082c64e2652e514 | Shell | 140 | 3 | . run_scripts/ffn_model/01_run_ffn_train.sh
python run_scripts/ffn_model/02_predict_ffn.py
python run_scripts/ffn_model/03_run_retrieval.py
|
5e49fd439665258cdbcb9ad678af8762e6d1c829a40ea004f92fc02f23d187cc | Shell | 140 | 3 | . run_scripts/gnn_model/01_run_gnn_train.sh
python run_scripts/gnn_model/02_predict_gnn.py
python run_scripts/gnn_model/03_run_retrieval.py
|
7e042e03d3d506d512fde9aee72aa7fc2c3d3035501f05bf54e3e6f1c0c4c635 | Shell | 141 | 6 | #!/bin/bash
set -e
# extract x[0] samples for plotting test results
echo "X0" > x0.dat
cat output |grep e+ |cut -d' ' -f1 >> x0.dat
./plot.R
|
4a3647c7f165c51169f3bf058b884fb5e4f5f670c10c05b14c18de20f4c450dc | Shell | 144 | 5 | #!/bin/bash
EXEC_PATH=$(dirname $0)
valgrind --tool=verrou --vr-verbose=no --rounding-mode=random ${EXEC_PATH}/checkStatRounding > $1/res.out
|
b7dd0aaa7b07f6cf9e8570a620d20b09414868ed45032c652eedbb67e411191b | Shell | 144 | 13 | #!/bin/bash
echo "-O0"
gcc test.c -o test -O0
./test
echo "-O3"
gcc test.c -o test -O3
./test
echo "-Ofast"
gcc test.c -o test -Ofast
./test
|
e34683b4847a32ef53b4a2623f7dc18ebc582b05d90a2c20e2987ddc6838622b | Shell | 145 | 3 | #!/bin/sh
cd feature_decoding
python featdec_fastl2lir_train.py config/vggsound_fmriprep_rep4_500voxel_vggishish_allunits_fastl2lir_alpha100.yaml |
223d91c7841bbee0b4edc1e6c4f68af132092a5594b1be1d79b29a8d89b54bca | Shell | 146 | 8 | #!/bin/sh
cat \
| sed "s/Exon_/EXON_/g" \
| sed "s/exon_/EXON_/g" \
| sed "s/Transcript_/TRANSCRIPT_/g" \
| sed "s/mRNA/protein_coding/g" \
|
c1e701425e2fd3b9307b9285a0f4ce8ed12ac354196c7c86d453f5b8635e422f | Shell | 146 | 6 | #!/bin/sh
mkdir -p m4
for i in src/backends/interflop-backend-*; do mkdir -p $i/m4; done
autoreconf -is -I $(realpath src/interflop-stdlib/m4/)
|
71eae7cd70ef14f34257577535fea53779c06bd887e29ce6a3f535f053357b2d | Shell | 147 | 3 | . run_scripts/molnetms/01_run_molnetms_train.sh
python run_scripts/molnetms/02_predict_molnetms.py
python run_scripts/molnetms/03_run_retrieval.py
|
879cdee01117008d6c0424f5d024575f97789ae5542964258828f0713747a6b4 | Shell | 147 | 3 | . run_scripts/graff_ms/01_run_graff_ms_train.sh
python run_scripts/graff_ms/02_predict_graff_ms.py
python run_scripts/graff_ms/03_run_retrieval.py
|
23f8ae54e9dc2c7e5a8f434733ade31d05c61d2cf33175c462648a66310fa897 | Shell | 149 | 6 | #!/bin/bash
bumpversion $1
git push && git push --tags
TAG=$(git describe --tags)
python setup.py sdist
twine upload dist/caveclient-${TAG:1}.tar.gz
|
4b1c261a7728c9a9d7af237ff4665659b6aef7eace9eec596a3fee542c64629b | Shell | 150 | 7 | set -e
for CHROM in 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 19 20
do
echo $CHROM
python normalize.py /data/drive1/hic_data/K562 25000 $CHROM
done
|
88672484dd3c2254cfcb328b64cac05919becc9b9c882a1cb96762c8e617786c | Shell | 151 | 5 | pip install -r requirements.txt
pip install pre-commit
pre-commit install
pip install -r docs/requirements.txt
git submodule update --init --recursive
|
caf69182b9c4ab5c0a3bca13de5298df49c44c015ef19adfddb56b8968d4a1c4 | Shell | 151 | 2 | #!/bin/sh
mdbQuery "select fileName, dccAccession from hg19" | sed -e 's/^.*fileName=//' -e 's/; dccAccession=/ /' -e 's/;//' | grep '\.' | sort
|
76530ab8409deb1621e1ca99172c9acc20e96c4bd51f61e4a2bb1ce098c1940d | Shell | 152 | 4 | #!/bin/bash
awk '{print $4}' indivBetaMLparamsadulthypot_DIVALV.res | sed '/^$/d' | awk '{printf "%8.6f\n", $1}' > p
paste results p > resultsDIV_beta
|
7ba01f903c29035d04e2ac05e1ace840a29650a275ff35424d2884130aa17b7d | Shell | 152 | 5 | #!/bin/bash
# Choose one of the following PLATFORMS: linux-cuda, linux-cpu, mac
PLATFORM=mac
docker build -t ghost --build-arg="PLATFORM=${PLATFORM}" . |
9b5d6b4bf7e04ad0375afeb18aa256b14ab4adc13fe7930627fe33dce39a12cc | Shell | 152 | 4 | #!/bin/bash
OUTDIR=$1
valgrind --tool=verrou --rounding-mode=random --libm=instrumented --IOmatch-clr=matchLast.script\
./unitTest >${OUTDIR}/res.dat
|
f4412e82b397c703da1d67f088641a9460d8150979fada202172415e7ca6fee2 | Shell | 152 | 2 | source /project/ag-moonraedler/MAtienza/cellsbi/envs/sbi/bin/activate
python /project/ls-raedler/software/onedcellsim/onedcellsim/simulations/viewer.py |
daadb84bca53b23dbe497c3ee4e0e89d17d3515341883989803d6385dfe9962f | Shell | 154 | 7 | #!/bin/bash
set +e
source /home/bdemedeiros/software/miniconda3/etc/profile.d/conda.sh
conda activate varKoder
varKoder convert cgr varKodes cgrs -n 20
|
81a93f5ef4685cd62203d9584d32563175811a74dce420c90a77afd7a4089094 | Shell | 155 | 7 | #!/usr/bin/env bash
set -e
FOLDER=$1
bgdata_out=`bgdata get intogen/pon/hmf`
data_path=`echo ${bgdata_out} | awk '{print $NF}'`
cp ${data_path} ${FOLDER}/ |
b2efc22e16e89be92e0ca1050d411d3b98506c9c9de27952d647da4562af422f | Shell | 156 | 13 | #!/bin/bash
echo "-O0"
gcc test.c -o test -lm -O0
./test
echo "-O3"
gcc test.c -o test -lm -O3
./test
echo "-Ofast"
gcc test.c -o test -lm -Ofast
./test
|
b89d2a13aee2f87f8a6be474a7f4842fc1fe4c0d45cc076561d2b0fb3b399dd5 | Shell | 156 | 3 | #!/bin/bash
set -e
../autoconf/tap-driver.sh --test-name testplan.test --log-file testplan.log --trs-file testplan.trs --color-tests yes -- ./testplan.test
|
57a959a387562ed505d80b2f2cadeaa8e73585ff0aadd002d3cec0141bc7a4f6 | Shell | 159 | 3 | bash get_gm12878.sh 5000 22
python ../minimds.py hic_data/GM12878_combined_22_5kb.bed
python ../minimds.py --partitioned hic_data/GM12878_combined_22_5kb.bed
|
697c9f9c47ba93952b01842614ade11905f568b1a75327176361c844b91b5ef0 | Shell | 161 | 7 | #!/usr/bin/env bash
set -e
FOLDER=$1
bgdata_out=`bgdata get intogen/hotmaps/info`
data_path=`echo ${bgdata_out} | awk '{print $NF}'`
cp ${data_path} ${FOLDER}/
|
ef1cad838e1fb8497db8991a70f44ad5fa4c78a4ced1c42621138999e879735d | Shell | 161 | 8 | #!/usr/bin/env bash
PATH=$(getconf PATH)
export PATH=$PWD/.Python/bin:$PATH
export PYTHONPATH=$PWD/.Python/bin
pip3 install --upgrade pip
pip3 install multiqc
|
04e923430b92a0b310385061673eaed73665796b0405763901b2613ceb309aa3 | Shell | 162 | 4 | #!/bin/bash
python -m pip install "git+https://github.com/fsspec/kerchunk" --no-cache-dir
python -m pip install hdf5plugin --no-binary hdf5plugin --no-cache-dir
|
3f21b433742515c3578e39dbce24cf64b9ebba20b80f9193de133aec21983fc6 | Shell | 162 | 2 | latexdiff main-first-submission.tex main-R1.tex > EVL3-25-0079-R1-diff.tex
latexdiff EVL3-25-0079-R1-main.tex EVL3-25-0079-R2-main.tex > EVL3-25-0079-R2-diff.tex
|
b1cea24709d323aaf67a8de4c3ab3b12a6b2c60ab5edbd354f03621683e7965c | Shell | 162 | 3 | #!/bin/bash
rm -Rf ./*~ out_bitmask out_mca s_bitmask s_mca test_{float,double} test.log ./*.ll ./*.o .*.o log compute_sig* check_status.py run_parallel ./tmp.*
|
c650405a3a5b8d244b9c595b2c617d7b0516e447b8d9bef0ca973633d924e6ab | Shell | 163 | 10 | #!/usr/bin/env bash
mkdir Refs
cd Refs
curl -L -o out.zip "https://www.dropbox.com/sh/y5ly6bswf4qqrg9/AACWrqJ74AN8RRPLVD9xe38Fa?dl=1" --http1.1
unzip out.zip
|
19cdd35cff45a4d08ecf6fd3a8ac851adfb712040763de0e1f0940141ed3d7bb | Shell | 165 | 2 | python launcher_scripts/run_from_config.py configs/scarf/scarf_train_nist.yaml
python launcher_scripts/run_from_config.py configs/scarf/scarf_train_nist_ablate.yaml
|
2963862dc7facbb424bea557050f265ed90dbf8ee4ad4ee2b80016bc5e440acc | Shell | 165 | 13 | #!/bin/bash
if [ "$1" == "1" ]; then
echo "written to stdout"
fi
if [ "$2" == "1" ]; then
echo "written to stderr" 1>&2;
fi
if [ "$3" == "1" ]; then
exit 1
fi
|
4af0625c19e719b7414d389cda4c76d0a8f2eea2daf301ab10c57cb73b18184b | Shell | 165 | 4 | #!/bin/bash
awk '{print $4}' indivBetaMLparamsadulthypot_DIVALVdropout.res | sed '/^$/d' | awk '{printf "%8.6f\n", $1}' > p
paste dropoutput p > results_dropoutput
|
0870414cc822dff4ef5770fe4aa1630607b868a4a2d6e70af160cb3bc2136c30 | Shell | 166 | 10 | #!/usr/bin/env bash
pbin=""
fl=$(readlink $0)
if [[ -z "$fl" ]]; then
pbin=$(dirname $0)
else
pbin=$(dirname $fl)
fi
export PATH=$pbin:$PATH
$pbin/tophat "$@"
|
4504aef3013121a812cb4ac1dbc2250107bb5ecd20bbae8453a084d61a00e8e3 | Shell | 167 | 2 | python launcher_scripts/run_from_config.py configs/marason/marason_train_nist20.yaml
python launcher_scripts/run_from_config.py configs/marason/marason_train_msg.yaml
|
a3c1c263d7dc9cc8279a13b0915e8d9007af22e264895515607993fc688a789e | Shell | 168 | 3 | #!/bin/sh -f
cd /opt/pcstudio
/usr/local/pcstudio-venv/bin/python3 /opt/pcstudio/bin/studio.py -c /opt/pcstudio/config/PhysiCell_settings.xml --galaxy --samples --biwt
|
a7070cf491e397b4fe3dfabf356d6829c54cc4b3f94bc25ee3b93fbb6e343646 | Shell | 168 | 13 | #!/bin/bash
set -e
# Build binaries
make all
# Extract pre-generated references
make mpfr_reference
# Check vprec backend against mpfr_reference
./check.sh
exit $?
|
de26276e26deab750acf6bb291a598a5f74fde7a8230c748b82311864e91a0f9 | Shell | 168 | 7 | #!/usr/bin/env bash
set -e
FOLDER=$1
bgdata_out=`bgdata get intogen/hotmaps/coordinates`
data_path=`echo ${bgdata_out} | awk '{print $NF}'`
cp ${data_path} ${FOLDER}/
|
1dfec9648bb6650d7b47a9463139ee47a4e6e3de455d54f17d8657e9b7c1bea9 | Shell | 172 | 9 | #!/bin/sh -e
zcat ORI/c_elegans.PRJNA13758.WS241.annotations.gff3.gz \
| grep WormBase \
| sed "s/Transcript://g" \
| sed "s/Gene://g" \
> genes.gff
|
f070edd6b63aa2057fbade4d15ec0f62def1dc74c3276db6b060dc593616fd5b | Shell | 172 | 7 | #!/bin/bash
# Cleans up resources and shuts down containers, useful for local development of slurm-docker-cluster
set -eou pipefail
pushd cluster
docker compose down
popd
|
adb5e6dfc512a1aa957c4867f6542df8c70aacc6ad5312f7d596786166991b36 | Shell | 173 | 9 | #!/bin/sh -e
# run @PROG_CLASS@
JAVA_HOME="@JAVA_HOME@"
CLASSPATH="@CLASSPATH@"
export JAVA_HOME CLASSPATH
exec ${JAVA_HOME}/bin/java -Xms256m -Xmx512m @PROG_CLASS@ "$@"
|
95befe4750dd1ee61ae64d36cb150025f0a0db98ac84c492b624531bce89300c | Shell | 175 | 3 | . run_scripts/massformer_model/01_run_massformer_train.sh
python run_scripts/massformer_model/02_predict_massformer.py
python run_scripts/massformer_model/03_run_retrieval.py
|
78127ac133d211e12dbcce67dc2b61d5d3c52d3f88381be451c01eab0a60495d | Shell | 177 | 2 | python launcher_scripts/run_from_config.py configs/marason/marason_inten_train_nist.yaml
python launcher_scripts/run_from_config.py configs/marason/marason_inten_train_msg.yaml
|
c247a90725621a25bcd8def4c82abfbea34f087ed997dcf826792acbd2fe3b6c | Shell | 177 | 10 | #!/bin/sh -e
dir=$1
scripts=`dirname $0`
for pdb in `find $dir -iname "*.ent.gz"`
do
pdbId=`basename $pdb .ent.gz`
gunzip -c $pdb | $scripts/pdbCompoundLines.py $pdbId
done
|
652b73d0317ee79513fa2b4aff0b1fabb66a61b644b6623732319910c931e33f | Shell | 182 | 8 | #!/bin/bash
set -eu
pip3 install -U pandas tqdm joblib
OUTPUT_DIRPATH="images"
CSV_FILEPATH="Task2/book32-listing.csv"
python3 download_images.py ${OUTPUT_DIRPATH} ${CSV_FILEPATH}
|
589392384efab8a83633ed6a70fb7b9e6e82c6d7e57f16c230143fc8c3b53648 | Shell | 186 | 9 | #!/bin/sh
gunzip -c ORI/Sbicolor_79_cds.fa.gz \
| sed "s/^>S.*\|PACid:/>PAC:/g" \
> cds.fa
gunzip -c ORI/Sbicolor_79_protein.fa.gz \
| sed "s/^>S.*\|PACid:/>PAC:/g" \
> protein.fa
|
71765ddec6301d1e9f33b5bcdea096cd8a480d2cb0ff146ae6fc7c9df3e4058f | Shell | 187 | 8 | #!/bin/sh
snakemake --jobs 500 \
--use-conda \
--default-resources "mem_mb=8192" "runtime=240" \
--resources pdfReport=1 \
--slurm \
$*
|
ec1c32a9446da9ba0283cf41ff0ffaed4c4ebbb7687bd44204cd878ee0a71b6d | Shell | 187 | 7 | #!/bin/bash -l
#SBATCH --output=/scratch_tmp/users/%u/%j.out
#SBATCH --job-name=gpu
#SBATCH --gres=gpu
singularity exec --nv \
segreg_ubuntu20.sif \
python3.8 scan_xyzTz_batch.py
|
a075681cd49426ac9da9fd6c8b014907751abc8ab82c1f4922589b7f5d3a2777 | Shell | 189 | 9 | #!/bin/bash
DIR=$1
if test "x$CMD_ROUNDING" = "x"
then
CMD_ROUNDING="random"
fi
valgrind --tool=verrou --rounding-mode=${CMD_ROUNDING} --libm=instrumented ./main_libm > $DIR/res.dat
|
fa67379f8efde107dbb63e65bb0bbecef99cbc0fd5f6173b918a7e8ab001aa36 | Shell | 190 | 8 | #!/usr/bin/env bash
# Copyright Beman Dawes, 2010
# Distributed under the Boost Software License, Version 1.0.
# See www.boost.org/LICENSE_1_0.txt
bjam $* >bjam.log
grep "error" <bjam.log
|
ecfd55a00c595cfe9fd82d367351e6b87cc330b556e4e7d1c98be151cf49efff | Shell | 191 | 7 | #!/bin/bash
export mydir=$(dirname $0)
export project_prefix="--project_prefix May29"
for i in {0..14} ; do
export SLURM_ARRAY_TASK_ID=$i
bash $mydir/run-rna-protein-common.sh $*
done |
8827a03a9b1feecd04b824703c9a635ebfe40131e2d3767e132d78ac1e3af1a4 | Shell | 192 | 13 | #!/bin/bash
dropbox=../../dropbox
data=schneider50k
save_dir=$dropbox/cooked_$data
python get_canonical_smiles.py \
-dropbox $dropbox \
-data_name $data \
-save_dir $save_dir
|
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