sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3535c3cab51e7ab2de31a5d3bb7352f4ff8396f8b150000976bbba3dd9f3fd6d | Shell | 143 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_PairwiseSequenceAlignment "
./ex_PairwiseSequenceAlignment
|
481d608e259ade25ebe48d893b15b261c82ddeb5e3aade5f52a43b70fceee1fd | Shell | 144 | 4 | IK=2
NU=120
NP=5
/Applications/MATLAB_R2021a.app/bin/matlab -nodesktop -nosplash -nodisplay -r "run ie_fmm3dbie_sqrtscaling(${IK},${NU},${NP})"
|
786f5d437e4b3bcdf39499672a140d46a007f443df9516f5c364dc6a4797b545 | Shell | 144 | 3 | #!/bin/bash
cat data/adc_np_ord.txt | awk 'NR==1{for (i=3; i<=NF; i++) print $i}' | xargs -n 1 -P 4 bash code/analysis/ordinal/03_regression.sh |
b22c6281ebdc931ff423135c2d653cca62911a13585e1640b97f1cb2ea172051 | Shell | 144 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_mmCif test_inputs/2GB1.cif"
./ex_mmCif test_inputs/2GB1.cif
|
fb974d75a884aece6254983d824557acac71972277d3a7dc3905fcd6b81adefc | Shell | 146 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py seg /opt/elephant/script/train_configs/check_overfitting_Fluo-N3DH-CE_versatile002.json
|
5a4ac8e5c803c70d73b6acaaefa219972303ee033434a70759fd291e81fbd6e2 | Shell | 148 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py seg /opt/elephant/script/train_configs/check_overfitting_Fluo-N3DH-CE_t000-t100-t194.json
|
8ba4d2d0dc2cf42df86f5ad8115924514477ee6247921a1a98707c4b8613dad1 | Shell | 148 | 2 | python $SCHNARC/run_schnarc.py train schnet --split 100 10 --batch_size 10 --tradeoffs tradeoffs.yaml $SCHNARC/../examples/CH2NH2+/CH2NH2+.db TEST
|
36fd9b837c6e9f4ecd0eb494fca5a2bcbc5c1f57d152a3734220fa80b2d082f0 | Shell | 151 | 9 | #!/bin/bash
# Prepare diamond index for database
INPUT=$1
OUTPUT=$2
diamond makedb -p 8 --in $IN -d $OUT
echo "Diamond index created for $INPUT."
|
c10b31ae6d35753ceba0ee4d5ee04e8469a26ed379b0200f16525a9b23043799 | Shell | 151 | 3 | echo "# Running ex_HierarchicalClustering1B example-inputs/fasta_distances 811 195"
./ex_HierarchicalClustering1B test_inputs/fasta_distances 811 195
|
527565d696490ea95bebf3ac5576dd17dd8cdb43ab41cb21cd831446de0d76d1 | Shell | 153 | 4 | #!/bin/bash
echo -e "# Running ./ex_ramachandran_kd_tree ./test_inputs/val-rama.dat 4 10.0"
./ex_ramachandran_kd_tree ./test_inputs/val-rama.dat 4 10.0
|
ab5ac1f83472abb25d4b3f57262b70c8acc37439bec357b0f94cdf28fa64d379 | Shell | 153 | 5 | #!/bin/bash
python3 TI_sim_1d.py 2000 2020 900 1200
python3 TI_sim.py 2000 2020 900 1200 0
python3 TI_sim.py 2000 2020 900 1200 1
python3 plot_TI_sim.py
|
49ca5cedf9f58833c19e6f2820d42775b2a9bdf1398b1f68df91940bc5218478 | Shell | 155 | 3 | #!/bin/sh
optuna studies --storage "postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}" | grep kubernetes > /dev/null
echo $?
|
ceabf5e908976c924bb2c9011e4acd5590c30a771625e5c1cf8d8c925bce7562 | Shell | 155 | 7 | cd "$SRC"/textdistance
pip3 install .
# Build fuzzers in $OUT
for fuzzer in $(find fuzzing -name '*_fuzzer.py');do
compile_python_fuzzer "$fuzzer"
done
|
b6b5ea368300b9aeef08940d03b5d69ab90e57a1daad508d820e2a48b4d378f6 | Shell | 156 | 4 | mkdir -p Datasets/CoFusion/room4
cd Datasets/CoFusion/room4
wget http://visual.cs.ucl.ac.uk/pubs/cofusion/data/room4-full.tar.gz
tar -xvzf room4-full.tar.gz |
b70b208922e2b50f84e7e4be99cddd58fd2010ff400b2f0157aafdd88ef056d1 | Shell | 156 | 6 | #!/bin/bash
#====================
# find related pairs
#====================
plink --bfile data/adc/adc_np_pruned --genome --min 0.18 --out data/adc/adc_np |
c48511a401be69fe150ec74d95ccf61e4c7f4a74a4e83bb428fab0f3b57d83f2 | Shell | 156 | 2 | mkdir reconnet_0_04 #Create a folder to save the caffe models (measurement rate is 0.04)
../../../build/tools/caffe train --solver ReconNet_solver.prototxt
|
f00b1273e168e36d1d3a7800bd5edad18e25539d2cf039ade86ff447d5d26096 | Shell | 157 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_evaluate_chi test_inputs/2kwi.pdb"
./ex_evaluate_chi test_inputs/2kwi.pdb
|
e47eea0897fb30c34e13dfbd4ec618fbb3b24a0cf5a4a14f5869e04774dbffe1 | Shell | 158 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ex_pdb_to_fasta test_inputs/5edw.pdb"
./ex_pdb_to_fasta test_inputs/5edw.pdb
|
111dfda0dd306b240bdcfc26eda11ece7e13d53d5a317de16d72c0941fff5eb5 | Shell | 160 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_cabs_rotamers test_inputs/2gb1.pdb"
./ex_cabs_rotamers test_inputs/2gb1.pdb
|
c59ee1880936421aaba193d5d4f5ec60142d668ff2c78e963fca7611c3403083 | Shell | 160 | 4 | pip install --upgrade pip
pip install numpy
pip install opencv-python
pip install http://download.pytorch.org/whl/cu80/torch-0.3.1-cp27-cp27mu-linux_x86_64.whl
|
cd9f7c2d92aab51fe60dcae7e04ab646e17f26271a1e19d55952d64f1038cbfd | Shell | 160 | 9 | #!/bin/sh
python segment_cacs_predict.py \
-m ../model/SegmentCACS_0001619_unet.pt \
-d ../data \
-p ../prediction \
-f mhd \
-gpu cuda \
|
595cfd32988b7ddfaceef7d8f11da26964567ddf393b6e94d3c20cabc42989dc | Shell | 161 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_define_rotamer test_inputs/5edw.pdb"
./ex_define_rotamer test_inputs/5edw.pdb
|
be7aeb2a5efcac4e650f9d0f97d3285b48f300229e2cba3c7ce22f9674eeab1e | Shell | 161 | 10 | if [[ $# -ne 1 ]]; then
echo "train.sh <gpu>"
exit 1
fi
gpu=$1
echo "export CUDA_VISIBLE_DEVICES=${gpu}"
export CUDA_VISIBLE_DEVICES=${gpu}
python main.py |
c43c00b0d0e874c043d4fcbc4c90aad2d52a1842106085319d40761200e7670c | Shell | 162 | 10 | #!/usr/bin/bash
CONDA='/home/analyst/anaconda3'
snakemake -s "./Snakefile_GATK" \
--cores 20 \
--resources mem_gb=50 \
--use-conda \
--conda-prefix $CONDA
|
1e649f52252d68030c634e9ab63e2d0308c40f1f067972b2bf6acddcd4d69070 | Shell | 163 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_find_side_group test_inputs/2gb1.pdb"
./ex_find_side_group test_inputs/2gb1.pdb
|
205aeb32fc232b529f8b66854eb95dab5de3579d5a663938e1cb1ac415f058fe | Shell | 163 | 6 | #!/bin/bash
for i in $(seq $4)
do
getorf -find 0 -min $3 -outseq "$2/getorf_p" -sequence $1
getorf -find 2 -min $3 -outseq "$2/getorf_d" -sequence $1
done
|
3e95f94786e81586456bc7c35348c5f8bfa113db41b3934b80a7d7fec983b976 | Shell | 163 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ex_hssp_to_fasta test_inputs/1dm1.hssp"
./ex_hssp_to_fasta test_inputs/1dm1.hssp
|
db4d0e9fa84ecb4d07fba40fab6e5ce68511795adba2d11993aa540a23b934c7 | Shell | 163 | 8 | #! /bin/tcsh
#SBATCH --job-name="DF"
cd $SLURM_SUBMIT_DIR
/data/PNAI/yuba/software/cafemol_mod/bin/cafemol input.inp -machinefile $SLURM_JOB_NODELIST > runlog
|
6b9c107c8d66642e7bf2d949eb93e0744454169a23e3d4721009bcb4092ed6a1 | Shell | 164 | 10 | #!/bin/bash
echo "# Running: ./tasks -i=test_inputs/ls_task.xml"
./tasks -i=test_inputs/ls_task.xml
mkdir -p outputs_from_test
mv *.txt ./outputs_from_test/
|
c00186a85cc65be7eaf08124676fe141b6d44993ac94d6fb55fa8944df1f7e66 | Shell | 164 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_MonomerStructure test_inputs/AA3.cif"
./ex_MonomerStructure test_inputs/AA3.cif
|
18da19658e4cf2e504545bce0a2e4edfaaed6a7e96af0e793a6dcb93edc5f4a5 | Shell | 165 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_bf_by_residue ./test_inputs/4mcb.pdb"
./ex_bf_by_residue ./test_inputs/2gb1.pdb
|
ad4b74ec6a741fd62424ddf562661d99d6ba8f4161316e0b5458f0a2a2c133b6 | Shell | 165 | 2 | gfortran -O3 -fPIC -fopenmp -march=native -std=legacy flattriquad.f90 ../src/lpeval_flattri.f90 ../src/potint2.f90 -lfmm3d -lfmm3dbie -L/mnt/home/mrachh/lib
./a.out
|
e6060c33502adbf565dc5846be066a5b2733fece46e22d56dd18bfceb55e0ed6 | Shell | 165 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_evaluate_phi_psi test_inputs/2kwi.pdb"
./ex_evaluate_phi_psi test_inputs/2kwi.pdb
|
b2f68194e0420458f88e77afef016d35f7574ca30740b86a1f958092e2993424 | Shell | 166 | 13 | #!/bin/bash
set -e
VERSION=`cat VERSION.txt`
rm -f ./*simg
docker build -t trinityrnaseq/trinotate:$VERSION .
docker build -t trinityrnaseq/trinotate:latest .
|
f65823eeac9971a05f4483300e4e6a615b0ef37b4872b0b8fb8c74eb093bcd56 | Shell | 166 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ex_NcbiSimilarityMatrixFactory BLOSUM45"
./ex_NcbiSimilarityMatrixFactory BLOSUM45
|
3be19aa1d83d5b619eb08c6017e412184bc6ac91ab2f21b0e84e7ea5fd13d040 | Shell | 167 | 8 | sudo rmmod dma_proxy
if [ "$BIOEMUM_TARGET" = "vpk120" ]; then
sudo fpgautil -R -n Full
else
sudo xmutil unloadapp
sudo xmutil loadapp k26-starter-kits
fi |
c6c3d47813df6197eef9554befe9519250dc261feb1f3bd7ff96c3b3ce441220 | Shell | 167 | 6 | #!/bin/bash
for i in $(seq $4)
do
getorf -find 1 -min $3 -outseq "$2/getorf_3_p" -sequence $1
getorf -find 3 -min $3 -outseq "$2/getorf_3_d" -sequence $1
done
|
84b83031b59312dd1c12dbae50adb156f12665883eb119f0d62eadce6d06f431 | Shell | 168 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_vdw_interactions test_inputs/2gb1.pdb"
./ap_vdw_interactions test_inputs/5edw.pdb
|
479221d3f43093baa1ad6427d67db25d14ce90d203492d812e00d6531f0bd259 | Shell | 170 | 9 |
source scripts/samples.sh
for i in ${SAMPLES[@]};
do
cat results/star_pass1/${i}/${i}.SJ.out.tab | awk '$7 >0' > results/star_pass1/${i}/${i}.SJ.out.exp.tab
done
|
511474b3842b2f8afbbec848caeddb1081fb8acb8338d3195464d8b3ab2ad579 | Shell | 171 | 2 | python ../src/main_vis_aud_audio2text_graph.py --prefix gemini2.5 --signal graph100_H --api xxx--config ../configs/gemini2.5pro_SI_baseline_aud2text_conv_graph100_H.json
|
8ec23f73bb87cdf8d995bd90d34dc072391d3e3aca9614529b8850dd80211a10 | Shell | 171 | 3 | #!/bin/bash
aws cloudformation create-stack --stack-name chunkflow --template-body file://template.yml --capabilities CAPABILITY_IAM --tags User=jingpeng,Tool=chunkflow
|
9fd1de2d2a9c3b0e57a92783291ea4a3aa0f9fa3c182059657ea0ffeed365c1c | Shell | 171 | 11 | #!/bin/bash
# $-N traj_00001
PRIMARY_DIR=/global/mai/SHARC_3.0_tests/tests/RUNNING_TESTS/scripts_setup_traj/State_2/TRAJ_00001/
cd $PRIMARY_DIR
$SHARC/sharc.x input
|
a014b0ab801217f557fe8ad9ee73c975abd4c20c400878e12cbd6da636a0259d | Shell | 171 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_Sequence test_inputs/3wn7.pdb A 366 405"
./ex_Sequence test_inputs/3wn7.pdb A 366 405
|
08ba51e0a46fa5f1b9247f2530463cb0d47ec079c1741d50cf707a053843995c | Shell | 172 | 4 | #!/usr/bin/env bash
set -euo pipefail
project_root="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)"
exec "$project_root/scripts/launch_observatory.sh" --smoke "$@"
|
a53e63aaaf38c2db9054ddcbd168fe724e1a33f22f046e7937b8c9a437a530de | Shell | 172 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_BetaStructuresGraph test_inputs/2fdo.pdb"
./ex_BetaStructuresGraph test_inputs/2fdo.pdb
|
41d5bfc23f7be8a36745591339d068f2768e6e2bd2e9b962dac6d1cc662293a4 | Shell | 174 | 4 | #!/bin/bash
echo "# Running ./ap_filter_fasta test_inputs/ferrodoxins.fasta test_inputs/5edw.fasta"
./ap_filter_fasta test_inputs/ferrodoxins.fasta test_inputs/5edw.fasta
|
e84408d697c845891d9d4c63b2037399dee3586cedb4e8b617ca27448d60f2cf | Shell | 175 | 7 | #!/bin/bash
# Get Instance ID
EC2_INSTANCE_ID=$(ec2metadata --instance-id)
# Set password for nginx to Instance ID
htpasswd -b -c /opt/h2oai/htpasswd h2oai $EC2_INSTANCE_ID
|
4677b8bdcd10b78a2c3365ce026b97e7e474b01fe28bcef8af05c84c297e200b | Shell | 176 | 8 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "# Running ./ex_BuildPolymerChain 30.0 5 15"
./ex_BuildPolymerChain 30.0 5 15 > out.pdb
mv out.pdb outputs_from_test/out.pdb
|
936f013d680585d3c216886c2cbd879a05f4d01e694e594bef2c2f8be71a33f3 | Shell | 176 | 16 | mkdir results
mkdir scripts
mkdir data
cd data
mkdir raw
mkdir processed
cd processed
mkdir bam
mkdir bed
mkdir sam
mkdir trimmed
mkdir txt
mkdir rds
mkdir coverage
cd ../../
|
81fad44524a9dbf0da4ea7c593fa26148fbb282bd1d1702e3d6610fdba01bb9c | Shell | 177 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_NeighborGrid3D test_inputs/2gb1.pdb A:12"
./ex_NeighborGrid3D test_inputs/2gb1.pdb 2.0 A:12
|
16bddd41fbd35caffdcbde65a0001b8d7c153f6921ea49285b0eaabbea534675 | Shell | 179 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_ligand_interactions test_inputs/5ldk.pdb ATP"
./ap_ligand_interactions test_inputs/5ldk.pdb ATP
|
b46db4444a79f1003f967a6e135c124a2f94108c274596ed96ccb9dd89d1f931 | Shell | 180 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_interdigitated_strands test_inputs/2fdo.pdb"
./ap_interdigitated_strands test_inputs/2fdo.pdb
|
dfbb4f59b054a9ba3caec00a1b690af1220be8c22dcbf119e093b96d5b890d62 | Shell | 180 | 4 |
samtools view -h -D CB:/data/barcodes.tsv --keep-tag CB,RG /data/possorted_genome_bam.bam
samtools view -h -D CB:/data/barcodes.tsv /data/possorted_genome_bam.bam | head -n 300 |
b4a95b5b74f7c0f572aa730d9b24d8fb1e47054da1466a8e662fef4dda4b30b9 | Shell | 182 | 4 | # Helper script to run the stats.py script
# Adjust the path to the results directory
RESULTS_DIR=./results
python3 stats.py -o $RESULTS_DIR --models_subdir statsmodels $RESULTS_DIR
|
fc3a92e0fff055bad051cbe3c73373764b578f1cf10cf0924942d27a5403a284 | Shell | 182 | 4 | #!/bin/bash
seq 1 22 | sudo xargs -P 22 -n 1 bash -c 'bcftools merge --force-samples -Oz -o /data_global/ACT_imputed/chr$0.dose.vcf.gz data/imputed/ACT_NHW/ACT*/chr$0.dose.vcf.gz'
|
50daecc80814d64f6413dbbced5cef0692d34fa1e270d9c474011d690f097d7b | Shell | 183 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_ligand_trajectory test_inputs/2kwi.pdb GNP 3.5"
./ap_ligand_trajectory test_inputs/2kwi.pdb GNP 3.5
|
34af40227f185fe9bb0edf4f2ab9465d2ae1b5e21c46757d66bdf6809366488c | Shell | 184 | 7 | #!/bin/bash
PYTHONPATH="${PYTHONPATH}:$PWD/../"
printf -v cmd "%s" "python ../pyseg/scripts/tests/mcf_synthetic_test.py do_short"
echo $cmd
$cmd | tee $PWD/results/synthetic_test.log |
50d7bac6467ace1ec0b80185d4de9b3701940b2c66b7e06fdbd1515b57f69d07 | Shell | 184 | 9 | #!/bin/bash
# Build glove
cd glove && make
cd ..
# Generate embedding for each token
python3 glove_embedding.py
cd glove && bash demo.sh
cd ..
cp ./glove/vectors.txt ./data/vectors.txt |
8e7e001b083f6c46a4f90e6b0b0862fdf044f56a96fb9859ee18bf249ca81b1c | Shell | 184 | 5 | #!/bin/bash
# Install pytorch
pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu116
# Install requirements
pip install -r requirements.txt
|
e8e199728f77a488eed3fc0142cded7692c1f229970fb0160fc62e48a99626e0 | Shell | 184 | 9 | #!/bin/bash
CONDA='/home/USER/anaconda3'
snakemake -s "./Snakefile_Nirvana" \
--cores 35 \
--resources mem_gb=80 \
--use-conda \
--conda-prefix $CONDA
|
d524a9944fbada419b3e6d252b158cfd0b41ef44fa5d1cb690f9a5d4b735ea2e | Shell | 185 | 6 | #! /usr/bin/env sh
set -e
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
pytest
|
94c031acb22dcc5888e3e27ac49707d1033ee3dac28b51f0f345f62b8658b78e | Shell | 186 | 6 | #!/bin/bash
set -ex
singularity run -e ../Docker/trinotate.simg bash -c "export TRINOTATE_HOME=/usr/local/src/Trinotate && ./runMe.sh && ./runMe.add_expression_prep_TrinotateWeb.sh"
|
e0af02809f7df3f011cf145f5d43c56eff1aae178f78bcc51791b22967bc9adf | Shell | 187 | 5 | #!/bin/bash
echo "# Running ./ap_find_in_fasta ./test_inputs/ferrodoxins.fasta test_inputs/seq_id_list.txt"
./ap_find_in_fasta test_inputs/ferrodoxins.fasta test_inputs/seq_id_list.txt
|
f25e645af34019df2b0a37c8742ac43ccff21b6df3f46951d9f7bf7d2e189f5d | Shell | 187 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_FastaMatchProtocol test_inputs/unique100.fasta"
./ex_FastaMatchProtocol test_inputs/unique100.fasta 4
|
d5de37ad640b55214c121914c8725e6752f03e0c183bc417a42ca99599acef34 | Shell | 189 | 14 | #!/bin/bash
pheno=$1
covar=$2
gene_annot=$3
out=$4
magma \
--bfile data/mega/mega_np \
--pheno file="$pheno" \
--covar file="$pheno" \
--gene-annot "$gene_annot" \
--out "$out" |
2f7e79f49dd59e521930eb5b373169ac51fe87e253575b78f55d14cc0df54fec | Shell | 190 | 5 | #!/bin/sh
export DISPLAY=:99
sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &
curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
sh ci-build.sh
|
7516bac2ff6545470c23f6c390ce247f3ee7242852bf153b9b416fdd45f66d4c | Shell | 190 | 2 | sudo docker run -it --mount source=/home/hiwi/challenge_submission_2021/results,target=/workspace/results,type=bind --rm --net=host --gpus '"device=0"' -e PORT=2000 transfuser-agent:latest
|
77347cdfff00548b41fd79a4650b380f61ddd738e37e6f8fec9c15002d98dab3 | Shell | 191 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_test_train_li13-t4_seg.json seg /opt/elephant/script/train_configs/li13-t4.json
|
b601a81078bfc732fd34044f76c4540e1f1f477864dee84dff3181e0f568dbbd | Shell | 191 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running: ./ap_blastxml_to_fasta test_inputs/1K25_01+PBP_C2.psi"
./ap_blastxml_to_fasta test_inputs/1K25_01+PBP_C2.psi
|
909d9b9aea73da33c61abc193bb4ee4c005aea5c4e120b9e3777400f8e2edad5 | Shell | 192 | 7 | #!/bin/bash
PYTHONPATH="${PYTHONPATH}:$PWD/../"
printf -v cmd "%s" "python ../tutorials/exp_ssmb/class/plane_align_class_test.py"
echo $cmd
$cmd | tee $PWD/results/plane_align_class_test.log |
3acf45ff9729d40be4d9f8559fd05f33cc8fa888d7a0cc2f662dbc724c8746f0 | Shell | 193 | 7 | #!/bin/bash
transcriptome=$1
output=$2
awk -F " " '/^>/ {print substr($1, 2, index($1, "t")-2) "\t" substr($1, 2)}' $transcriptome > $output
echo "gene_trans_map were created successfully!"
|
508fa116835d287bfb8b654dc4e13c92a5aabb9b277f86721cb7cbc511592e54 | Shell | 193 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_test_train_li13-t4_flow.json flow /opt/elephant/script/train_configs/li13-t4.json
|
af24011d6b3d0b26e19f0e61cd29dcde1df174deba270aeac2ec97f349cbd8f5 | Shell | 194 | 5 | #!/bin/bash
echo -e "Running ./ex_goodman_kruskal_rank_correlation test_inputs/example_contingency_matrix.txt"
./ex_goodman_kruskal_rank_correlation test_inputs/example_contingency_matrix.txt
|
2a9bc10c99ba63bb2b09325dff6ce6ec466209acb3abf7811b8a642e466c617c | Shell | 195 | 5 | #!/bin/bash
# Sabotage local tox environment so that `sinfo` is not working any more
if [ -n "$NO_SLURM" ]; then
echo "ofnis" >| $VIRTUAL_ENV/bin/sinfo && chmod a+x $VIRTUAL_ENV/bin/sinfo
fi
|
60296efa5d6225d258b0abb672f6aea5df76c7251f70853a7f1031073c0865fd | Shell | 195 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./rg.py test_inputs/1cey.pdb"
python3 ./rg.py test_inputs/1cey.pdb
|
6c5ecb58cf5905f769a6298cc5429ee6120f0c8fcd796685bacc5f98ac31fbb7 | Shell | 195 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_train_seg_li13-t4_20220111.json seg /opt/elephant/script/train_configs/li13-t4.json
|
77452118b1c6c25301b7158b1275a15e623600c3b9879dc6d5aee2c9696ac0ca | Shell | 195 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
echo -e "Running: ./str_calc -in::pdb=./test_inputs/2gb1.pdb -calc:hbonds:bb"
./str_calc -in::pdb=./test_inputs/2gb1.pdb -calc:hbonds:bb
|
38788a00afcd6cd3108926dd6ccf2e5240a249a98db5c7a58fde7e207d9c2eda | Shell | 196 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo "#Running ./ap_blast_nonredundant test_inputs/1K25_01+PBP_C2.psi 0.5"
./ap_blast_nonredundant test_inputs/1K25_01+PBP_C2.psi 0.5
|
cbea6f378d37f070c54922fd28ad42ee4f81447f877affa8f992ef7339ae228c | Shell | 196 | 6 | #$ -N GWAMA_ModelAveraged
#$ -cwd
#$ -q single15.q
#$ -S /bin/bash
Rscript /data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/Dyslexia/dyslexiaevol/clap-beat_dyslexia/GWAMA_MA.R
|
e32d664dfe1f40e05a1a28c8d8ccc3fd98a7d7ed43ea563219ccdbd92c4863bf | Shell | 196 | 13 | #!/bin/sh
#SBATCH --partition=shared-gpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --time=12:00:00
module load GCCcore/8.2.0
module load FFmpeg/4.1.3
CMD="python vac.py"
srun $CMD
|
2b68c3a49283e9c1c5cad75b22f83aaf32ba9cb07e3e124bd59d940299a6ff23 | Shell | 197 | 6 | sudo ./stop_kernel_module.sh
sudo make -C /lib/modules/$(uname -r)/build M=$(pwd) modules
#For debugging: generate disassembly output:
#objdump -dS bcm2835_spi_display.ko > bcm2835_spi_display.S
|
64d54f364e48c1b8e94b13975f3d8bbffaa94a5511c302740e0e1a3f76f414d0 | Shell | 197 | 8 | #!/bin/bash
out=$'/console.out'
ckpt_dir=$'./checkpoints/'
date=$(date +%y-%m-%d-%H-%M)
nohup \
python train_multilabel.py --image-size '232 300' --augment 1 \
> "./log/$date$_console.out" &
|
0743de649e335294517f23a9dc10af6a88fd3f7c89d0a64f2b8fc18d9f734cde | Shell | 198 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_molecule_diffusion test_inputs/ar_tra.pdb AR 27.6214"
./ap_molecule_diffusion test_inputs/ar_tra.pdb AR 27.6214
|
23a87f01b0020e1b85146449a5f4104ef3c89d9e0eda968066ae8421141a19b2 | Shell | 198 | 5 | LLNAME=flattrirouts
MWNAME=${LLNAME}.mw
GATEWAY=${LLNAME}.c
../../mwrap/mwrap -c99complex -mex -${LLNAME} -c ${GATEWAY} ${MWNAME}
../../mwrap/mwrap -c99complex -list -mex ${LLNAME} -mb ${MWNAME}
|
423915cfea0cf11cdad5974388bb66c2252e81d54823bf5c65c469ca9de5f45a | Shell | 198 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='8'
JAVA_INSTALL_VERSION=311
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-8u311-linux-x64.tar.gz
|
a4af8e74a290c91852169ea2ca4d091e4522685e6874cae5b0b0267464ba7d09 | Shell | 198 | 7 | #!/bin/bash
echo -e "Running ./ap_OnlineStatistics"
./ap_OnlineStatistics
echo -e "Running ./ap_OnlineStatistics test_inputs/random_normal.txt"
./ap_OnlineStatistics test_inputs/random_normal.txt
|
c8e20d242ae282ada2ddb28afc8b4aa99a34f21f6da9b037a50135dbd6d37f0f | Shell | 198 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_protein_peptide_interface ./test_inputs/1dt7.pdb 7.0"
./ex_protein_peptide_interface ./test_inputs/1dt7.pdb 7.0
|
ebf5f03fe548a1556d6a738cee13edbf311794256a9be028828a68806d11870a | Shell | 198 | 5 | list=$1
cat $list | xargs -n 1 -P 100 -I {} bash -c '
timeout 600s xvfb-run -d /home/vkzohj/public/vaa3d_for_neutube/start_vaa3d.sh -x neuTube \
-f neutube_trace -i {} -p 1 > /dev/null
' |
f438ac688efbf79172ad6b256ec56c137b74d9c8e799308f4e5be06bcda7664e | Shell | 198 | 5 | cd ~/git/FMM3D/
make install
cd ~/git/01_TES_Package/Apr20_2022_fmm3dbie
gfortran -O3 -fPIC -fopenmp -march=native -std=legacy convert_geom_go3.f90 -lfmm3d -lfmm3dbie -L/mnt/home/mrachh/lib
./a.out
|
e7e02b1a57934df5ccd244e045fac853c26eee8d3840ca5cca718e453ba1f6e3 | Shell | 199 | 6 | #!/bin/bash
seq 1 22 | \
sudo xargs -P 22 -n 1 \
bash -c 'bcftools merge data/imputed/ADC_NHW/ADC*/chr$0.dose.vcf.gz --force-samples -Oz -o /data_global/ADC_imputed/chr$0_all_adcs.dose.vcf.gz'
|
5a2f0b425b169979f2c6dab9fd8502e9bfe502d32f2a60df1a7909ab84ed4602 | Shell | 200 | 9 | #!/usr/bin/env bash
#SBATCH --job-name=deschamps
#SBATCH --partition=etna-shared
#SBATCH --account=nano
#SBATCH --qos=normal
#SBATCH --nodes=1
#SBATCH --time=96:00:00
#SBATCH --mem=1000mb
./deschamps
|
d6c558d2ab28fc88f96832fffea596c6d6719ffe198a59120dd309ad94acdf96 | Shell | 201 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='10'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-10.0.2_linux-x64_bin.tar.gz |
332c31f4380fedd4ba2651e0d963054add0c65ac1f4e91d1a1d091f0c96b86d3 | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='15'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-15.0.2_linux-x64_bin.tar.gz
|
48c369692d75290ccdf237bc3a87dde6786151d16f2d7568d1e030eaebe66392 | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='13'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-13.0.2_linux-x64_bin.tar.gz
|
5533b3036da1e6d3f488ef55e29bb5d2169a390c4a2c2ec629fc043b4fb5b230 | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='16'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-16.0.2_linux-x64_bin.tar.gz
|
a6a8d3b3010b1ffa13421e90e067d73eb87ed48c488a62909c4358cd6c788650 | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='17'
JAVA_INSTALL_VERSION=0
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-17.0.0_linux-x64_bin.tar.gz
|
b336abac1cbfe901bb9aac3ce194839f9a304fa47c4b7c2ae6e746316acc1f9b | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='12'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-12.0.2_linux-x64_bin.tar.gz
|
b9728344b0f086728e5b8412bae13c0fa544d33295e1a5da252db819a7ef7f52 | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='14'
JAVA_INSTALL_VERSION=2
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-14.0.2_linux-x64_bin.tar.gz
|
e0cb809e3f67c6b7055ff332e0ad3edd3434b6c4852651b7672f23f416bfc8c3 | Shell | 202 | 4 | #This script takes PDB file with only CA atoms as first argument, then predicts ss2 and rebuilds backbone
../bin/heca_program -in:pdb=$1 -out:ss2=temp.ss2
../bin/deep_bbq -in:pdb=$1 -in:ss2=temp.ss2
|
ef5f24c8ef546ec9f119af645bb69803c9837c4bf422affbb20dfdb280e890ba | Shell | 202 | 6 | #! /bin/bash
JAVA_INSTALL_VERSION_MAJOR='11'
JAVA_INSTALL_VERSION=3
JAVA_INSTALL_PATH=/usr/opt/java-${JAVA_INSTALL_VERSION_MAJOR}-${JAVA_INSTALL_VERSION}/
JDK_FILE=/tmp/jdk-11.0.3_linux-x64_bin.tar.gz
|
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