sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
08255782a76a1c4cb042bc67c45064f5b1268bc132bedc96dcafd9640a4e11a7 | Shell | 259 | 10 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=6:00:00
#SBATCH --job-name=rel_bootstrap
#SBATCH --account=proj9
#SBATCH --partition=prod
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
python -u compute_reliability_bootstrap.py $1 |
4d90621b1bf9a8fc7e5346a9ae20142b070795d6028ee18c4ea0622a63d70f23 | Shell | 259 | 12 | #!/bin/bash
rm bin/*
rm -rf BasesToIndices/build/
rm -rf CS_caller/build/
rm -rf CS_Candidate/build/
rm -rf CS_Consensus/build/
rm -rf CS_FindRepeats/build/
rm -rf CS_Observations/build/
rm -rf GFF/build/
rm -rf refine/build/
rm -rf sort-fastq-on-bam/build/
|
a1e35647a731f31a28a3c4559960d68c7e71409fe6286d060eed68392b8ec86b | Shell | 259 | 9 | #!/bin/bash -l
#SBATCH --time=8:00:00
#SBATCH --ntasks=1
#SBATCH --mem=320g
#SBATCH --mail-type=ALL
#SBATCH --mail-user=west0883@umn.edu
#SBATCH -p ram1t
module load matlab
matlab -nodisplay -r "maxNumCompThreads(1)" < SVD_forMSI_forhemo.m ; exit;
|
0db707727a1a7a9497d7d2c1e002088a00828ed96007733cd888592dcaee2fb6 | Shell | 261 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_ReduceSequenceAlphabet to print all known alphabets"
./ex_ReduceSequenceAlphabet
echo -e "# Running ./ex_ReduceSequenceAlphabet lz-mj.16"
./ex_ReduceSequenceAlphabet lz-mj.16
|
03412c7837af623688929acc219d6d4b2fc23fbb6a8d92b6879a68fd0838023b | Shell | 263 | 10 | #!/bin/bash
VERSION=`cat VERSION.txt`
singularity build trinotate.v${VERSION}.simg docker://trinityrnaseq/trinotate:$VERSION
singularity exec -e trinotate.v${VERSION}.simg /usr/local/src/Trinotate/Trinotate
ln -sf trinotate.v${VERSION}.simg trinotate.simg
|
5fb9b1bb6c267a364cada6ab998c69bf17183e4152a16db86be01c8914ef241c | Shell | 263 | 10 | #!/bin/bash
. /opt/venv/bin/activate
cd /groups/branson/home/leea30/git/apt.aldl/deepnet
# numCores2use=7
export PYTHONPATH="/groups/branson/home/leea30/git/dpk:/groups/branson/home/leea30/git/imgaug"
python apt_dpk_exps.py "$@"
# "--expname $1 --exptype $2
|
514a8f7f79d1617abe522e8f7d96c301a89caa4ffdf77a7a5a0b2db0182c604d | Shell | 264 | 7 | #!/bin/bash
echo -e "#Running ./ex_KDE_1D test_inputs/normal.txt 0.4"
./ex_KDE_1D test_inputs/normal.txt 0.4
echo -e "#Running ./ex_KDE_1D test_inputs/THR_chi1.dat 0.1 -3.14159 3.13149 periodic"
./ex_KDE_1D test_inputs/THR_chi1.dat 0.1 -3.14159 3.13149 periodic
|
1983c8505b38bc11e4f4c6cbf00e33f3b6b694e6e6d6876bbf595d1ea3a46dc5 | Shell | 265 | 4 | #!/bin/bash
awk 'BEGIN{FS="\t";OFS=" "}NR>1{print "hs"substr($4,4),$6,$7,$9}' $1 |sort -r -k 4 |awk 'NR<201{print $0}' > data/circos_input.txt
sed -i "s/hg[0-9]\+/$2/g" circos.conf
circos -conf circos.conf --outputdir $3 -debug_group summary,timer > data/circos.log |
1d733a3d04df5129a5f1db1c8dc999261c5e9eff3f304f4238c33823e003cfe2 | Shell | 265 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_symmetry_in_pdb test_inputs/5edw.pdb"
./ap_symmetry_in_pdb test_inputs/5edw.pdb
echo -e "Running ./ap_symmetry_in_pdb test_inputs/3dcg.pdb"
./ap_symmetry_in_pdb test_inputs/3dcg.pdb
|
7d0f9c44af6035f8679e1455b05fd87735ed7ed1dabc867e8c29f8b17a6d5f35 | Shell | 265 | 9 | phenos=$(cat data/mega/mega_np_ord.pheno | awk 'NR==1{for (i=3; i<NF; i++) printf $i "\n"; print $NF}')
for pheno in $phenos
do
./code/gwas/clump.sh \
data/mega/mega_np \
output/gwas/mega/"$pheno"_ord_results.txt \
output/gwas/mega/"$pheno"_ord_results
done
|
b8dd80c7119c9f32b402cdee4ee60d1e39cae12dd14672ec0cda5abbe6ab51b3 | Shell | 265 | 5 | #!/bin/bash
mkdir ./projects_folder
touch ./bin/settings.ini
echo "liftover_hg19_hg38 = ../src/cppNGS-TEST/data_in/hg19ToHg38.over.chain.gz" >> ./bin/settings.ini
echo "liftover_hg38_hg19 = ../src/cppNGS-TEST/data_in/hg38ToHg19.over.chain.gz" >> ./bin/settings.ini
|
81ca77ae0b74487b78368091b3636f1c3765ee04961882fcb3e781211902f2d0 | Shell | 266 | 11 | #!/bin/bash
autopep8_params="--in-place --max-line-length=120"
pylint_params="--rcfile=.pylintrc"
files=`find leaderboard/ -type f -name "*.py"`
for file in ${files[@]}
do
autopep8 $file ${autopep8_params}
pylint --rcfile=.pylintrc ${pylint_params} $file
done
|
59a907881c9829c599d35ff06aefa0afec5902d6c31aa947670ba9cbd42532cb | Shell | 269 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_orient_pdb test_inputs/2kwi.pdb B 391 418 > helix_rotated.pdb"
./ap_orient_pdb test_inputs/2kwi.pdb B 391 418 > helix_rotated.pdb
mkdir -p outputs_from_test
mv *.pdb outputs_from_test/
|
7bb6150b4fc9335f152533c44ec8d08c5cd5fff51621bf864ebfaa775497848d | Shell | 269 | 8 | #!/bin/bash
echo -e "Running: ./ex_monomer_io -in::monomers::cif=./test_inputs/HEM.cif -out:file=monomers_new.txt"
./ex_monomer_io --in::monomers::cif=./test_inputs/HEM.cif -out:file=monomers_new.txt
mkdir -p outputs_from_test
mv monomers_new.txt outputs_from_test/
|
c69a32e4f2568cfa0486dbdf4cdf27cf05bdcf377168d65635e360e2516a3ace | Shell | 270 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./radial_distribution_function.py test_inputs/ar_tra.pdb 27.6214"
python3 ./radial_distribution_function.py test_inputs/ar_tra.pdb 27.6214
|
ad1e66cc5fb6a12cc2d92231e2e727e70643e02eb981c3970f3073fecdc87d85 | Shell | 271 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p ./outputs_from_test
echo "#Running python3 filter_scorefile.py -f test_inputs/1pgxA-abinitio.fsc"
python3 filter_scorefile.py -f test_inputs/1pgxA-abinitio.fsc
|
07fd92962f8c51a1da3ae34f789cf4aa52100fc8ffcc176ba2542bcb7f9e5329 | Shell | 272 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./crmsd_on_ligands.py HEM test_inputs/5ofq.pdb test_inputs/4rm4.pdb"
python3 crmsd_on_ligands.py HEM test_inputs/5ofq.pdb test_inputs/4rm4.pdb
|
2dcd17cc3f8be99f19fd184dace9a7a2a5283b518a848af19a1608d86325d314 | Shell | 272 | 13 | bfile=data/mega/mega_np
plink \
--bfile "$bfile" \
--exclude raw_data/inversion.regions.txt \
--indep-pairwise 15000 1500 0.2 \
--out tmp/mega_np_prune
plink \
--bfile "$bfile" \
--extract tmp/mega_np_prune.prune.in \
--make-bed \
--out tmp/mega_np_prune |
cbd187ad9fb280d86d4b9c7fd01e4739d058b9701512d250015563b350bc57d8 | Shell | 272 | 8 | #!/bin/sh
# paranoia: sometimes autoconf doesn't get things right the first time
autoreconf --verbose --install --symlink --force
autoreconf --verbose --install --symlink --force
autoreconf --verbose --install --symlink --force
./configure --enable-maintainer-mode "$@"
|
44bfbba0019928027dc6f661eeb0ba8a2fe7612a2cf6a0601d6cd0dcc62b3374 | Shell | 273 | 10 | #!/usr/bin/with-contenv bash
# From http://www.derekmpowell.com/posts/2018/02/docker-tutorial-3/
GIT_USER=${GIT_USER:=none}
GIT_EMAIL=${GIT_EMAIL:=none}
if [ "$GIT_USER" != none ]; then
echo -e "[user]\n\tname=$GIT_USER\n\temail=$GIT_EMAIL" > /home/$USER/.gitconfig
fi
|
dcc68c88011fa1669abca3515eff545a23578346f87206859628c5234c4b2ea0 | Shell | 274 | 6 | # legacy.
#!/bin/sh
curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz
curl http://download.tensorflow.org/models/resnet_v1_101_2016_08_28.tar.gz | tar xvz
curl http://download.tensorflow.org/models/resnet_v1_152_2016_08_28.tar.gz | tar xvz |
3b75a7965d4d2951dd3155a986adb395a6ff40a1eaf3b2ebe336a02ca2fb35a3 | Shell | 275 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./tmscore.py test_inputs/2gb1-model1.pdb test_inputs/2gb1-model2.pdb"
python3 ./tmscore.py test_inputs/2gb1-model1.pdb test_inputs/2gb1-model2.pdb
|
0354c28dd227d77c29c72ba768eb79f7cbca6cefc51f991ddc3a8ff19e97fec7 | Shell | 277 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./align_sequences.py test_inputs/2azaA.fasta test_inputs/2pcyA.fasta"
python3 ./align_sequences.py test_inputs/2azaA.fasta test_inputs/2pcyA.fasta
|
3e63a205c27756104631651308a4ca841c605d6eb4e0dd5e57176f644a91630f | Shell | 277 | 6 | python baseline_aug.py > logs_baseline.txt
python baseline_aug_vgg.py > logs_vgg.txt
python baseline.py > logs.txt
python baseline_aug_predict.py > logs_baseline_predict.txt
python baseline_aug_vgg_predict.py > logs_vgg_predict.txt
python baseline_predict.py > logs_predict.txt |
6e8dfb939b7fd25ca2f73590a2280fbf9a492fcd5b1f812cdfb83aeddcb46d2c | Shell | 277 | 5 | ARGS="cohort_csv='`pwd`/tutorials/tutorial2/cohort.csv';"
ARGS="$ARGS config_path='`pwd`/tutorials/tutorial2/mappers.json';"
ARGS="$ARGS output_dir='`pwd`/results/tutorial2_mappers';"
ARGS="$ARGS data_root='`pwd`';"
matlab -nodesktop -r "$ARGS run('code/analysis/run_main.m')"
|
e6aa94dfdee38f1272707dbb9637560a757c53513048d82a79a781df107b28c0 | Shell | 277 | 14 |
source config.sh
source scripts/samples.sh
for i in ${SAMPLES[@]};
do
salmon quant -i $sal_index_mm -l A \
--validateMappings \
-1 fastq/trim/${i}_R1trim.fastq.gz \
-2 fastq/trim/${i}_R2trim.fastq.gz \
-p 12 -o results/salmon/${i} \
--numBootstraps 10
done
|
1043d2c8af31adaaf2c32cc872b636a18419b9c5f9cee36be0e77813499cc5eb | Shell | 278 | 12 | #!/bin/bash -l
sudo pip3 install silence_tensorflow
sudo pip3 install tensorflow-addons
sudo pip3 install einops==0.4.0
sudo pip3 install scipy
sudo pip3 install wandb==0.13.1
sudo pip3 install scikit-learn
sudo pip3 install numpy==1.26.4
sudo pip3 install pandas
wandb login
|
9c36ab92eb4b1b3c5b0c643a9eb0684d62fa40bcd1601a6b47d35e17ecdb15d8 | Shell | 278 | 8 | #!/bin/bash
cd /home/sfeng77/jobs/EAA/downstream/GSEA/random_SNP/scripts/output_gene_list/top_outliers/iterate/GSEA_top_500_genes/more_permutation_reps/results
# script to submit dags for each environmental variable
for dag in $(ls */split_*)
do
condor_submit_dag $dag
done |
a0f90a5c30192231d4e3f14c4a0ae3cdc32e11d56bab0febefd13f63e2c657e2 | Shell | 279 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../../data"
echo -e "Running ./ex_MMEnergy test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb"
./ex_MMEnergy test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb
|
3aaab17e75406f251b1bb1449382ab6f6fc50961fbb2a5f159cbc1c529ffe999 | Shell | 280 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
for i in 2gb1 1rrx 5l3z 5lpc
do
echo -e "# Running ./ex_cabsbb_representation test_inputs/"$i".pdb"
./ex_cabsbb_representation test_inputs/$i.pdb > outputs_from_test/$i-cabsbb.pdb
done
|
7519185bef86126005ee8d8841b48321f46632f1d09b5ee92fa058fe653cdc61 | Shell | 280 | 12 | #!/bin/bash
STAGES='color-correction normalization registration puncta-extraction'
stage_idx=2
for s in ${STAGES}; do
./runPipeline.sh -y -P -e ${s} | tee run-stage${stage_idx}-${s}-perf.log
mv logs logs-stage${stage_idx}-${s}
stage_idx=$(( $stage_idx + 1 ))
done
|
8a3eee331ce94a67a9c898cdd8ccc5c738b19dac8fabeb5169044192d4ac3e88 | Shell | 280 | 11 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=5:00:00
#SBATCH --job-name=sc_enhanced
#SBATCH --account=proj102
#SBATCH --partition=prod
#SBATCH --output=logs/reliab_all
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
python -u compute_reliab_basic.py |
002503c98330e0d9715eaf0a74d385d3a2a0aca7533184d10c0227539b7b925c | Shell | 281 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo "#Running ./ap_aligned_pdb 1uox_1uox_1.pir 1uox.pdb 1uox.pdb"
./ap_aligned_pdb test_inputs/1uox_1uox_1.pir test_inputs/1uox.pdb test_inputs/1uox.pdb
mkdir -p outputs_from_test
mv query.pdb tmplt.pdb outputs_from_test |
f312be900b8c750da6621b7b62b54c635182dcaaf4dfbff27ac402ec72fd459f | Shell | 281 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_selection_protocols test_inputs/5edw.pdb"
./ex_selection_protocols test_inputs/5edw.pdb
echo -e "Running ./ex_selection_protocols test_inputs/3dcg.pdb"
./ex_selection_protocols test_inputs/3dcg.pdb
|
25ee968938ce715b18499cab492a2ff119362fa1994964bc02607b9aa607b8ae | Shell | 282 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "Running: ./ap_reorder_profile_columns test_inputs/d1or4A_.asn1"
./ap_reorder_profile_columns test_inputs/d1or4A_.asn1 > d1or4A_reordered.txt
mv d1or4A_reordered.txt outputs_from_test
|
b29cf02168b8f528c5560460d73cf43e1e6386e5bc32047c859088502d042472 | Shell | 282 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../../data"
echo "Running: ./ex_MMNonBonded test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb"
./ex_MMNonBonded test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb
|
499b60b53397600ae88d66b792ecbf31e6fe9198d3e3ce23e95682de06746414 | Shell | 283 | 15 | #!/bin/sh
#SBATCH --partition=shared-gpu
#SBATCH --gpus=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --time=12:00:00
module load GCCcore/8.2.0 Singularity/3.4.0-Go-1.12
OPENPOSE_SIMG=audio.simg
CMD="python train_net.py"
srun singularity exec --nv $OPENPOSE_SIMG $CMD
|
8b4985eb5857ce120ec373014278152f859c2d7978d0545bfe3937a12bd9edb6 | Shell | 283 | 11 | #!/bin/bash
for FOLDER in *; do
if [ -f $FOLDER/test_all.sh ]; then
cd $FOLDER
./test_all.sh
[ $? -eq 0 ] || exit 1
sleep 1
cd ..
fi
done
echo -e "\n-----------------------------------\n| Successfully ran all unittests. |\n-----------------------------------" |
ca3cce7503a973a108ab4451be3191f31457e7b50459c52cf9e17cf59a1e2f0f | Shell | 283 | 9 | #!/usr/bin/env bash
## autobuild.sh: automatically rebuild mansucript outputs and the webpage when content changes
## Depends on watchdog https://github.com/gorakhargosh/watchdog
watchmedo shell-command \
--wait \
--command='bash build/build.sh && manubot webpage' \
content
|
1ece2bac5bcf20495e2e6c1e39e0072b1b647f763a5ded6ca30e8207968f2f35 | Shell | 284 | 15 | #!/bin/sh
#SBATCH --partition=shared-gpu
#SBATCH --gpus=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --time=12:00:00
module load GCCcore/8.2.0 Singularity/3.4.0-Go-1.12
OPENPOSE_SIMG=audio.simg
CMD="python prediction.py"
srun singularity exec --nv $OPENPOSE_SIMG $CMD
|
29d498e3766c6685c6d4d98b2950f99ff6284f7f87f7e5ee017addb10c73d3e0 | Shell | 284 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 caonly_multimodel.py test_inputs/cat_list o.pdb"
python3 caonly_multimodel.py test_inputs/cat_list o.pdb
mkdir -p outputs_from_test
mv o.pdb outputs_from_test
|
0c200bfe23d22de704d954e97252f91ee202366d6081fa6c20f34048247538b7 | Shell | 285 | 5 | ARGS="cohort_csv='`pwd`/tutorials/tutorial2/cohort.csv';"
ARGS="$ARGS config_path='`pwd`/tutorials/tutorial2/mappers_adv.json';"
ARGS="$ARGS output_dir='`pwd`/results/tutorial2_mappers_adv';"
ARGS="$ARGS data_root='`pwd`';"
matlab -nodesktop -r "$ARGS run('code/analysis/run_main.m')"
|
17a917138596e12f3e83385f7f5e7338bce1628dbfb640b5d460834df96d4134 | Shell | 285 | 11 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=22:00:00
#SBATCH --job-name=sc_enhanced
#SBATCH --account=proj102
#SBATCH --partition=prod
#SBATCH --output=logs/sc_enhanced
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
python -u simplex_counts_enhanced.py |
39ac3113e67b5c5b991e8ddb93c70a2315ff943198e2833d9695dc1e6d0891c6 | Shell | 287 | 5 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../../data"
echo -e "Running ./ex_MMBondEnergy test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb"
./ex_MMBondEnergy test_inputs/amber03_atoms.par test_inputs/amber03_ffbonded.itp test_inputs/2gb1.pdb
|
4a271bcf373c3101133348f0ee0338273aa2c9cf6f292daf84c1e652ef44f95e | Shell | 287 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
for pdb in test_inputs/*model*pdb
do
echo -e "#Running ./ap_Crmsd test_inputs/2gb1.pdb" $pdb
./ap_Crmsd test_inputs/2gb1.pdb $pdb
done
echo -e "#Running ./ap_Crmsd test_inputs/1cey.pdb"
./ap_Crmsd test_inputs/1cey.pdb
|
3d3018f536cd5f18e4a47f0bd7f26ae172a151cf25dc5ee070888f8005be09f6 | Shell | 288 | 8 | #!/usr/bin/env bash
CUDA_VISIBLE_DEVICES=2 ./test_expr.py \
-f ../../data/test_sequences.fa.gz \
-o ./test_bert.exprtop20.300bp.sample100.hidden512.clu50.nonfreeze \
--flank 150 \
--model_path ./train_bert.exprtop20.300bp.sample100.hidden512.clu50.nonfreeze \
--batch_size 128
|
e7bb4647b2aef68b22b8e5a2b30de80bc80194657854785d46e550e195e0fa77 | Shell | 288 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 hhpred_to_modeller.py test_inputs/CYP51F.hhpred"
python3 hhpred_to_modeller.py test_inputs/CYP51F.hhpred 1 2
mkdir -p outputs_from_test
mv *.pir outputs_from_test/
|
fa28f817db666fa45b5cfea9c61c8c08a252c231f69f98b017c4857e064c9cfe | Shell | 289 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 pdb_to_fasta.py test_inputs/2kwi.pdb test_inputs/4mcb.pdb test_inputs/5edw.pdb"
python3 pdb_to_fasta.py test_inputs/2kwi.pdb test_inputs/4mcb.pdb test_inputs/5edw.pdb
|
fa9b65095d132d7fd276b9df01b9ebd2cd129eab088d55dd35be8887af21abc1 | Shell | 289 | 14 | #!/usr/bin/env bash
# Halt on error
set -e
OUTDIR="./results-v1"
SEED=123456789
LEXP="data/LearningExp_190501_S5_001_log.txt"
echo "Seed: $SEED"
echo "Starting run with experiment data: $LEXP"
python3 train.py --as_humans "$LEXP" --seed "$SEED" --debug --iterations 5 --outdir "tmp/"
|
fcedf01547f87dd52b228e2341e82c23959340c083707aef90b3bce23b6d9309 | Shell | 290 | 6 | mkdir -p output/vis/scannet/scans
cd output/vis/scannet/scans
# you can also download the scene0000_00.zip manually through
# link: https://caiyun.139.com/m/i?1A5CvaOo7hbTa password: bLE7
wget https://cvg-data.inf.ethz.ch/nice-slam/vis/scannet/scans/scene0000_00.zip
unzip scene0000_00.zip |
db713ee4b4a43ef4000f298907006392bb730a5039ca837f09d5cbba7bd5214d | Shell | 292 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./dssp test_inputs/2gb1.pdb"
./ap_dssp test_inputs/2gb1.pdb
echo -e "Running ./dssp test_inputs/5edw.pdb"
./ap_dssp test_inputs/5edw.pdb
echo -e "Running ./dssp test_inputs/3dcg.pdb"
./ap_dssp test_inputs/3dcg.pdb
|
da2ad0285f8c22f453251e541e4374cc298dcea31bb731e21258346df96988f8 | Shell | 293 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_local_BBQ_coordinates test_inputs/2gb1.pdb"
./ex_local_BBQ_coordinates test_inputs/2gb1.pdb
echo -e "# Running ./ex_local_BBQ_coordinates test_inputs/5edw.pdb"
./ex_local_BBQ_coordinates test_inputs/5edw.pdb
|
4fe07aab16a4981bb473bfe598fe9a9550efd6a98666af613134bef52ee14680 | Shell | 294 | 7 | #!/bin/sh
#
# Written by Minh Nguyen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd $CBIG_CODE_DIR/../
mkdir -p Standalone_Nguyen2020_RNNAD/
rsync -axD $CBIG_CODE_DIR/stable_projects/predict_phenotypes/Nguyen2020_RNNAD/ Standalone_Nguyen2020_RNNAD/
|
790db5e4bbf97387b0fe4a6fbcb87fe59db50c69ae93d34565913f94c825287e | Shell | 295 | 11 | PDIR=`pwd`
cd $PDIR/GEO1/WORK
${OVDIR}/scripts/read_civfl.py 2 > prep.out
cd $PDIR/GEO2/WORK
${OVDIR}/scripts/read_civfl.py 2 >> prep.out
cd $PDIR
rm -f ONEINT RUNFILE
${OVDIR}/scripts/seward_double-mol.py GEO1 GEO2 run >> prep.out
${OVDIR}/../bin/wfoverlap.x -f ciov_bin.in > ciov_bin.out
|
f5caad06248e09159ab7565d33194d0c21bea8b3e3fc0d5b3e7470bb16a60d0b | Shell | 295 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_Pdb test_inputs/2gb1.pdb"
./ex_Pdb test_inputs/2gb1.pdb
echo -e "Running ./ex_Pdb test_inputs/5edw.pdb"
./ex_Pdb test_inputs/5edw.pdb
echo -e "Running ./ex_Pdb test_inputs/3dcg.pdb"
./ex_Pdb test_inputs/3dcg.pdb
|
7ec0c3038b97f222a02b4bfa303ae314463d2c05d809d4e2b41b4054d4b1d608 | Shell | 297 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_ligand_clustering Clo test_inputs/file_list.txt 5 6.0 10.0 "
./ap_ligand_clustering Clo test_inputs/file_list.txt 5 6.0 10.0
mkdir -p outputs_from_test
mv clusters-10.00.txt clusters-6.00.txt outputs_from_test
|
af211dc72d41a03118b6f4e2fb0664460f8aaf0a4a76876946afc991420c9bb7 | Shell | 298 | 5 | ARGS="cohort_csv='`pwd`/tutorials/tutorial3/cohort.csv';"
ARGS="$ARGS config_path='`pwd`/tutorials/tutorial3/mappers.json';"
ARGS="$ARGS output_dir='`pwd`/results/tutorial3_mappers';"
ARGS="$ARGS data_root='`pwd`/tutorials/tutorial3/';"
matlab -nodesktop -r "$ARGS run('code/analysis/run_main.m')"
|
3e58da032eb07e92e4a6aebe7b98344655efeb9e2f9386370746221d3e29c8a1 | Shell | 300 | 6 | [ -f all.txt ] || find ~/data/enhanced_soma_images/out -name *pbd > all.txt
find ~/data/enhanced_soma_images/out -name *_neutube.swc | sed 's/_neutube.swc//' > done.txt
sort all.txt done.txt done.txt | uniq -u | shuf > unfinished.txt
wc -l unfinished.txt
mkdir -p list
split -n 3 unfinished.txt list/ |
5d44a5afb5a47f1b2de0f83cf52429b19a1eee8feb9852771810b630ac1d35f5 | Shell | 302 | 15 | #!/bin/bash
input=$1
output=$2
sample=$3
log=$4
#sed '/^>/ s/\//_/g; /^>/ s/$/_${sample}/' $input > $output 2> ${log}
#echo "gene_trans_map were created successfully!"
#!/bin/bash
sed "/^>/ s/\//_/g; /^>/ s/$/_${sample}/" $input > $output 2> $log
echo "Fasta header were modified successfully!"
|
962ea1189bb067c133a7af271fd270d563998b5b305f27e438459a974e299a2b | Shell | 302 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 pdb_info.py test_inputs/2kwi.pdb test_inputs/4mcb.pdb test_inputs/5edw.pdb"
python3 pdb_info.py test_inputs/2kwi.pdb test_inputs/4mcb.pdb test_inputs/5edw.pdb test_inputs/6xra.pdb
|
70e22d41cf285c5a96bc54f0b3562d0c090a25b236cf90f52136a7aec30e4022 | Shell | 304 | 20 | #/bin/bash
# $PRIMARYDIR and SCRADIR are set
COPY_DIR=$SCRADIR/TRAJ
PRIMARYDIR=$(pwd)
mkdir -p $COPY_DIR
cp -r $PRIMARYDIR/* $COPY_DIR
cd $COPY_DIR
$SHARC/sharc.x input
err=$?
cp $COPY_DIR/output.* $PRIMARYDIR
if [ ! $err == 0 ];
then
cp $COPY_DIR/QM/* $PRIMARYDIR/QM/
fi
rm -r $COPY_DIR
exit $err
|
81ea77a8fb512d0a92b78d4d2fdc4ec3357e47c04aee064eeba77c9f16b5b897 | Shell | 304 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 pdb_from_clustering.py test_inputs/clusters-10.00.txt Clo"
python3 pdb_from_clustering.py test_inputs/clusters-10.00.txt Clo
mkdir -p outputs_from_test
mv c*.pdb outputs_from_test/
|
fb2eb06afa5b73d09eed0c8886544402ad42efb528ed431fda11bd79b0f9d33c | Shell | 304 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_ligand_contacts test_inputs/5edw.pdb TTP 3.5"
./ap_ligand_contacts test_inputs/5edw.pdb TTP 3.5
echo -e "# Running ./ap_ligand_contacts test_inputs/2kwi.pdb GNP 4.0"
./ap_ligand_contacts test_inputs/2kwi.pdb GNP 4.0
|
b4176da55e56574dd702a30f7c3db05215ec188ef49f5ccce6c2eb4d22d474b2 | Shell | 305 | 13 | #!/bin/bash
# Install required packages
pip install -r requirements.txt
# Download spike trains for TriDy
cd ./TriDy
curl -O https://zenodo.org/record/4290212/files/input_data.zip
unzip input_data.zip
for f in $(ls input_data/); do mv ${f} data; done
# Extract data
cd data && python extract_data.py
|
40ff8082ddd4f97a1961ce2d17c2b56b6364f185d8d3450ee45fbe318c005599 | Shell | 307 | 13 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=20:00:00
#SBATCH --job-name=other_metrics
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/other_metrics
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
python -u compute_other_metrics.py
echo "Exit code $?" |
eda9585075fdb36aee48d98d5f9e597769ffc2291098e1070c1f5f44b9dabd72 | Shell | 308 | 6 | mkdir -p Datasets
cd Datasets
# you can also download the Replica.zip manually through
# link: https://caiyun.139.com/m/i?1A5Ch5C3abNiL password: v3fY (the zip is split into smaller zips because of the size limitation of caiyun)
wget https://cvg-data.inf.ethz.ch/nice-slam/data/Replica.zip
unzip Replica.zip
|
467d0a48182e7bc6de4cd70b7ae5a433994e65a13824fafa96193172c481c207 | Shell | 309 | 7 | #!/bin/bash
echo -e "#Running ./ap_fit_VonMises_mixture test_inputs/THR_chi1.dat -1.05 30 0.0 30 1.05 30"
./ap_fit_VonMises_mixture test_inputs/THR_chi1.dat -1.05 30 -3.0 30 1.05 30
echo -e "#Running ./ap_fit_VonMises_mixture test_inputs/THR_chi1.dat 3"
./ap_fit_VonMises_mixture test_inputs/THR_chi1.dat 3
|
9fee2e1ff4cbecbdab1f11e9f8ba19b4a8770a5f74a88ae5bdc79ec1fe540974 | Shell | 309 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./ligand_crmsd_on_cofactor.py HEM 1YN test_inputs/*.pdb"
mkdir -p outputs_from_test
python3 ligand_crmsd_on_cofactor.py HEM 1YN test_inputs/*.pdb
mv 1YN-by-HEM.pdb ./1YN-by-HEM.pdb
|
e917843a45207e7b99ca4ff07ecb16616d0fb416d0618626d6884a946b6e7a11 | Shell | 310 | 16 | #!/bin/bash
path2bedtools=/hpc/hub_oudenaarden/avo/bin/bedtools2/bin/
if [ $# -ne 1 ]
then
echo "Please, give:"
echo "1) input bam file"
echo "2) output file"
exit
fi
${path2bedtools}/bamToBed -i $1 -split | awk -F '\t|:' '{col=NF; cell=col-2; umi=col-4; print $0"\t"$cell"\t"$umi}' > $2
|
1038d08caf6fde8c2ed7228cc1457e51f3ba7f3a00b5286bc372a6847eea3d4c | Shell | 313 | 10 | #!/bin/bash
echo -e "Running ./ex_chi2_independence_test"
./ex_chi2_independence_test
echo -e "Running ./ex_chi2_independence_test 4 1.51"
./ex_chi2_independence_test 4 1.51
echo -e "Running ./ex_chi2_independence_test test_inputs/chi2_test_data.txt"
./ex_chi2_independence_test test_inputs/chi2_test_data.txt
|
53764f1183c047a00b4bf597fc15a71d042bcf730ef5d1929e70f33e1573716a | Shell | 313 | 8 | #!/bin/bash
for i in `seq 0 25`;
do
printf -v cmd "%s" "relion_reconstruct --i ../../../../data/tutorials/synth_sumb/class/mbf_align_all/class_ap_r_ali_k$i""_split.star --o ../../../../data/tutorials/synth_sumb/class/mbf_align_all/dr_class_ap_r_ali_k$i"".mrc --angpix 2.62 --maxres 45"
echo $cmd
$cmd
done
|
8772891462e26b6ef172361ddd8c2e4b6555356aa6bec374546e5d9ff6ed5ec8 | Shell | 313 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test/
echo -e "# Running ./ex_REMC_Ar 512 0.5 10 1 100 100 105 110"
./ex_REMC_Ar 512 0.5 10 1 100 100 105 110
# Comment the line below to keep also trajectories from each replica
rm ar_tra-?.pdb
mv *.pdb *.dat outputs_from_test/
|
5ed1280cb24f81ef39c98dc8fa46ecd1c0b99b7470958a28504163a472f4d068 | Shell | 314 | 11 | PDIR=`pwd`
cd $PDIR/GEO1/WORK
${OVDIR}/scripts/read_civfl.py 2 0.99980001 -ms 0.5 > prep.out
cd $PDIR/GEO2/WORK
${OVDIR}/scripts/read_civfl.py 2 0.99980001 -ms 0.5 >> prep.out
cd $PDIR
rm -f ONEINT RUNFILE
${OVDIR}/scripts/seward_double-mol.py GEO1 GEO2 run >> prep.out
${OVDIR}/../bin/wfoverlap.x > ciovl.out
|
ae4a64af16b51952d2a2e21a10bb9dbb4b505f8529e81bab024635d92a5151fc | Shell | 314 | 7 | #!/bin/bash
#SBATCH --job-name=movements # Task name
#SBATCH --error=/home/intoumanis/sugar/code/logs/movements.err # Error output file
#SBATCH --output=/home/intoumanis/sugar/code/logs/movements.out # Output file
module load R/v4.0.3 # Load R module
srun Rscript check_movements.R # Run Rscript with file test.r |
7161f1eb24b552a1be62ff1ef1e6ab4006e289659c200dd3d507f12e1e5497fc | Shell | 316 | 5 | #!/bin/bash
wget https://flir.netx.net/file/asset/54401/original/attachment/spinnaker_python-3.1.0.79-cp310-cp310-linux_x86_64.tar.gz
mkdir PySpin
tar -xvf spinnaker_python-3.1.0.79-cp310-cp310-linux_x86_64.tar.gz -C PySpin
python3 -m pip install --user PySpin/spinnaker_python-3.1.0.79-cp310-cp310-linux_x86_64.whl
|
d47ff00e3cca375d1a49ffe561d6025b969ea22c8f59f559b3c221686cf80b88 | Shell | 317 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_filter_msa test_inputs/conservation_test_msa.aln"
./ap_filter_msa test_inputs/conservation_test_msa.aln
echo -e "#Running ./ap_filter_msa test_inputs/CYP109B1.aln M5R670_9BACI"
./ap_filter_msa test_inputs/CYP109B1.aln M5R670_9BACI
|
43845c7915e61f92b1ee07285382866657e128adc229028e8a321c5d48890c9e | Shell | 318 | 13 | partition=defq
shape=circle
timestep=0.01
eval=70000000
for refinement in 0 1 2 3
do
python3 main.py --submit-ex3 --partition=$partition mechanotransduction --mesh-folder meshes-mechanotransduction/${shape}_refined_${refinement} --time-step $timestep --e-val $eval --axisymmetric --well-mixed
sleep 5
done
|
d63c930f7cc7606e27d2f676080393aa2292fb0620d559644065ce2f881c0f74 | Shell | 318 | 17 | #!/bin/bash
set -ex
## Installing Anaconda
if [ -d "soft/miniconda3" ]
then
rm -r soft/miniconda3
else
mkdir -p soft
fi
sysPath=$PWD
cd /tmp
wget --no-check-certificate https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash ./miniconda.sh -b -p $sysPath/soft/miniconda3
|
7f34b1794bd31cdbccb59ebb73dcfbe144942dda3508ed872fea562f7f427fe8 | Shell | 319 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_crmsd_on_common_subset -in:pdb:native=6h60.pdb -select:chains=A -select:bb -in:pdb=6h60_A_rebuilt.pdb"
./ap_crmsd_on_common_subset -in:pdb:native=test_inputs/6h60.pdb -select:chains=A -select:bb -in:pdb=test_inputs/6h60_A_rebuilt.pdb
|
dd24525b45741538e1a6d06b963760e1bc7de70772eb742a42f7c3dfb42e33ed | Shell | 320 | 12 | #!/bin/sh
#SBATCH --ntasks=8
#SBATCH -N 1
#SBATCH --ntasks-per-node=10
#SBATCH --mem=80G
#SBATCH --partition=medium
#SBATCH -o logs/slurm/slurm-%j-%a.out
#SBATCH -e logs/errors/error-%j-%a.out
#SBATCH -t 2-00:00:00
module load python
python data_processing_granger_causality_preset_hpc.py $SLURM_ARRAY_TASK_ID $1 $2 $3
|
564069df7b9e83f771f6335c757cb851d7b6106205c569aa19c4375dfcf15b35 | Shell | 321 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_local_coordinates_three_atoms test_inputs/2gb1.pdb"
./ex_local_coordinates_three_atoms test_inputs/2gb1.pdb
echo -e "Running ./ex_local_coordinates_three_atoms test_inputs/5edw.pdb"
./ex_local_coordinates_three_atoms test_inputs/5edw.pdb... |
e2359eafd33bc3ec25ce3c04f35e71fe020d90c9cc475b8541bb1b3c8d622cf2 | Shell | 321 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_Residue test_inputs/2gb1.pdb"
./ex_Residue test_inputs/2gb1.pdb
echo -e "Running ./ex_Residue test_inputs/5edw.pdb"
./ex_Residue test_inputs/5edw.pdb
echo -e "Running ./ex_Residue test_inputs/3dcg.pdb"
./ex_Residue test_inputs/3dcg.pdb ... |
08cb5a66b6ffec8b1242bcca4973e8be6455a2e02f7e0e7599635da00374d1a3 | Shell | 322 | 14 | #!/bin/bash
#
# This script will reformat bed files for LAVA.
# Add rownumbers
for i in *.bed; do
awk 'NR>1 {print $1, $2, $3}' $i > tmp && mv tmp ${i}
nl -n ln $i > tmp && mv tmp ${i}
awk '{gsub("chr", "", $2); print}' $i > tmp && mv tmp ${i}
echo -e "LOC CHR START STOP" | cat - $i > tmp && mv tmp ${i};
don... |
0b8aa44b39b178282aac3b79f61dae7f767ae3164b7f472b5b3cf68b4b7a263b | Shell | 322 | 5 | #!/bin/sh
model="configs/abide_schaefer100/TUs_graph_classification_ContrastPool_abide_schaefer100_100k.json"
echo ${model}
python main.py --config $model --gpu_id 0 --node_feat_transform pearson --max_time 60 --init_lr 1e-2 --threshold 0.0 --batch_size 20 --dropout 0.0 --contrast --pool_ratio 0.5 --lambda1 1e-3 --L ... |
df437c769fb5e5d0ea170a0f18008c759be503db3fecaf151b3ee868a43bb84e | Shell | 322 | 26 | #/bin/bash
# $PRIMARYDIR and SCRADIR are set
COPY_DIR=$SCRADIR/TRAJ
PRIMARYDIR=$(pwd)
export PATH=$SHARC:$PATH
mkdir -p $COPY_DIR
cp -r $PRIMARYDIR/* $COPY_DIR
cd $COPY_DIR
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$orca
$orca/orca orca.inp > orca.log
err=$?
cp $COPY_DIR/* $PRIMARYDIR
rm -r $COPY_DIR
exit $err
... |
4486964f5e7453c3d05085b34693faa8151799d09083126c4ba9c192b9f442ee | Shell | 325 | 16 |
source config.sh
source samples.sh
for i in ${SAMPLES[$(($LSB_JOBINDEX - 1))]};
do
$bbduk -Xmx7g t=4 \
in1=fastq/trim/${i}_R1trim.fastq.gz \
in2=fastq/trim/${i}_R2trim.fastq.gz \
out1=fastq/trim/${i}_R1trim125.fastq.gz \
out2=fastq/trim/${i}_R2trim125.fastq.gz \
ftr=124 \
minlength=125
d... |
f7da67db751e490b02a634898c3dc4089e5e85399288de852e645658781f90e6 | Shell | 327 | 13 | #!/bin/bash
# ------- Path Setup -------
source ~/.bashrc
# ------- Package Setup -------
conda activate quacc
conda install -c conda-forge openbabel
pip install uv
uv pip install -r tests/requirements.txt "quacc[dev] @ ."
# ------- Request and run Slurm job -------
salloc -N 1 -n 32 -t 00:10:00 tests/jenkins/hpc_te... |
7ffbd2f9eca25160c2d55786d799b0e6c3abd770c2934464bc9e6c362d2f2ca5 | Shell | 330 | 15 | #!/bin/bash
#SBATCH --account=def-khill22
#SBATCH --cpus-per-task=1
#SBATCH --gpus-per-node=1
#SBATCH --mem=64000M
#SBATCH --time=1:00:00
module avail python
module load python/3.10
#virtualenv --no-download ENV
source ENV/bin/activate
#pip install -r requirements.txt
python3 src/cluster.py --dataset="01_Cypriniforme... |
e1b25e3c0f8ab72d104aefed2885e32e9c9e6e5326b259ab4f1a52912634ec30 | Shell | 330 | 14 |
# annotate variants to genes for MAGMA gene-based analysis
# build: hg38
# gene window: 100 Mb
cat raw_data/NCBI38.gene.loc | \
awk '{print $6, $2, $3, $4, $5, $1}' \
> tmp/hg38.gene.loc
magma \
--snp-loc data/adc/adc_np.bim \
--gene-loc tmp/hg38.gene.loc \
--annotate window=10 \
--out data/adc/snp_gene_... |
e691ceaf042e527e6bd166e9701ba8bdfbac4e546dc028d17908a0bd8cd5a435 | Shell | 331 | 3 | #!/bin/bash
gwas_snp=/hpc/users/songl05/PF_25BR/data/gwas_sig.avinput
/sc/arion/projects/roussp01b/resources/software/annovar/table_annovar.pl $gwas_snp /sc/arion/projects/roussp01b/resources/software/annovar/humandb/ -buildver hg38 -out /hpc/users/songl05/PF_25BR/data/gwas_sig.anno -protocol refGene -operation gx -n... |
0d3c8ca9323832495ca812612a613dba4d69014d1d335f1a03250c7db80e3bad | Shell | 332 | 17 | #!/bin/bash
#SBATCH --job-name="Test1FMM3D"
#SBATCH -D .
#SBATCH --output="test_1.out"
#SBATCH --error="test_1.err"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=16G
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=2:00:00
module purge
module load matlab/R2023a
matlab -nodisplay -nosplash -r ... |
58979f5b4e149ad66b6e7f27c305435bc41677eb9cc7a116c435cc3ff98d60e0 | Shell | 332 | 17 | #!/bin/bash
#SBATCH --job-name="Test2FMM3D"
#SBATCH -D .
#SBATCH --output="test_2.out"
#SBATCH --error="test_2.err"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=16G
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=2:00:00
module purge
module load matlab/R2023a
matlab -nodisplay -nosplash -r ... |
8c9269548f94dd275aaac6e9e47a5321785fa04e0ba843eeddad4207bf979588 | Shell | 332 | 6 | export OMP_NUM_THREADS=1
$OVDIR/../bin/wfoverlap.x -f ciovl.in > ciovl.out.1thr || exit $?
$OVDIR/../bin/wfoverlap.x -f ciovl.in.lumorb > ciovl.out.lumorb || exit $?
export OMP_NUM_THREADS=2
$OVDIR/../bin/wfoverlap.x -f ciovl.in > ciovl.out.2thr || exit $?
$OVDIR/../bin/wfoverlap.x -f ciovl.in.direct > ciovl.out.direct... |
e1ba6511f10a9307c17fb034ffe5173f438b01331c990aa9b4e4d0b3ad03529e | Shell | 334 | 22 | #/bin/bash
# $PRIMARYDIR and SCRADIR are set
COPY_DIR=$SCRADIR/TRAJ
PRIMARYDIR=$(pwd)
mkdir -p $COPY_DIR
cp -r $PRIMARYDIR/* $COPY_DIR
cd $COPY_DIR
. $SHARC/sharcvars.sh
$SHARC/pysharc_lvc.py input
err=$?
cp $COPY_DIR/output.* $PRIMARYDIR
if [ ! $err == 0 ];
then
cp $COPY_DIR/QM/* $PRIMARYDIR/QM/
fi
rm -r $COPY_... |
552cbe73c53a9504299d3b36622e6382e91e48de00223691081a923ac8208c3f | Shell | 335 | 13 | #!/bin/sh
#SBATCH --job-name=createevents
#SBATCH --output=/home/intoumanis/sugar/code/logs/createevents.out
#SBATCH --error=/home/intoumanis/sugar/code/logs/createevents.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=01:00:00
module load R
srun Rscript create_events_in_volumes.R
e... |
97383336ccfbee0fae44b102564c1bb0692edf72e6a75b01ed9874acf17700d5 | Shell | 335 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 ./list_pdb_ligands.py test_inputs/5edw.pdb"
python3 ./list_pdb_ligands.py test_inputs/5edw.pdb
echo "#Running python3 ./list_pdb_ligands.py test_inputs/5ofq.pdb"
python3 ./list_pdb_ligands.py test_... |
d5f1d13d16d7d71c79512ab71a35297360804fa407e1b8e74b91925c737e90ec | Shell | 335 | 17 | #!/bin/bash
./pretrain_expr.py \
--fasta ../../data/train_sequences.fa.gz \
--resume \
--batch-size 128 \
--device 0 \
--num-hidden-layers 3 \
--fraction-per-epoch 0.2 \
--num-workers 3 \
-lr 0.0001 \
--hidden-size 512 \
--num-attention-heads 8 \
--flank 200 \
-o bert.exprtop20.480bp.hidden512... |
2978fecc4932bc09d459ea6c04dae73484bbd14e8500620745ce0cf68f9ce890 | Shell | 336 | 13 | CUDA_VISIBLE_DEVICES=6 python -m torch.distributed.launch \
--nproc_per_node=1 \
--master_port=$((RANDOM + 10000)) \
start.py \
--dataset Geometry3K \
--use_MLM_pretrain
CUDA_VISIBLE_DEVICES=6 python -m torch.distributed.launch \
--nproc_per_node=1 \
--master_port=$((RANDOM + 10000)) \
start.py \
--dataset PGPS9K \
--... |
3fd925cf42f71d33d3a2a42df35a477fc731ed880bdacd634a7fb07d55a77825 | Shell | 336 | 10 | #!/bin/bash
# OTB2015
mkdir OTB2015 && cd OTB2015
baseurl="http://cvlab.hanyang.ac.kr/tracker_benchmark"
wget "$baseurl/datasets.html"
cat datasets.html | grep '\.zip' | sed -e 's/\.zip".*/.zip/' | sed -e s'/.*"//' >files.txt
cat files.txt | xargs -n 1 -P 8 -I {} wget -c "$baseurl/{}"
ls *.zip | xargs -n 1 unzip
rm -r ... |
6874133272aef9eb2b5a704d75d5bf600c7c9fb966ecc1c2ac78458c6526fa24 | Shell | 337 | 13 | #!/bin/bash
set -ex
## Installing third parties packages
# Install latest DisPerSe from source
wget --no-check-certificate https://github.com/thierry-sousbie/DisPerSE/archive/refs/heads/master.tar.gz
mv master.tar.gz install/disperse/latest/sources/disperse_latest.tar.gz
cd install/disperse/latest
chmod u+x install.s... |
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