sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e3f3c1ebd8e2080ed1f91d645ead32f2ec84004b44800efe30a113cf080a5e5d | Shell | 337 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_Structure test_inputs/2gb1.pdb"
./ex_Structure test_inputs/2gb1.pdb
echo -e "# Running ./ex_Structure test_inputs/5edw.pdb"
./ex_Structure test_inputs/5edw.pdb
echo -e "# Running ./ex_Structure test_inputs/3dcg.pdb"
./ex_Structure test... |
f96d2e51514b0077f4c319c85fb82834e45c3b88396c06592d7ff0c742304437 | Shell | 337 | 7 | ls list/* | while read list; do
# qsub -l walltime=48:00:00 -l nodes=1:ppn=100 -N ntb -j oe -o /dev/null -d . -V run.sh
bash run.sh $list
done
find /home/vkzohj/data/enhanced_soma_images/out -name *_neutube.swc -exec cp -p --parents -r -u {} ~/public/projects/230k/ntb \;
mv home/vkzohj/data/enhanced_soma_images... |
0ab8aa02bb92aa7e661f2891e9fd2f8f3d578dd863a77f3ce0b94b81c2371a26 | Shell | 339 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_sasa test_inputs/2gb1.pdb"
./ap_sasa test_inputs/2gb1.pdb 1.6 > 2gb1_sasa.pdb
echo -e "Running ./ap_sasa test_inputs/5edw.pdb"
./ap_sasa test_inputs/5edw.pdb 2.2 > 5edw_sasa.pdb
mkdir -p outputs_from_test
mv 2gb1_sasa.pdb 5edw_sasa.pdb ... |
bc223c00a7a81b2091ab05d3c914b21397b796b03e8eabc6affa07b1f1edf1bd | Shell | 339 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ex_structure_to_molecule test_inputs/4rm4.pdb HEM"
./ex_structure_to_molecule test_inputs/4rm4.pdb HEM
echo -e "# Running ./ex_structure_to_molecule test_inputs/1lw5.pdb LLP"
./ex_structure_to_molecule test_i... |
530dbeb0b3959ded97c66c1ec044fdd94ce672b562d2e2dc4b3b5a51e02c6397 | Shell | 342 | 6 | #!/bin/bash
fileid="1oyknOulq_j0w9kzOKKIHdTLo5HphT99h"
filename="default_model.zip"
curl -c ./cookie -s -L "https://drive.google.com/uc?export=download&id=${fileid}" > /dev/null
curl -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename}
un... |
cdbdeea797f0c769265f59bd8c46647b53d6998c12164622772078caa9155a36 | Shell | 342 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../../data" #../../../../../data"
# Here we tabulate R13 potential for ALA(helical)-HIS(helical) in CABS model
echo -e 'Running ./ex_MeanFieldDistributions "forcefield/cabs/R13_cabs.dat" 0.02 2.0 15.0 AD.HH'
./ex_MeanFieldDistributions "forcefield/cabs/R13_cabs.dat"... |
f12a6d74e93f1e0c3716ef22dfd767bc946ddb901fafc43ad1b69dd119505793 | Shell | 342 | 9 | #!/bin/bash
#PBS -N tan_tracking_V100
#PBS -l nodes=1:ppn=8:gpus=1:V100_32,mem=8gbs,walltime=4:00:00
run=$1
tag=$2
cd /scratch/tantan132/extended-event-modeling/
source activate sem-pysot-37-new
python tracking/tracking_to_correct_label.py -c configs/config_tracking_to_correct_label.ini --run $run --tag $tag 2>&1 | te... |
5843a3006b606f5aef87ba7e1154abd513bb3174edebba404dcf93c32e28ae0c | Shell | 343 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./find_rings.py test_inputs/MES_ideal.pdb"
python3 ./find_rings.py test_inputs/MES_ideal.pdb
echo -e "#Running python3 ./find_rings.py test_inputs/9ZB_ideal.pdb"
python3 ./find_rings.py test_... |
7f2682bbaeb197ae43498e61284ad0f3016e17816dcfd9daa06d407c30dcc000 | Shell | 343 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./check_structure.py test_inputs/3dcg.pdb"
python3 ./check_structure.py test_inputs/3dcg.pdb
echo -e "#Running python3 ./check_structure.py test_inputs/2gb1.pdb"
python3 ./check_structure.py... |
2df7d73b0f2ace1b34331c555e3b7eb7200b26cb28cb26f496698ed34ea93144 | Shell | 344 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 betastructures_graph.py test_inputs/2gb1.pdb"
python3 betastructures_graph.py test_inputs/2gb1.pdb
echo "#Running python3 betastructures_graph.py test_inputs/5edw.pdb"
python3 betastructures_graph.... |
97933d385441ecebd0a3251555d3bc6df29ccd58e3d05a74ff946594914c9091 | Shell | 344 | 17 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=6:00:00
#SBATCH --exclusive
#SBATCH --job-name=correlations
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/add_rc
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
echo `date`
python -u add_rc_manipulations.py
echo `da... |
39e52be6f4eb7699292c1b8aa7a040a8d1a18329c72d898adb8df04ab94ce45b | Shell | 346 | 16 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=24:00:00
#SBATCH --job-name=simplex_lists
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/simplex_lists_max
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
#python -u run_simplex_lists.py
python -u run_max_simplex_lists... |
e849d86f616371320ebfb844a787ecf9730d2488b82f3207877b187f71931440 | Shell | 346 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p outputs_from_test
echo "#Running python3 ./score_rms_plot.py -f test_inputs/1pgxA-abinitio.fsc test_inputs/1pgxA-abinitio-bis.fsc"
python3 score_rms_plot.py -f test_inputs/1pgxA-abinitio.fsc test_inputs/1pgxA-abi... |
851c56ddfbf8a7eb8b0a103f9b6a7aaa4ff0c3ae433ce2c2a096381f00fea213 | Shell | 350 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N stemness_brca
#PBS -q ct160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ERBB2' 'ESR1' 'MKI67' 'PGR' 'PLAU')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./source/stemness.sh ${BioMarkers[${... |
d80c568da41a153778cd8ede2a89e0b35794aad717b6fe302757469fea82baf8 | Shell | 351 | 10 | #! /usr/bin/bash
SCRIPT_FILE_NAME="$0"
SCRIPT_FILE_PATH=$(realpath "${SCRIPT_FILE_NAME}")
SCRIPT_FOLDER_PATH=$(dirname "${SCRIPT_FILE_PATH}")
cd "${SCRIPT_FOLDER_PATH}"
/groups/scicompsoft/home/taylora/.miniconda3-blurgh/envs/apt_20230427_tf211_pytorch113_ampere/bin/python \
./run-coco-from-apt-training-with-db-w... |
967563ecb69a234112a8bec06d718903ae3f12cc40288b0d89c3164d48d97b29 | Shell | 355 | 9 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "# Running ./ap_Hexbins " > outputs_from_test/normal_2d.dat
./ap_Hexbins >> outputs_from_test/normal_2d.dat
echo -e "# Running ./ap_Hexbins test_inputs/LEU_chi1_chi2_rad.dat 3.6" > outputs_from_test/LEU_rotamers.dat
./ap_Hexbins test_inputs/LEU_chi1_chi2_rad.dat 3.6 >> o... |
13201d23bcb6bf0dd80fce397378239e2ad7f9669cac0fa4761320e5d90eda93 | Shell | 356 | 8 | #!/bin/bash
# Run the executable jar for tracking with three input parameters:
# input_sequence output_sequence config_file
# Prerequisities: CUDA-compatible GPU, Ubuntu 18.04, Java Runtime Environment 8
java -jar elephant-ctc-0.0.1-SNAPSHOT.jar "../${dataset}/${seq}" "../${dataset}/${seq}_RES-${config}" "run_config... |
402b508f2991c53e290562cfc6300ca789e8893f18e649aba88c55d9e767e0d2 | Shell | 356 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N nonstemness_brca
#PBS -q ct160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ERBB2' 'ESR1' 'MKI67' 'PGR' 'PLAU')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./source/nonstemness.sh ${BioMark... |
8b1c7da519ee05978122c21083b583182799f031636e8aee0f19c2d0427f9b46 | Shell | 356 | 14 | #!/bin/bash -l
#SBATCH --time=5:00:00
#SBATCH --ntasks=1
#SBATCH --mem=225g
#SBATCH --mail-type=ALL
#SBATCH --mail-user=west0883@umn.edu
#SBATCH -p ram1t
#SBATCH --array=539
# Use '%A' for array-job ID, '%J' for job ID and '%a' for task ID
module load matlab
matlab -nodisplay -nodesktop -r "SVD_forMSI_func... |
ee1f7801849b0aa5bf87d308c1398febe536a0929b0e8f687f9821eebe13cbda | Shell | 356 | 14 | #!/bin/bash -l
#SBATCH --time=2:00:00
#SBATCH --ntasks=1
#SBATCH --mem=200g
#SBATCH --mail-type=ALL
#SBATCH --mail-user=west0883@umn.edu
#SBATCH -p ram1t
#SBATCH --array=109
# Use '%A' for array-job ID, '%J' for job ID and '%a' for task ID
module load matlab
matlab -nodisplay -nodesktop -r "SVD_forMSI_fun... |
f3e79231439540ad97564860db28526afd256b4f02244b000cc7928a5102792e | Shell | 357 | 14 | #!/bin/bash
# ------- Path Setup -------
source ~/.bashrc
# ------- Package Setup -------
module load anaconda3/2024.10
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... |
82476b7388c83a8c2359f67f09eab0f40434b5f685b97dd24336d4cca8907689 | Shell | 358 | 14 | #!/bin/bash
#example: bash basic_benchmark_fq.sh ../testdata/bmdata/SRR976159_1.fastq.gz 66 fqgz_out
infile=$1
min=$2
outdir=$3
mkdir -p $3
time orfipy --min $2 --bed b --outdir $3 --between-stops $1
time orfipy --min $2 --dna d --pep p --outdir $3 --between-stops $1
time orfm -m $2 -t "$3/orfm_d" $1 > "$3/orfm_p"
t... |
4d9e747573321e06000cffc8a5b8e293b074afa8f78e38a0fc124b899abd4bfa | Shell | 361 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_MSAColumnConservation test_inputs/conservation_test_msa.aln"
./ap_MSAColumnConservation test_inputs/conservation_test_msa.aln
echo -e "#Running ./ap_MSAColumnConservation test_inputs/CYP109B1.aln M5R670_9BACI"
./ap_MSAColumnConservation... |
5a4703b2537a4f62daa25eb7075b2a4c5c333e2197175e76521f17380eaddbb4 | Shell | 362 | 9 | #!/bin/bash
base=$(pwd)
res_dir="${base}/results/figure4"
ARGUMENTS="++red_method=autoencoder ++base_dir=${base} ++hydra.run.dir=${res_dir} ++clustering.agglomerative.n_clusters=[7]
++testing.plot=false ++plotting.superfamily=null ++plotting.subfamily=null ++reload_families=true"
python pipeline/run_pipeline.py $A... |
6c81d43421b232b1748b4e61b8bb995e62277dd723b2f603a2852417ac02f1e9 | Shell | 362 | 18 | #!/bin/bash
folder="/etc/tucam/"
if [ ! -d "$folder" ]; then
mkdir "$folder"
fi
# copy the tucsen usb camera config file
cp tuusb.conf /etc/tucam
cp 50-tuusb.rules /etc/udev/rules.d
# copy the tucsen camera libraries
cp libphxapi-86_64.so /usr/lib
cp libTUCam.so /usr/lib
cp libTUCam.so.1 /usr/lib
cp libTUCam.so.1... |
375a19407778857b4b00cadd115bd47ed286c5be22c47bce3586db9701b41c19 | Shell | 365 | 17 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=10G
threads=1
if [ $# -ne 1 ]
then
echo "Please, give:"
echo "1) fastqfile to trim"
exit
fi
input==$1
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/trim.sh $1" | qsub -cwd -N trim-$1 -o trim-$1.out -e trim-$1.err -m eas -M ${email} -pe threade... |
3a11fa1550a8df846acfa64d893d4a60c81405fd1e47ee105989b9f4e19592cd | Shell | 365 | 14 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ap_MC_water 256 298 10 100"
./ap_MC_water 64 298 10 10
mv final.pdb start.pdb
echo -e "# Running ./ap_MC_water start.pdb 298 10 100"
./ap_MC_water start.pdb 298 10 10
rm -rf water.pdb start.pdb
mkdir -p outputs... |
54662bcc596eabf752c099ef4adbfc20ae3e0d00aeceeb4ccbf532b031602601 | Shell | 365 | 10 | #!/bin/bash
cd BigBrainWarp
source scripts/init.sh
# data-driven cytoarchitectural axis of DMN from BigBrain to fsaverage
dataDir=~/GitHub/DMN/output/
bigbrainwarp --in_space bigbrain --out_space fsaverage --wd $dataDir \
--in_lh $dataDir/tpl-bigbrain_hemi-L_desc-DMN.txt \
--in_rh $dataDir/tpl-bigbrain_hemi-R_... |
63ca569454b84fd06c82a37f3bc3781d28259fd94055a234b1934719b4f73a64 | Shell | 367 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_build_crystal test_inputs/5edw.pdb > 5edw_uc.pdb"
./ap_build_crystal test_inputs/5edw.pdb > 5edw_uc.pdb
echo -e "Running ./ex_Remark290 test_inputs/3dcg.pdb > 3dcg_uc.pdb"
./ap_build_crystal test_inputs/3dcg.pdb > 3dcg_uc.pdb
mkdir -p o... |
bbb6817e399e0592af7d8f0cc2b31ebdf2f95862bec979aa0d2658f0d5f61019 | Shell | 367 | 11 | #!/bin/bash
sudo apt update
# sudo apt install nvidia-driver-530
cd ~/Downloads
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb
sudo dpkg -i cuda-keyring_1.1-1_all.deb
sudo apt-get update
sudo apt-get -y install cuda
pip install cuda-python
pip install cupy-cud... |
d6d16254dca31346ab91077125b9112282d4b5a4ad65a800bfcedec7b0b47163 | Shell | 367 | 6 | export SHARC=/global/mai/SHARC_3.0_tests/install/sharc/bin
export PYSHARC=/global/mai/SHARC_3.0_tests/install/sharc/pysharc
export SHARCLIB=/global/mai/SHARC_3.0_tests/install/sharc/lib
export ANACONDA=/user/mai/anaconda/miniconda3/envs/pysharc_3.0_test
export PYTHONPATH=$SHARCLIB:$PYSHARC:$PYTHONPATH
export LD_LIBRARY... |
472acb121e3aee349dba770f23431a6e8e5103aaf0af17ac1d68b57b1ffc8799 | Shell | 368 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N stemness_luad
#PBS -q cf160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ALCAM' 'CADM1' 'EPCAM' 'HIF1A' 'PKM' 'PTK7' 'SLC2A1')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./source/stemness.... |
b779e823e6941f52436f7cd03d495d1e577b5468848a25e2d99d11dc51194da6 | Shell | 368 | 14 | #!/bin/sh
juliapath=`which julia`
compiled_code="./SimplicialTS/Simplicial.so"
nthreads=$1
input_file=$2
output_file_scaffold=$3
scaffold_flag=2 # Flag 1-> frequency, Flag 2 -> persistence
##Launching the code
time julia -J ${compiled_code} --threads ${nthreads} simplicial_multivariate.jl ${input_file} -s ${output... |
d9f3027323a86b64cf767b85a69f6a688bae4eff2200df9ce6988d4668127913 | Shell | 368 | 20 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=10G
threads=1
if [ $# -ne 1 ]
then
echo "Please, give:"
echo "1) fastqfile to trim"
exit
fi
input==$1
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/trim.sh $1" | qsub -cwd -N trim-$1 -o trim-$1.out -e trim-$1.err -m eas -M ${email} -pe threade... |
fbfbeae794065a3a7d2d289d83d589e7dde2b741bdb8705ebfbff5822434f94e | Shell | 368 | 18 | #!/bin/sh
prefix=$1
tmp=tmp.$$
exps="521 1279 2203 4253 11213 19937 44497 86243 132049 216091"
for mexp in $exps; do
compare=dSFMT.${mexp}.out.txt
command=${prefix}-M${mexp}
./$command -v > $tmp
if diff -q -w $tmp $compare; then
echo $command output check OK
rm -f $tmp
else
echo $command output c... |
b4247e17098d791f0f14b0119c4fa06ca6e711f33c50455761baee5284d21163 | Shell | 369 | 8 | #!/bin/sh
Rscript ../utils/5-regulator-stability-scregclust.R "pbmc"
Rscript ../utils/5-regulator-stability-wgcna.R "pbmc"
Rscript ../utils/5-regulator-stability-hdwgcna.R "pbmc"
Rscript ../utils/5-regulator-stability-ppcor.R "pbmc"
Rscript ../utils/5-regulator-stability-kmeans-grnboost2.R "pbmc"
Rscript ../utils/5-re... |
d6d030ad7232096e9785c7660cd3a476d300eeb09f2feedf3d402260be1783ab | Shell | 369 | 8 | #!/bin/sh
Rscript ../utils/5-regulator-stability-scregclust.R "wang"
Rscript ../utils/5-regulator-stability-wgcna.R "wang"
Rscript ../utils/5-regulator-stability-hdwgcna.R "wang"
Rscript ../utils/5-regulator-stability-ppcor.R "wang"
Rscript ../utils/5-regulator-stability-kmeans-grnboost2.R "wang"
Rscript ../utils/5-re... |
3b465067b6f62721aa754ddd4edf9825d16d683ef30b4efe3396705e61f6483e | Shell | 371 | 22 | #!/bin/bash
subj_ids=$1
ses=baselineYear1Arm1
if [ -z "$1" ]; then
echo
echo "Error: Missing list. Provide subject list w/o 'sub-' prefix in positon 1."
echo
exit 1
fi
n=0
cat $subj_ids | while read line ; do
sed -e "s|SUBJECT|${line}|g; s|SESSION|${ses}|g" ./templates/abcd_firstlvl.txt > ./batch_abcd/first${n... |
aafb5836836401a7b9892ac622b5d933a09dd344c5b85942eb158840abc1d234 | Shell | 371 | 15 | #!/bin/bash -l
#SBATCH --time=12:00:00
#SBATCH --ntasks=1
#SBATCH --mem=25g
#SBATCH --mail-type=ALL
#SBATCH --mail-user=west0883@umn.edu
#SBATCH -p ram256g
#SBATCH --array=1087,1088,1096
# Use '%A' for array-job ID, '%J' for job ID and '%a' for task ID
module load matlab
matlab -nodisplay -nodesktop -r "c... |
c778e13322357a3bf589e164bbd6c6b227d95d73e47f769588daca6a15390aa9 | Shell | 371 | 6 | #!/bin/bash
# download continuous .wav recording of robot counting (https://freesound.org/people/EnjoyPA/sounds/203066/; CC0)
wget https://zenodo.org/record/7358140/files/Counting-from-1-to-20.wav?download=1 -O Counting-from-1-to-20.wav
# download segmented stroop mat file
wget https://zenodo.org/record/7358140/files/... |
11ba5c83485d9bcbc85aabd86784d51162260bf67763ea2ade19210ee8dce6df | Shell | 372 | 23 | #/bin/bash
source $ADF/adfrc.sh
export PYTHONPATH=$ADF/scripting/:$PYTHONPATH
# $PRIMARYDIR and SCRADIR are set
COPY_DIR=$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_DI... |
0a25fdc9eac08cc2e4c263618014a5513230211458ed3db0c25a9bac6464ed2f | Shell | 373 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_peptide_hydrogen test_inputs/2gb1.pdb"
./ex_peptide_hydrogen test_inputs/2gb1.pdb
echo -e "Running ./ex_peptide_hydrogen test_inputs/5edw.pdb"
./ex_peptide_hydrogen test_inputs/5edw.pdb
echo -e "Running ./ex_peptide_hydrogen test_inputs/... |
6feeb87711a69523cf4ee5ce47c4438fd103098475ead932759fc779649fbeaf | Shell | 373 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_BackboneHBondMap test_inputs/2gb1.pdb"
./ap_BackboneHBondMap test_inputs/2gb1.pdb
echo -e "Running ./ap_BackboneHBondMap test_inputs/5edw.pdb"
./ap_BackboneHBondMap test_inputs/5edw.pdb
echo -e "Running ./ap_BackboneHBondMap test_inputs/... |
208266ada9004b4a5b82ae14bb816e41adc1f8390ae5fdcb82a19f7c7b9f6418 | Shell | 374 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N nonstemness_luad
#PBS -q cf160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ALCAM' 'CADM1' 'EPCAM' 'HIF1A' 'PKM' 'PTK7' 'SLC2A1')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./source/nonste... |
b94b3a5e4ae394fb9eab379aeb7757307fd6fd9c35c5c5b3d08adc75b5094c62 | Shell | 374 | 7 | ARGS="cohort_csv='`pwd`/tutorials/tutorial3/cohort_wtask.csv';"
ARGS="$ARGS config_path='`pwd`/tutorials/tutorial3/mappers_wtask.json';"
ARGS="$ARGS output_dir='`pwd`/results/tutorial3_mappers_wtask';"
ARGS="$ARGS data_root='`pwd`/tutorials/tutorial3/';"
ARGS="${ARGS} poolsize=8;" # generate 8 parallel workers
matlab ... |
272d7156001a78e0420214ac958d8f285321b28b9806b6f02cffe1cf7c745f49 | Shell | 376 | 23 | #/bin/bash
source $ADF/adfrc.sh
export PYTHONPATH=$ADFHOME/scripting/:$PYTHONPATH
# $PRIMARYDIR and SCRADIR are set
COPY_DIR=$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 $COP... |
f226e8082dc37929a9194c28119a2d9499545765753b5e1ddf54dffddd0ecd73 | Shell | 376 | 13 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
n_limit=$1
job_tag=$2
curr_user=`whoami`
njobs=$( ssh headnode "qstat | grep ${curr_user} | grep ${job_tag} | wc -l" )
while [ $njobs -gt ${n_limit} ]
do
njobs=$( ssh headnode "qstat | grep ... |
f6a9413d0c75a9592fbbed40e699e327fa75e6f35a4a829add0ecd47b38c6f1d | Shell | 376 | 10 | #!/bin/bash
python3 pointElec_sim.py 0.5 0 700 0 500
python3 pointElec_sim.py 1 300 1800 300 900
python3 pointElec_sim.py 2 1000 9000 1000 5000
python3 pointElec_sim.py 4 6000 30000 6000 17000
python3 pointElec_sim.py 8 10000 170000 10000 80000
python3 pointElec_sim.py 16 100000 500000 100000 300000
python3 unifor... |
0e8772623a716185b4cadc034157f13d4722b80ff839592dd07e7a3d8455a865 | Shell | 377 | 15 | #!/bin/bash
path2trimgalore=/hpc/hub_oudenaarden/aalemany/bin/TrimGalore-0.4.3
path2cutadapt=/hpc/hub_oudenaarden/aalemany/bin
if [ $# -ne 1 ]
then
echo "Please, give input file to trim"
exit
fi
file2trim=$1
${path2trimgalore}/trim_galore --path_to_cutadapt ${path2cutadapt}/cutadapt ${file2trim}
mv ${file2trim}... |
accc665ebec4f00dc7753f7b8034936dc09063d349aad12eaf3c0a70470656ab | Shell | 377 | 13 | #!/bin/bash
# Remove packages no longer required
sudo apt-get autoremove
# Delete all apt cache
sudo apt-get clean
# Delete journal logs older than 3 days
sudo journalctl --vacuum-time=3d
# Delete older versions of snap packages
set -eu
snap list --all | awk '/disabled/{print $1, $3}' |
while read snapname revision; ... |
1a433958258cae4d87b1eb352ab878e9e147426f2bf57b87d682c52308236ec3 | Shell | 378 | 15 | #!/bin/bash
H2O_DIR="../../../../../.."
cd $H2O_DIR
GRADLE="./gradlew"
$GRADLE clean
NOHUP_DIR="./h2o-algos/build/jmh/nohup"
NOHUP_FILE="$NOHUP_DIR/$(date +%Y-%m-%d).out"
mkdir $NOHUP_DIR -p
BENCH_CMD="nohup $GRADLE :h2o-algos:jmh >$NOHUP_FILE"
$BENCH_CMD
# run only one benchmark
# BENCH_CMD="nohup $GRADLE :h2o-algo... |
7543bced1c49a905c0e4ebbcabe014730337b25c29d564065c4670f756ef18b3 | Shell | 378 | 15 | #!/bin/bash
path2trimgalore=/hpc/hub_oudenaarden/aalemany/bin/TrimGalore-0.4.3
path2cutadapt=/hpc/hub_oudenaarden/aalemany/bin/
if [ $# -ne 1 ]
then
echo "Please, give input file to trim"
exit
fi
file2trim=$1
${path2trimgalore}/trim_galore --path_to_cutadapt ${path2cutadapt}/cutadapt ${file2trim}
mv ${file2trim... |
ed02afa6a9f49ebea1929f9834fe9fecfcbd5caf19528d1c1da98254becd56f2 | Shell | 379 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N stemness_coad
#PBS -q cf160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ABCB1' 'ABCC1' 'ABCG2' 'ALCAM' 'ALDH1A1' 'CD44' 'EPCAM' 'PROM1')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./sourc... |
4041fb532edfe53177a917639393245f99e09dd480823331141805c40edf7738 | Shell | 380 | 12 | #!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --mem=16G
#SBATCH --array=1-102
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/mantel-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" variants.txt`
module load anaconda/2023-01
python3 /m/cs/scratch/networks-pm/effects_externalfactors_on_fun... |
8a57e9a07cfbe80b8dd8234c9ee274f6e0ad9ef989517e9424c81c95cfbb2570 | Shell | 380 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ligand_rototranslation.py CAM test_inputs/2m56-ref.pdb test_inputs/00199.pdb test_inputs/00963.pdb test_inputs/04473.pdb"
python3 ligand_rototranslation.py CAM test_inputs/2m56-ref.pdb test_inpu... |
97fb3ef3c23272e7fa175430574e72d9d24289e115c58b91bc5333ccf76622fc | Shell | 380 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ex_chi_correlation test_inputs/2fd2.pdb test_inputs/5fd1.pdb"
./ex_chi_correlation test_inputs/2fd2.pdb test_inputs/5fd1.pdb
echo -e "#Running ex_chi_correlation test_inputs/1bgx_aligned.pdb test_inputs/1xo1_aligned.pdb"
./ex_chi_correlation... |
ca2937b6a922de6b11d63b8bf3db17ecdc02f2d7ac7268eaecea131d36899f5a | Shell | 381 | 10 | #!/bin/bash
$SHARC/wigner.py -n 1 -o initconds.ADF ADF.molden
$SHARC/wigner.py -n 1 -o initconds.COLUMBUS COLUMBUS.molden
$SHARC/wigner.py -n 1 -o initconds.GAUSSIAN GAUSSIAN.molden
$SHARC/wigner.py -n 1 -o initconds.MOLCAS MOLCAS.molden
$SHARC/wigner.py -n 1 -o initconds.MOLPRO MOLPRO.molden
$SHARC/wigner.py -n 1 -o ... |
341733c89354f729977aa6ff826d9a101f10bacb1fc04decac74fbebf23f4fff | Shell | 382 | 14 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p outputs_from_test
echo "#Running python3 pdb_to_ss2.py test_inputs/2gb1.pdb 2gb1.ss2"
python3 pdb_to_ss2.py test_inputs/2gb1.pdb 2gb1.ss2
mv 2gb1.ss2 outputs_from_test
echo "#Running python3 pdb_to_ss2.py test_... |
4941f6dc2f4be932b0ae756ac97a2744ceb8d42d34ffd0ccd1f3813e0b6deee0 | Shell | 382 | 14 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p outputs_from_test
echo "#Running python3 pdb_to_seq.py test_inputs/2gb1.pdb 2gb1.ss2"
python3 pdb_to_seq.py test_inputs/2gb1.pdb 2gb1.ss2
mv 2gb1.ss2 outputs_from_test
echo "#Running python3 pdb_to_seq.py test_... |
8b3b0fe8b03f55e992490eea0aab7d62bf5d106181bcb69c6b101787f83ee4a0 | Shell | 384 | 15 | scrna_path=$1
spatial_path=$2
celltype_key=$3
output_path=$4
dir_path=`dirname $scrna_path`
dataset=`echo $dir_path | rev | cut -d/ -f1 | rev`
celltype_path=`echo $celltype_key`
prefix='STRIDE'
echo $dataset
echo $celltype_path
STRIDE deconvolve --sc-count $scrna_path \
--sc-celltype $celltype_path \
--st-count $spati... |
0ef6b05d80bd45054319e24c694b527411b9392db1bfde165c8b96e2abef896b | Shell | 385 | 11 | #!/bin/bash
echo "# Running ./ap_hhpred_converter ./test_inputs/CYP51F.hhpred -f"
./ap_hhpred_converter ./test_inputs/CYP51F.hhpred -f
echo "# Running ./ap_hhpred_converter ./test_inputs/CYP51F.hhpred -p"
./ap_hhpred_converter ./test_inputs/CYP51F.hhpred -p
echo "# Running ./ap_hhpred_converter ./test_inputs/CYP51F.h... |
a31774644477679e036f38b8e84df4e39290aef02cb32d47669875e5755672cf | Shell | 385 | 19 | #!/bin/bash
#PBS -l select=1:ncpus=4
#PBS -N nonstemness_coad
#PBS -q cf160
#PBS -P ACD110174
#PBS -J 1-10
#PBS -j oe
#PBS -M r08942073@ntu.edu.tw
#PBS -m be
BioMarkers=('' 'ABCB1' 'ABCC1' 'ABCG2' 'ALCAM' 'ALDH1A1' 'CD44' 'EPCAM' 'PROM1')
cd $PBS_O_WORKDIR
module purge
echo "${BioMarkers[${PBS_ARRAY_INDEX}]}"
./so... |
16f2d1d21e0a3bf0739364d0ea971aaf1bc2adfd2af059ff583b3bd1148a25a9 | Shell | 387 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ex_MC_Ar 256 0.5 97 10 100 1.0"
./ex_MC_Ar 256 0.5 97 10 1000 1.0
mv final.pdb start.pdb
echo -e "# Running ./ex_MC_Ar start.pdb 0.5 97 10 100 3.0"
./ex_MC_Ar start.pdb 0.5 97 10 100 3.0
rm -rf ar_tra.pdb star... |
a0d8656d0ca463b3454ce542ce5641afb749b931be84b7e572886391ea628ade | Shell | 387 | 12 | #!/bin/bash
#SBATCH --time=06:00:00
#SBATCH --mem=32G
#SBATCH --array=61-120
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/beta-%j.out
#SBATCH --cpus-per-task=8
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" variants.txt`
module load anaconda/2023-01
python3 /m/cs/scratch/networks-pm/effects_externalfactors_on_func... |
c01a69da6c786d5b61be8da88065bc566049e1730251a366298f838e044ed4a3 | Shell | 387 | 12 | #!/usr/bin/env bash
# Download and install CARLA
mkdir carla
cd carla
wget https://carla-releases.s3.us-east-005.backblazeb2.com/Linux/CARLA_0.9.10.1.tar.gz
wget https://carla-releases.s3.us-east-005.backblazeb2.com/Linux/AdditionalMaps_0.9.10.1.tar.gz
tar -xf CARLA_0.9.10.1.tar.gz
tar -xf AdditionalMaps_0.9.10.1.tar.... |
e47a1c570f50c3c00be245d3f3cd9cb0a1189fcb90e11cd6334f2b6e6c968256 | Shell | 387 | 15 | #!/usr/bin/env bash
mkdir data
cd data
# Download license file
wget https://s3.eu-central-1.amazonaws.com/avg-projects/transfuser/data/LICENSE.txt
# Download 2022 dataset
for scenario in left ll lr right rl rr s1 s3 s4 s7 s8 s9 s10
do
wget https://s3.eu-central-1.amazonaws.com/avg-projects/transfuser/data/2022_data... |
ba17d4b31cdd571a64cb0ed981bf0ff3579dcb8a0ff0964b3bd60648478ee4ba | Shell | 388 | 20 | #!/usr/bin/env bash
set -euo pipefail
mode="${1:-}"
if [ "$mode" != "--check" ] && [ "$mode" != "--write" ]; then
echo "Usage: $0 --check|--write" >&2
exit 1
fi
files=()
while IFS= read -r -d '' file; do
if [ -f "$file" ] && [ ! -L "$file" ]; then
files+=("$file")
fi
done < <(git ls-files -z -- '*.md')
... |
3cb8ba4adcabcf1fbc4c5e06365e8e5ffa4c82798a0958bd127dcd1ebe729ceb | Shell | 392 | 16 | #../bin/agfusion \
# --gene5prime ENSG00000100325 \
# --gene3prime GGNBP2 \
# --junction5prime 30228234 \
# --junction3prime 34910661 \
# --out ASCC2-GGNBP2 \
# --genome GRCh37
agfusion annotate \
--gene5prime ENSG00000066468 \
--gene3prime ENSG00000197959 \
--junction5prime 121485532 \
--junction3prime... |
bf0a8d7dbff30a2b0fcec91b10adc6d5566e8ab5cffefa796d994aa7959923f8 | Shell | 394 | 17 | #!/bin/bash
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
i=0
for publicDnsName in $(cat nodes-public)
do
i=$((i+1))
echo Stopping on node ${i}: ${publicDnsName}...
ssh -o StrictHostKeyChecking=no -i ${AWS_SSH_PRIVATE_K... |
06ce1144c7d5221c3eec88e4fd0968f3a88764347e89a76f50c977a9a6b2cc1b | Shell | 396 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
./strc -ip=test_inputs/4rm4.pdb -op=4rm4A.pdb -strc:renumber -select::chains=A
./strc -ip=test_inputs/5ofq.pdb -op=5ofqA.pdb -strc:renumber -select::chains=A
echo -e "# Running ./ap_LocalStructureMatch 7 4rm4A.pdb 5ofqA.pdb | sort -nk3 | head -10000"
./ap_Loc... |
d83153dd490540c493e22f7289d92024008f39db6973149d67c335a02a669109 | Shell | 396 | 3 | echo "-------Testing..."
python3 test.py --seed 42 --valid_batch_size 1024 --valid_workers 8 --seqsize 150 --temp .TEMPDIR --use_single_channel --singleton_definition integer --gpu 0 --ks 7 --blocks 256 128 128 64 64 64 64 --resize_factor 4 --se_reduction 4 --final_ch 18 --target test_sequences.txt --delimiter tab --ou... |
ebaa9e5b5b7ea068959b450388da044aa63c91b6d38a157bc8803e4691b566c3 | Shell | 397 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_structure_iterators test_inputs/2gb1.pdb"
./ex_structure_iterators test_inputs/2gb1.pdb
echo -e "# Running ./ex_structure_iterators test_inputs/5edw.pdb"
./ex_structure_iterators test_inputs/5edw.pdb
echo -e "# Running ./ex_structure_i... |
6cf9f909bc26926772d67075c4aadac18bd8edaa9df6923581d983ff118fb86d | Shell | 399 | 18 | #!/bin/bash
#SBATCH --job-name="SWISS_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/swiss_15.out"
#SBATCH --error="output_amr/swiss_15.err"
#SBATCH --ntasks=1
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matla... |
bc3e42f6ed813fcb6999be7577ec44b4107cc8a68d184998071410c32f53da8a | Shell | 399 | 11 | #!/bin/bash
CHR=$1
cat /data_global/UKY_ADC/TOPMedImputation/preQC/chr$CHR.alladcs.bim | xargs -n 6 bash -c 'grep -E -w -m1 "$3[ \t].*$4[ \t].*$5|$3[ \t].*$5[ \t].*$4" /data_global/code/rs/hg38/ucsc.hg38.snp151.chr'$CHR'.linker | (printf $1; printf " ";cut -f 3 -d " " | tr -d "\n";printf "\n") | awk '\''$2!="" {prin... |
25ad1705908aea6fd40106191b1199cfda63ba2ba79040ccad5a6567c78c9dda | Shell | 400 | 18 | #!/bin/bash
#SBATCH --job-name="1_GER_AMR"
#SBATCH -D .
#SBATCH --output="output_amr/german_1.out"
#SBATCH --error="output_amr/german_1.err"
#SBATCH --ntasks=1
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matla... |
46b6c4266e9e428260de96daf2c823896eec10a00ded08f8ecdd09e083695bd6 | Shell | 400 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_rescore_alignment test_inputs/2azaA_2pcyA-ali.fasta BLOSUM62 -10 -2"
./ap_rescore_alignment test_inputs/2azaA_2pcyA-ali.fasta BLOSUM62 -10 -2
echo -e "# Running ./ap_rescore_alignment test_inputs/optimal_global_ali.fasta BLOSUM62 -10 ... |
17d8c45d05d61c2a4f6586de118971564decd78db34f0c54b93bd1069dab11c0 | Shell | 403 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_stacking_interactions test_inputs/2gb1.pdb"
./ap_stacking_interactions test_inputs/2gb1.pdb
echo -e "Running ./ap_stacking_interactions test_inputs/5edw.pdb"
./ap_stacking_interactions test_inputs/5edw.pdb
echo -e "Running ./ap_stacking_... |
54bdcb3eaeee16172a8e065fea5bd6ecc753f75e53084e8f26cfb94f8cbc8260 | Shell | 403 | 12 | #$ -N genomicSEM
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# This script will run the genomicSEM_multivarGWAS.R script
# see https://github.com/GenomicSEM/GenomicSEM/wiki/5.-User-Specified-Models-with-SNP-Effects
#-----
module purge
module load R/R-4.0.3
Rscript /data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPT... |
fcfb0661bba274bcbb58e65a35dfc0d9ae41af4906c40fdd0b5a6b3f94e6d423 | Shell | 403 | 18 | #!/bin/bash
#SBATCH --job-name="SN_11"
#SBATCH -D .
#SBATCH --output="output_amr/simNIBS_11.out"
#SBATCH --error="output_amr/simNIBS_11.err"
#SBATCH --ntasks=1
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=16
#SBATCH --partition=short
#SBATCH --time=22:00:00
#SBATCH --exclude=compute-3-01
module purge
module load matla... |
142833fe41ddec0c84788362d286fb8e4a1287c9e723d62592d3845391beb372 | Shell | 404 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p ./outputs_from_test
echo "#Running python3 ./read_scorefile.py test_inputs/1pgxA-abinitio.fsc"
python3 read_scorefile.py test_inputs/1pgxA-abinitio.fsc
echo "#Running python3 ./read_scorefile.py test_inputs/1pg... |
69d5b2f6779b92ae00d91d5ced4e1a8ccff72facb5cfa466991c9019e47aba68 | Shell | 404 | 6 | $OVDIR/../bin/wfoverlap.x -f dyson1.in > dyson1.out || exit $?
$OVDIR/../bin/wfoverlap.x -f dyson2.in > dyson2.out || exit $?
$OVDIR/../bin/wfoverlap.x -f dyson3.in > dyson3.out || exit $?
$OVDIR/../bin/wfoverlap.x -f dyson4.in > dyson4.out || exit $?
$OVDIR/../bin/wfoverlap.x -f dyson_quart_0.5.in > dyson_quart_0.5.ou... |
e30e0352430cfd02d6152a149435d851e5e803166b21c417ddd69e67f4e3cb0c | Shell | 404 | 15 | #! /usr/bin/env sh
set -e
# If there's a prestart.sh script in the /app directory, run it before starting
PRE_START_PATH=/app/prestart.sh
echo "Checking for script in $PRE_START_PATH"
if [ -f $PRE_START_PATH ] ; then
echo "Running script $PRE_START_PATH"
. $PRE_START_PATH
else
echo "There is no script $PRE... |
7455724e0fc55cac5c239eb825359c885687ad6edb0ad683df6c8f3365e04cfb | Shell | 405 | 20 | #!/bin/bash
#SBATCH --partition cpu_short,cpu_medium,cpu_long
#SBATCH --mem=20G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH -t 00-12:00:00
#SBATCH --job-name=CalcTD
#SBATCH --mail-type=FAIL
export JULIA_BIN=/gpfs/scratch/asslaj01/julia-1.10.0/bin/julia
set -Eeo pipefail
echo $HOSTNAME
$JUL... |
75f7b2490c5037da842a42d01d8ff1d40345adcf02eb4ac0a00a01cdd771215b | Shell | 408 | 19 | #!/bin/bash
#SBATCH --job-name=FT_SWISS
#SBATCH -D .
#SBATCH --output=ftoutput/ftswiss_%a.out
#SBATCH --error=ftoutput/ftswiss_%a.err
#SBATCH --array=1-15
#SBATCH --mem=32G
#SBATCH --cpus-per-task=12
#SBATCH --time=12:00:00
#SBATCH --partition=short
#SBATCH --exclude=compute-3-01
module purge
module load matlab/R202... |
f85f0d54e701044e131a68d4e8004493d234ac131ba530f22624775ac0e0f303 | Shell | 408 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
mkdir -p ./outputs_from_test
echo "#Running python3 hist_from_scorefile.py -f test_inputs/1pgxA-abinitio.fsc test_inputs/1pgxA-abinitio-bis.fsc -c score -min -50.0 -max -10.0"
python3 hist_from_scorefile.py -f test_input... |
a659ed6661cac9def13c9fe6bde0b47da91eb444d54432ab199a7491c1b55ebb | Shell | 409 | 16 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=30:00:00
Dmem=30G
threads=12
if [ $# -ne 1 ]
then
echo "Please, give"
echo "1) root input fastq lanes"
echo "2) protocol (celseq1, celseq2, nla)"
exit
fi
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/map.sh $1 $2" | qsub -cwd -N map-$1 -o map-${1}.out -e... |
02ebebbb11daac5daf1b041883e879272d6f6dcc6cb8a5c8c22296a9fffcc74e | Shell | 412 | 13 | #!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=20G
#SBATCH --array=1-24
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H5-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/effects... |
19c43f5984c808d10d913f1b464c7d7973010fbc7c990e9aaa8eb577c579c415 | Shell | 412 | 13 | #!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=20G
#SBATCH --array=1-24
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H6-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/effects... |
3bee685ee8fa129f5ecbba8ca4a94d3b9d75803b07e73fc5ca5ac2579e4cb171 | Shell | 412 | 13 | #!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=20G
#SBATCH --array=1-24
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H7-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/effects... |
5849b6fb707689315967557de8d960a720f1b9fd1348b64a2b1d3fd07773a2b4 | Shell | 412 | 19 | #!/bin/bash
#SBATCH --job-name=FT_GERMAN
#SBATCH -D .
#SBATCH --output=ftoutput/ftgerman_%a.out
#SBATCH --error=ftoutput/ftgerman_%a.err
#SBATCH --array=1-15
#SBATCH --mem=32G
#SBATCH --cpus-per-task=12
#SBATCH --time=12:00:00
#SBATCH --partition=short
#SBATCH --exclude=compute-3-01
module purge
module load matlab/R... |
c813b2b216c71b6e3534be4689a7cff69bb75644312cddaee707aeddd16c1b3d | Shell | 412 | 19 | #!/bin/bash
#SBATCH --job-name=FT_SIM
#SBATCH -D .
#SBATCH --output=ftoutput/ftsimNIBS_%a.out
#SBATCH --error=ftoutput/ftsimNIBS_%a.err
#SBATCH --array=1-15
#SBATCH --mem=32G
#SBATCH --cpus-per-task=12
#SBATCH --time=12:00:00
#SBATCH --partition=short
#SBATCH --exclude=compute-3-01
module purge
module load matlab/R2... |
9311a8e32e312c804ef2f79b3a31e5cf898bd5e5af34488529640ce21c2062d5 | Shell | 413 | 17 | #!/usr/bin/env bash
# Halt on error
set -e
OUTDIR="./results-v1"
# Iterate over different seeds here
for SEED in 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000; do
echo "Seed: $SEED"
for LEXP in data/LearningExp_*.txt; do
echo "Starting run with experiment data: $LEXP"
python3 train.py --as_humans "$LEXP... |
0247451aeb0a1d2587e083b08741da4762b8ee35a600d92cd084d44e409d0a1a | Shell | 415 | 17 | #where fsaverage and litong_dxh live
export SUBJECTS_DIR=/home/xianchige/YZY/20220523data/sub-01/
mri_surf2surf \
--hemi lh \
--srcsubject fsaverage \
--trgsubject sub-01 \
--sval fsaverageKastner2015Labels-LH.mgz \
--tval sub-01_lh.Kastner2015Labels.mgz
mri_surf2surf \
--hemi rh \
--srcsubject fsaverage \
--trgsubjec... |
7b80a3879bc13d3070735ecfcb365bd0617e8869196f75eefce7c12304ddc60c | Shell | 415 | 15 | samplot plot -n MSA1_CingCx_ONT MSA1_CingCx_ILM -b /Volumes/ritd-ag-project-rd00bt-cprou78/sample1/MSAsample1cing.ONT.aligning.minimap.bam /Volumes/ritd-ag-project-rd00bt-cprou78/sample1/IlluminaWGS_sample1/D5-78408_merged.bam.dup_marked.bam -o /Volumes/ritd-ag-project-rd00bt-cprou78/sample1/IlluminaWGS_sample1/samp... |
9c606f3b28e55430fe29141c87d33a0df6fe0ececc00bde1d5241af013f57a15 | Shell | 415 | 21 | #!/bin/bash
echo "removing log files"
rm -f processGenome.* binB* mapB* *done *.fa.* bowtieBUILT bwaBUILT indexB*
if [ $# == 1 ] && [ "$1" == "all" ]
then
echo "removing simulated reads"
# rm -f *frags
echo "removing bwa and bowtie indices"
# rm -f *.fa.*
echo "removing chromosome specific files"
rm -f re... |
d35e5620e60f6e49fba7d0c2b92e0dadb972b901e2225b9b94546391f5173635 | Shell | 415 | 10 | #!/bin/bash
wget https://flir.netx.net/file/asset/54398/original/attachment/spinnaker-3.1.0.79-amd64-pkg.tar.gz
tar -xvf spinnaker-3.1.0.79-amd64-pkg.tar.gz
sudo apt-get install libavcodec58 libavformat58 \
libswscale5 libswresample3 libavutil56 libusb-1.0-0 \
libpcre2-16-0 libdouble-conversion3 libxcb-xinput0 \
libxcb... |
50077f2079275b1e7e7b29797594e45d342327ac74597dcb6b234be1646c6a28 | Shell | 416 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ap_PairwiseCrmsd ./test_inputs/2gb1.pdb ./test_inputs/2gb1-model1.pdb \
./test_inputs/2gb1-model2.pdb ./test_inputs/2gb1-model3.pdb ./test_inputs/2gb1-model4.pdb"
./ap_PairwiseCrmsd ./test_inputs/2gb1.pdb ./test_inputs/2gb1-model1.pdb ... |
172a30fcb33f787fa6cfd7aa50654939d55ef4d30a145edba152244e703dfba8 | Shell | 417 | 13 | #!/bin/bash
#SBATCH --time=00:40:00
#SBATCH --mem=10G
#SBATCH --array=1-72
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H6-fakecorr-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" nodes.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/... |
471c81e62a425da08a475aafbd63ff7d031475cd8b2690fd7b1d527bf03e86b5 | Shell | 417 | 18 | #!/bin/bash
#SBATCH --job-name="VOLUMETRIC_PAT1"
#SBATCH -D .
#SBATCH --output="vol_output/dipole_%a.out"
#SBATCH --error="vol_output/dipole_%a.err"
#SBATCH --array=2
#SBATCH --mem=1024GB
#SBATCH --cpus-per-task=24
#SBATCH --exclude=compute-3-[01-07]
#SBATCH --partition=short
#SBATCH --time=22:00:00
module purge
mod... |
73975c746b867149fc8cea4cadafd24112e886a1cf3782d361ec477b21424f5b | Shell | 417 | 13 | #!/bin/bash
#SBATCH --time=00:40:00
#SBATCH --mem=10G
#SBATCH --array=1-72
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H7-fakecorr-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" nodes.txt`
module load anaconda/2023-01
export PYTHONUNBUFFERED=true
python3 /m/cs/scratch/networks-pm/... |
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