sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4234e293a6a45c18a9ec974458ed6d576090737bb82d26b4f7130d562a3decf9 | Shell | 203 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_set_dihedral ./test_inputs/2gb1.pdb 18 -80.4 90.4 180.0"
./ex_set_dihedral ./test_inputs/2gb1.pdb 18 -80.4 90.4 180.0
|
0ec65d3e489a0b41fd9739d5dfd971388df920e0fe0f4e5e3732640cdf4447f4 | Shell | 204 | 12 | #! /bin/sh
git checkout gh-pages
git merge master
cd doc
make html
cd ..
rsync -av ./doc/_build/html/* ./
git add .
git commit -m "Update documentation"
git push origin gh-pages
git checkout master
|
c0a4eda8229dc8e971ac4a149432f14b09933da0a9cc1bc8937ab625320c39f7 | Shell | 204 | 8 | #!/bin/bash
out=$'/console.out'
ckpt_dir=$'./checkpoints/'
date=$(date +%y-%m-%d-%H-%M)
nohup \
python eval_multilabel.py --image-size '232 300' --augmented 1 --tta \
> "./log/$date$_console.out" &
|
492bb096b71835b6121fd5cfdf0a772e2738c6866a2ed8b0dd869b895ca93e5c | Shell | 205 | 6 | #!/bin/bash
set -ex
docker run --rm -it -v `pwd`:/data -e TRINOTATE_HOME=/usr/local/src/Trinotate trinityrnaseq/trinotate bash -c 'cd /data && ./runMe.sh && ./runMe.add_expression_prep_TrinotateWeb.sh'
|
f53e1128070b44ebdbc06112db03a50c2f441cbfdca47303d0218f1122923230 | Shell | 205 | 4 |
python code/prep/merge_plink_filesets.py -b data/rosmap/rosmap_adc -b1 data/act/act_np -o data/act/act_rosmap_adc
king -b data/act/act_rosmap_adc.bed --related --degree 2 --prefix data/act/act_rosmap_adc |
cca6ed2e68e9ee128084c698f3c62bc7733069c58afdd379c2d15d19813ca809 | Shell | 207 | 3 | cp octopi-research-malaria.desktop ~/.local/share/applications/
chmod u+x ~/.local/share/applications/octopi-research-malaria.desktop
cp ~/.local/share/applications/octopi-research-malaria.desktop ~/Desktop/ |
1f090a3d6b38dbc5a66651bf8e44cb75f8df7b9363e54b6a1f2838034ed9c82f | Shell | 208 | 7 | #!/bin/bash
echo -e "Running ./ap_pir_to_fasta test_inputs/example.pir"
./ap_pir_to_fasta test_inputs/example.pir
echo -e "Running ./ap_pir_to_fasta test_inputs/az.pir"
./ap_pir_to_fasta test_inputs/az.pir
|
23856e2293d848ce8f8d8d24937c9378f22a22cecb64a9844a782a599ff28d87 | Shell | 208 | 10 | #!/bin/sh
path=/media/lcao/DATA/T1_structure/cpp
for file in `cat $path/cpp.txt`
do
dcm2niix -z y -x y $path/$file
cp $path/$file/*Crop* $path/$file/${file}.nii.gz
gunzip $path/$file/${file}.nii.gz
done
|
62470f5f70787647b6fcb17d7fd7cb458d9dc2d9660e0d5aa3c25f32c7b19866 | Shell | 209 | 7 | #!/bin/bash
echo -e "#Running ./ex_BivariateNormal"
./ex_BivariateNormal
echo -e "#Running ./ex_BivariateNormal test_inputs/bivariate_normal.dat 0 1"
./ex_BivariateNormal test_inputs/bivariate_normal.dat 0 1 |
0085a1baa0a7d7598b1f4c6b450f5d52038e779d78555b807af589ea898ba7c7 | Shell | 210 | 5 | #!/usr/bin/env bash
CUDA_VISIBLE_DEVICES=2 ./submit.py \
-o ./pred_bert.exprtop20.300bp.sample100.hidden512.cdhit95.nonfreeze \
--test_path ./test_bert.exprtop20.300bp.sample100.hidden512.cdhit95.nonfreeze |
2961fcae3b925ce5f6319f291a06e804a39144d5917ae9f437c14a894c89abec | Shell | 210 | 7 | echo "Epoch 1/60:"
SLURM=1 python SFC_backprop/SFC_backprop_main.py --weight_mode rand_He
for i in {2..60}
do
echo "Epoch $i/60:"
SLURM=1 python SFC_backprop/SFC_backprop_main.py --weight_mode restore
done
|
aa5aef6bcd6ff8ce17539ff01f9e42ecc01c87a47ad2fdf61e8d8e5aca01caf5 | Shell | 210 | 12 | #!/bin/bash
#SBATCH --time=4:00:00
#SBATCH --mem=128000
#SBATCH -N 1
#SBATCH --cpus-per-task=4
#SBATCH --ntasks-per-node=1
#SBATCH --ntasks-per-socket=1
#SBATCH --gres=gpu:1
echo "args: ${@:1}"
python ${@:1}
|
b8fb873c2c1f5db3be1132af8e6130ff783e309195f897f11123516e78980d41 | Shell | 210 | 8 | #!/bin/bash
module load fsl
source $FSLDIR/etc/fslconf/fsl.sh
source /m/cs/scratch/networks-pm/software/deface/bin/activate
find $1 -type f -name '*_T1w.nii' -print -exec pydeface {} --outfile {} --force \;
|
365ed28fbd5c0b62608be3c3c7d7253aca43575193efb4c74d108191c64af4b9 | Shell | 211 | 7 |
STAR --runThreadN 12 \
--runMode genomeGenerate \
--genomeDir star279a_124_gencode_vM26 \
--genomeFastaFiles GRCm39_gencode_vM26_primary_assembly.fa \
--sjdbGTFfile GRCm38_gencode_vM26.gtf \
--sjdbOverhang 124
|
2f2ffb5339ce87cbde75ad5086ec40b4443f0b61958454a00a4552f34058c155 | Shell | 212 | 12 | set -e
mongosh <<EOF
db = db.getSiblingDB('$CIRRO_DATABASE')
db.createUser({
user: '$CIRRO_DATABASE_USER',
pwd: '$CIRRO_DATABASE_PASSWORD',
roles: [{ role: 'readWrite', db: '$CIRRO_DATABASE' }],
});
EOF
|
9f626054db62a077d7d51b096007f688ed600d746f90e7549e9ea3d6d953ec93 | Shell | 212 | 5 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "Running ./ex_Cart test_inputs/LEU_chi1_chi2_rad.dat > outputs_from_test/out_tree.txt"
./ex_Cart test_inputs/LEU_chi1_chi2_rad.dat > outputs_from_test/out_tree.txt
|
c54bbd09aadee50fc28d0ef6c29c2901ceaca694480b71abb52b7357b840f6e4 | Shell | 212 | 6 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "Running: ./deep_bbq -in::pdb=./test_inputs/2gb1.pdb -d=../../../../data"
./deep_bbq -in::pdb=./test_inputs/2gb1.pdb -d=../../../../data
mv *.pdb expected_outputs/ |
c823961a34042004d208e3f2b8de62186f04b013646ca645d471b0243ac66327 | Shell | 213 | 3 | $OVDIR/../bin/wfoverlap.x -f ciovl.in.ms0 > ciovl.out.ms0 || exit $?
$OVDIR/../bin/wfoverlap.x -f ciovl.in.ms1 > ciovl.out.ms1 || exit $?
$OVDIR/../bin/wfoverlap.x -f ciovl.in.ms-1 > ciovl.out.ms-1 || exit $?
|
7e24af81978a90d4ceec717271e21f44d90f4805be9a28959d39e782987ee9b4 | Shell | 214 | 8 | # Uncomment the next 3 lines if not using modules
module load modules/0-traditional
module load gcc/9.3.0
module load matlab
IK=2
NU=10
NP=5
matlab -nodesktop -nosplash -nodisplay -r "run test1(${IK},${NU},${NP})"
|
9f48dacb2ffaa750ad7030d793a030366592433aec92d66a16ddff32aef8dd57 | Shell | 216 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 cif_to_mol2.py test_inputs/HEM.cif HAEM"
python3 cif_to_mol2.py test_inputs/HEM.cif HAEM
|
da70e978970714523ad902367fa281011ef1909f0408069a36a43fcac93155c9 | Shell | 216 | 6 | #!/usr/bin/env bash
# TODO: specify the python version
(cd pybullet_tools/ikfast/franka_panda && python setup.py)
(cd pybullet_tools/ikfast/movo && python setup.py)
(cd pybullet_tools/ikfast/pr2 && python setup.py)
|
a0f2c684113798e70c4722e8733b06341e0fdc40a093f827f1c34f03a2b2b3cc | Shell | 217 | 12 | #!/bin/bash
#$-N init_00000
PRIMARY_DIR=/user/mai/Documents/NewSHARC/SHARC_2.1/TESTS/pysharc/RUNNING_TESTS/scripts_setup_init/ICOND_00000//
cd $PRIMARY_DIR
$SHARC/SHARC_Analytical.py QM.in >> QM.log 2>> QM.err
|
a20e56f006e5c2ec0f5a52bd364229e183adcd781e3f55f5dcedbc09bce8006c | Shell | 217 | 6 | #! /usr/bin/env bash
sal_index_mm="genome/salmon1.4.0_GRCm39_gencode_vM26_selective"
bbduk="bins/bbmap/bbduk.sh"
bbadapters="bins/bbmap/resources/adapters.fa"
rmats="bins/rMATS.4.0.2/rMATS-turbo-Linux-UCS2/rmats.py"
|
adce912e4faa45dc40835dc60690cb663b8acbf26aba5c84c1599e361224822c | Shell | 217 | 12 | #!/bin/bash
#$-N init_00001
PRIMARY_DIR=/user/mai/Documents/NewSHARC/SHARC_2.1/TESTS/pysharc/RUNNING_TESTS/scripts_setup_init/ICOND_00001//
cd $PRIMARY_DIR
$SHARC/SHARC_Analytical.py QM.in >> QM.log 2>> QM.err
|
5d12cbcd420e79af8e88a40ffd3edcff30b5a7caaa4a622af86718e3d593f5ed | Shell | 218 | 9 | #!/usr/bin/env bash
CUDA_VISIBLE_DEVICES=1,2 ./train_expr_group.py \
-f ../../data/train_sequences.fa.gz \
-o ./tmp \
--flank 150 \
--batch_size 64 \
--model_path ./bert.exprtop20.300bp.hidden512 \
--sample 1.0
|
80f4bc57fee8cdff973f339ef11598b10a25b3650220e75afb6197621d25f76b | Shell | 218 | 5 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# ./ap_shuffled_sequence_alignment test_inputs/input2.fasta BLOSUM80 10000"
./ap_shuffled_sequence_alignment test_inputs/input2.fasta BLOSUM80 10000
|
ce9ff4de43d61a4972376d219bb3f06c31c85a772b4ff016eeeb8ddcf47b1972 | Shell | 218 | 5 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_AlignmentPValuesProtocol test_inputs/small500_95identical.fasta"
./ap_AlignmentPValuesProtocol test_inputs/small500_95identical.fasta
|
ceff6cb85b2e7cd2a8bf91105b5f2a820062ee12834f37e0bb515e0e24299a6c | Shell | 219 | 16 | #!/bin/bash
if [ -d ICOND_00000 ];
then
rm -r ICOND_00000
fi
if [ -d ICOND_00001 ];
then
rm -r ICOND_00001
fi
if [ -f all_run_init.sh ];
then
rm -r all_run_init.sh
fi
$SHARC/setup_init.py < KEYSTROKES.setup_init |
a244ee79c29e816fc6aa1d90d194910b342d89889b0b6fe0ea50b827dca99a39 | Shell | 220 | 9 | #!/usr/bin/env bash
git pull --recurse-submodules
git submodule update --init --recursive
pip install -r requirements.txt
cd control_tools/ik
python setup.py build
cd ../../
./pddlstream/FastDownward/build.py release64
|
d3a311ba6bd1ae89f20169dc0c09aeb242394a257a918fa0acf2506a43fe8d27 | Shell | 221 | 6 | mkdir -p Datasets
cd Datasets
# you can also download the Demo.zip manually through
# link: https://caiyun.139.com/m/i?1A5ChPCwScw8P password: LR99
wget https://cvg-data.inf.ethz.ch/nice-slam/data/Demo.zip
unzip Demo.zip |
e99c91fb2841ae4d39c3722cdaa9c773d45f8c106ce4980590e7dbeda21c5983 | Shell | 221 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
for input in ./test_inputs/*.pdb; do
echo -e "#Running ./ap_ProteinArchitecture $input"
./ap_ProteinArchitecture $input
done
|
1524204f0aaea6b4e5da2e4364e4f282a5ec92e9fdae0b5c887dfa1d93ba3c8f | Shell | 222 | 8 | file=AA_CoilParameter.dat
echo $file
sed -i '' '/^$/d' $file #remove empty line
sed -i '' 's/://g' $file
sed -i '' 's/ / /g' $file
sed -i '' 's/ *$//' $file
awk '{print toupper($0)}' $file > tmp3 && mv tmp3 $file
#rm tmp* |
4a70ba11a13b5e140170a8d8e454866018eea14d53bd45ccdfb0346b1b191f00 | Shell | 222 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 toss_ligand.py test_inputs/2m56-ref.pdb X"
python3 toss_ligand.py test_inputs/2m56-ref.pdb X
|
e0436669fa6309f01e0d9bc479c02e963ffdcca72e3ab2bb262bf79729e3a975 | Shell | 222 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../../data"
echo -e "# Running ./ex_MMAtomTyping test_inputs/amber03_atoms.par test_inputs/2gb1.pdb"
./ex_MMAtomTyping test_inputs/amber03_atoms.par test_inputs/2gb1.pdb
|
81335208b468409333c217854de63489ceebe5e30b226c434df59909287d184c | Shell | 223 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 ./asn1_to_profile.py test_inputs/d1or4A_.asn1"
python3 ./asn1_to_profile.py test_inputs/d1or4A_.asn1
|
98cc99d25e96823c41823a880434be0f639b2a7351309295c3d650ec8f8b9362 | Shell | 223 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./contact_map.py test_inputs/2kwi.pdb 4.5"
python3 ./contact_map.py test_inputs/2kwi.pdb 4.5
|
9bc9786faab674433dc1d61bce3328022222d9213379b71aa4d49a87123b4b58 | Shell | 223 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
for pdb in 2gb1.pdb 3dcg.pdb 5edw.pdb
do
echo -e "Running ./ex_SelectPlanarCAGeometry test_inputs/$pdb"
./ex_SelectPlanarCAGeometry test_inputs/$pdb
done
|
d57b9ae0409b47a5d58263970ace6a20954e8f0460793e11a507affbacd07a52 | Shell | 223 | 11 | #!/bin/bash
< tmp/snp_list_index.tmp \
xargs -n 1 -P 22 -I % \
plink \
--bfile "$1" \
--extract data/tmp/ordinal_snp_list_%.tmp \
--allow-no-sex \
--recode A \
--out data/tmp/ordinal_snp_list_%
|
6d3987586e6a3b8e2fbc958975925577b64f52d6cce4dd462e0294da5be73581 | Shell | 224 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_caonly_multimodel test_inputs/cat_list"
./ap_caonly_multimodel test_inputs/cat_list
mkdir -p outputs_from_test
mv all.pdb outputs_from_test
|
46780f040445aa0faf0e8e6f235a886a289ae992b80e7d21f8fb748b898c4ee3 | Shell | 225 | 4 | # you can also download the cull_replica_mesh.zip manually through
# link: https://caiyun.139.com/m/i?1A5CvGNQmSDsI password: Dhhp
wget https://cvg-data.inf.ethz.ch/nice-slam/cull_replica_mesh.zip
unzip cull_replica_mesh.zip |
5736a48ecf6ff90651c0a0c7401e0fa302f42f5d028ee137e05ad7b57c17b96a | Shell | 225 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 msa_to_profile.py test_inputs/cyped.CYP109.aln"
python3 msa_to_profile.py test_inputs/cyped.CYP109.aln
|
8bd1952f608d6e3e80c9e2bea334e3196d0836f9c255c5124063ce5c0339f5e5 | Shell | 227 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./center_protein.py test_inputs/2kwi.pdb 51"
python3 ./center_protein.py test_inputs/2kwi.pdb 51
|
9b21d45e228b24c3431b01d68ce401f758f772d7c77fae062777d85d6c81232f | Shell | 227 | 8 | #! /bin/bash
python image_demo.py \
demo-input.jpg \
td-hm_hrnet-w48_8xb32-210e_coco-256x192.py \
td-hm_hrnet-w48_8xb32-210e_coco-256x192-0e67c616_20220913.pth \
--out-file demo-output.jpg \
--draw-heatmap
|
399da223e84bc5abdffe278a6e72257b9aef016e8354b112fc0795d09610782f | Shell | 228 | 2 | #!/bin/bash
cd .. && tar zcvf conceptnet-numberbatch/conceptnet-numberbatch-16.09.tar.gz conceptnet-numberbatch/data/*.gz conceptnet-numberbatch/README.md conceptnet-numberbatch/LICENSE.txt conceptnet-numberbatch/text_to_uri.py
|
86d6a52eb144b7b710b19c3acae39a62a7a6db6ae8954ba7d9066bbd8153cf9a | Shell | 228 | 7 | #!/bin/bash
echo -e "# Running ./ap_bootstrap_quantile 0.25"
./ap_bootstrap_quantile 0.25
echo -e "# Running ./ap_bootstrap_quantile 0.2 test_inputs/random_normal.txt"
./ap_bootstrap_quantile 0.2 test_inputs/random_normal.txt
|
fa1fc4293412bf1aa2bd6850ccaa46f7f240bbbbf1c6ea552a97bd44bcaf8cca | Shell | 229 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_Seqres test_inputs/2kwi.pdb"
./ex_Seqres test_inputs/2kwi.pdb
echo -e "Running ./ex_Seqres test_inputs/4mcb.pdb"
./ex_Seqres test_inputs/4mcb.pdb
|
41f8a3771eaf873d9a39e8d33d38244afedfdb242075a320dac62b63c568891c | Shell | 230 | 8 | #!/bin/bash
echo -e "#Running ./ex_P2QuantileEstimation"
./ex_P2QuantileEstimation
echo -e "#Running ./ex_P2QuantileEstimation test_inputs/random_N\(0,1\).txt 0.5"
./ex_P2QuantileEstimation test_inputs/random_N\(0,1\).txt 0.5
|
4381e4de3f18b6ef068ed7a0b6f66d231f963f31854e230bb63ddfb08400542d | Shell | 230 | 5 | export JAVA_HOME=/usr/lib/jvm/java-current-oracle
export HADOOP_SECURE_DN_USER=hdfs
export HADOOP_SECURE_DN_PID_DIR=/var/lib/hadoop-hdfs
export HADOOP_SECURE_DN_LOG_DIR=/var/log/hadoop-hdfs
export JSVC_HOME=/usr/lib/bigtop-utils/
|
4bf815d4d347d69cbeb86951009cf06c3c890082cccdee457220bcf50742cc9c | Shell | 230 | 7 | cd "$( dirname "${BASH_SOURCE[0]}" )"
echo "$(pwd)"
cd ..
cd ..
source venv/bin/activate || echo "activated"
mkdir -p tests/out
python bin/graphs.py --checkpoints tests/resources/kellis_list_exp.pickle --export tests/out/test.png
|
0bcc4c40fc82f4caa426d02d4f3fa72ef388d7ac723823821e6975f24fdbe897 | Shell | 233 | 2 | #! /usr/bin/env bash
ELEPHANT_PROFILE= kernprof -l -v -o ~/train.py.lprof /opt/elephant/script/train.py --baseconfig /opt/elephant/script/train_configs/base_profile_flow.json flow /opt/elephant/script/train_configs/profile_flow.json
|
a5bb513dedffa54b79686e57852171776fe881fe52cd8f8aec84ff39a27dcb15 | Shell | 233 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 seq_identity.py test_inputs/cyped.CYP109.fasta 0.3"
python3 seq_identity.py test_inputs/cyped.CYP109.fasta 0.3
|
49e585e52fe0030e8576def8fd2a684a8c078ff47ec36945a11508a758efcb88 | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=4-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=38G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,2,1,'ISCout2','decode_ISCout2_25_2_1') ; exit(0)"
|
594d17babfa1a227b1e560a12ce90387091d8826e2b1495c2f07a6c475419432 | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=38G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,4,1,'ISCout2','decode_ISCout2_25_4_1') ; exit(0)"
|
906118f690e3aee90ec0a44fa2f73b6884effd53c771f0ce0422ca09c2da6f92 | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=38G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,4,1,'ISCout1','decode_ISCout1_25_4_1') ; exit(0)"
|
b137ec1a5cad61d28b6cab958e60736c7dc2683ea519eeba9d44e59e1dad69df | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=3-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=48G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,1,1,'ISCout2','decode_ISCout2_25_1_1') ; exit(0)"
|
b3ce98744b695abd045ed8eae964fd0c5a6c037f549c9fc0be4b7b7a1b44c116 | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=38G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,1,1,'ISCout1','decode_ISCout1_25_1_1') ; exit(0)"
|
f9aa9fc6646d1131c2d120661d358be2051338b9f19de202468d4534dd43cf16 | Shell | 234 | 11 | #!/bin/bash
#SBATCH --time=1-00:00:00
#SBATCH --array=1-91
#SBATCH --mem=38G
#SBATCH --cpus-per-task=10
module load matlab
x=${SLURM_ARRAY_TASK_ID}
matlab -r "run_decode_par($x,25,2,1,'ISCout1','decode_ISCout1_25_2_1') ; exit(0)"
|
3c86424d44b4af1bfe4c089a712aa15530980343665469898cbbcc80e224300c | Shell | 235 | 19 | #!/bin/bash
if [ -s $1 ]
then
if [ $# -eq 1 ];
then
echo "y"
else
# check size if size is supplied
fsz=$(stat -c%s "$1")
if [ $2 -eq $fsz ];
then
echo "y"
else
echo "n"
fi
fi
else
echo "n"
fi
|
cf398c0e6376f5cfdc41438d77a1983eef2ccac1aa64a8b609255c90b3b5e16a | Shell | 235 | 19 | #!/bin/bash
if [ -e $1 ]
then
if [ $# -eq 1 ];
then
echo "y"
else
# check size if size is supplied
fsz=$(stat -c%s "$1")
if [ $2 -eq $fsz ];
then
echo "y"
else
echo "n"
fi
fi
else
echo "n"
fi
|
efcaba7efbeade6eed472e3753e68ddb03dae97a63491e1afe140bd67a449f12 | Shell | 235 | 10 | #!/usr/bin/bash
CONDA='/home/analyst/anaconda3'
snakemake -s "./Snakefile_SV_pipeline" \
--cores 20 \
--resources mem_gb=50 \
--use-conda \
--rerun-triggers mtime input \
--conda-prefix $CONDA
|
35d44ea3f79b37c55106c561782fd9553483650023d7a116f6b9319131e90074 | Shell | 236 | 15 |
if [ $# -ne 2 ]
then
echo "Please, give root for input and output fastq files"
exit
fi
fq=$1
outfq=$2
zcat ${fq}*R1* > ${outfq}_R1.fastq &
zcat ${fq}*R2* > ${outfq}_R2.fastq &
wait
gzip ${outfq}_R1.fastq &
gzip ${outfq}_R2.fastq
|
56f6021033c274da467e75741d232aed885137ae9859a8dccc11b2aebaefbc59 | Shell | 237 | 6 | mkdir -p Datasets
cd Datasets
# you can also download the Apartment.zip manually through
# link: https://caiyun.139.com/m/i?1A5CvuLuaPdhR password: kL2G
wget https://cvg-data.inf.ethz.ch/nice-slam/data/Apartment.zip
unzip Apartment.zip
|
ebcc1aa2c0a687dec9b14b8f7f4cb4df5a6b7b85bcf8eb8b09faaadd7383a41e | Shell | 237 | 8 | JOB_NAME="norbcapsule_`date +"%b%d_%H%M%S"`"
TAG="norbcapsule_local_gpu"
docker build -f DockerfileGPU -t $TAG $PWD
docker run -v \
$HOME/datasets/smallNORB:/root/datasets/smallNORB \
--runtime=nvidia $TAG \
--job_name $JOB_NAME
|
4a4c1ab7499b043afbd62a8c01980491228914ac215748ded785d1f7db9f5186 | Shell | 238 | 6 | mkdir -p output/vis
cd output/vis
# you can also download the Apartment.zip manually through
# link: https://caiyun.139.com/m/i?1A5CvuLsF50u6 password: yuh3
wget https://cvg-data.inf.ethz.ch/nice-slam/vis/Apartment.zip
unzip Apartment.zip |
9c21c87a9e8ba26dc876520b6c4053ceabbb48eae74a0092292b01fd224d0b69 | Shell | 238 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_LigandsOnGridProtocol 2.0 test_inputs/cat_list"
./ap_LigandsOnGridProtocol 2.0 test_inputs/cat_list
mkdir -p outputs_from_test
mv *.out outputs_from_test
|
14fba6eace1ebf92de4d8a92daecbed17f2a4ae4785acc17c6c30136a466d810 | Shell | 239 | 12 | #/bin/bash
CWD=/user/mai/Documents/NewSHARC/SHARC_2.1/TESTS/pysharc/RUNNING_TESTS/scripts_setup_init
cd $CWD/ICOND_00000//
bash run.sh
cd $CWD
echo ICOND_00000/ >> DONE
cd $CWD/ICOND_00001//
bash run.sh
cd $CWD
echo ICOND_00001/ >> DONE
|
6634b96524ba0c8ff12970ae31c5855fa02db4954abae3cac2890456272c7568 | Shell | 239 | 5 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_NWAligner test_inputs/input2.fasta test_inputs/ferrodoxins.fasta BLOSUM80"
./ap_NWAligner test_inputs/input2.fasta test_inputs/ferrodoxins.fasta BLOSUM80
|
bfdace12726f0748ef86b81c86ee7a1afb7e63d43929d7ff4deb5645fb34b91d | Shell | 240 | 7 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# call from ./107/fmri as ./scripts/extractData.sh $roi
# $roi = region to extract, e.g., Greymatter, LO, localizer
3dmaskdump -mask ./$1+orig ./epiFinal+orig > ../analysis/raw/$1.txt
|
e06a3cf64fb8af6fe6b12d45400c09513081171e3ff2976e34cf173fef483008 | Shell | 241 | 9 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_hbonds test_inputs/2gb1.pdb"
./ap_hbonds test_inputs/2gb1.pdb
echo -e "# Running ./ap_hbonds test_inputs/2kwi-1.pdb"
./ap_hbonds test_inputs/2kwi-1.pdb
|
701395f46b470e3b9acafbfe0fbc5f99051dfffae091934ad3c8d87eeb235dc9 | Shell | 242 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ap_atom_correlations test_inputs/2kwi.pdb | sort -nk 9 | grep -v e | tail -200"
./ap_atom_correlations test_inputs/2kwi.pdb | sort -nk 9 | grep -v e | tail -200
|
91b8ce5afba0795a51c92ce0e565a0e1589fca2c9cc8d88009aa39a0afa40691 | Shell | 242 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ap_LigandTossingMover test_inputs/2kwi.pdb GNP 5"
./ap_LigandTossingMover test_inputs/2kwi.pdb GNP 5
mv out.pdb outputs_from_test/
|
cafcc00fb25cf5026455b2c9d552721be353528ef2f4270e3671e5e23a0d12bc | Shell | 242 | 10 | cd train
# Get training data (Note that this data is downloaded from SRCNN website: http://mmlab.ie.cuhk.edu.hk/projects/SRCNN.html)
wget http://www.public.asu.edu/~kkulkar1/Training_Data.zip
unzip Training_Data.zip
rm Training_Data.zip
|
f5c9a0088c6612c5ea14944124e2491814303edac343d9777a270567143227c9 | Shell | 242 | 7 | #!/bin/bash
echo -e "Running ./ex_split_fasta test_inputs/5edw.fasta"
./ex_split_fasta test_inputs/5edw.fasta
mkdir -p outputs_from_test
mv *.fasta outputs_from_test # moves fasta files generated by ex_split_fasta to outputs_from_tests dir
|
13135b8092bc2d18f7b74913edbf1c6106573f0df31b43d4b32b9a3e02641cc8 | Shell | 243 | 7 | CUDA_VISIBLE_DEVICES=2,3 python train_unet_demo.py \
--challenge multicoil \
--data_path data_root_path \
--center_fractions 0.1171875 0.1171875 \
--accelerations 2 3 \
--mask_type equispaced_fraction \
--num_workers 2
|
5ffdd01258405887fa423caaf37a7d5f0fa6f77239859de546d2ec075d433b0b | Shell | 244 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "# Running ./ex_cabs_representation test_inputs/2gb1.pdb"
./ex_cabs_representation test_inputs/2gb1.pdb > out.pdb
mv out.pdb outputs_from_test/
|
6e81296efd37c69af9ecd2ce6c704324eb9eec4930994a189c30d0c031096595 | Shell | 244 | 5 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_SWAligner test_inputs/ferrodoxins.fasta test_inputs/ferrodoxins.fasta BLOSUM80"
./ap_SWAligner test_inputs/ferrodoxins.fasta test_inputs/input2.fasta BLOSUM80
|
7c2310fd347c872c2c77adcd6a3704a8823c226bf8430a6602e4da2e04e829d2 | Shell | 244 | 11 | source samples.sh
source config.sh
python $rmats --b1 wt_125.txt \
--b2 trt_125.txt \
--gtf GRCm38_gencode_vM26.gtf \
--od results/star_pass2/rmats -t paired \
--nthread 8 \
--readLength 125 \
--cstat 0.0001 \
--libType fr-secondstrand
|
03eb3e62fb70ab416f9036edfff925ff1dcf845c712ee825b175588b66d9e542 | Shell | 245 | 9 | #!/bin/bash
phenotype=$1
<data/tmp/snp_list_index.tmp xargs -n 1 \
Rscript --vanilla --slave code/analysis/ordinal/03a_regression.R \
data/plink/adc_np.covar \
data/adc_np_ord.txt data/related_rm/"$phenotype".remove \
$phenotype
|
6c42b96be0fedb2bb7d0a394b85553d127c5fb455777e8ff765850bbce5b5ec3 | Shell | 245 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 unwrap_pdb.py test_inputs/out_pbc.pdb 40"
python3 unwrap_pdb.py test_inputs/out_pbc.pdb 40
mkdir -p outputs_from_test
|
7461e668b2714d87497720c4a3b06fd30d27a6a206394a9a5dd2828accb7e66f | Shell | 245 | 7 | CUDA_VISIBLE_DEVICES=2,3 python train_varnet_demo.py \
--challenge multicoil \
--data_path data_root_path \
--center_fractions 0.1171875 0.1171875 \
--accelerations 2 3 \
--mask_type equispaced_fraction \
--num_workers 2
|
bda816c4c5a027c553457877bf40d861659d16468463cdd3a5f01c6b501e3163 | Shell | 245 | 8 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_pdb_to_pir test_inputs/2gb1.pdb"
./ap_pdb_to_pir test_inputs/2gb1.pdb
echo -e "Running ./ap_pdb_to_pir test_inputs/2kwi.pdb"
./ap_pdb_to_pir test_inputs/2kwi.pdb
|
135b9bfd05f0e489c673b023e9a33e2d11ef2a728da9edcba05cb2e07871d5b5 | Shell | 246 | 9 | #!/bin/bash
#SBATCH --time=04:00:00
#SBATCH --output=/home/intoumanis/sugar/code/logs/ROI.out
#SBATCH --error=/home/intoumanis/sugar/code/logs/ROI.err
module load Python/Anaconda_v11.2021
source activate expert_power
srun python extract_ROIs.py |
6105016c456bccc5b32fcbcb2de30ca424d556fe58fe271e5a7788eddfe16cff | Shell | 246 | 7 | #!/bin/bash
python3 non-invasive_sim.py 0 100 1000
python3 non-invasive_sim.py 1 100 1000
python3 non-invasive_sim.py 2 100 1000
python3 plot_summary_non-invasive.py 0
python3 plot_summary_non-invasive.py 1
python3 plot_summary_non-invasive.py 2
|
b7214f867266e890e1e81cd6f801d22e24ea3cd69d74fc66665b7e998cbc44de | Shell | 246 | 6 | #!/bin/bash
echo -e "# Running ./ex_plot_VonMises_mixture 0.487862 -3.00582 17.4059 0.0794212 -1.02886 112.164 0.432717 1.10223 68.0564"
./ex_plot_VonMises_mixture 0.487862 -3.00582 17.4059 0.0794212 -1.02886 112.164 0.432717 1.10223 68.0564
|
109c7206bc0ba0c65eca3093446dbd0c20f34be1d51ae1a82e2af4ae490057f9 | Shell | 247 | 20 | #! /bin/tcsh
#SBATCH --job-name="HoRNet"
cd $SLURM_SUBMIT_DIR
module load python/3.9
# Input prep
python input_prep.py
# UML
python UML.py
# DNN
module load cuDNN/7.6.5/CUDA-10.1 python/3.7
python Prediction.py
python Prediction_Cohort.py
|
b1ea119601c802519a00e4fb6b16a51b9c516f1ff90c1adc8f7c9b5bda301ba1 | Shell | 247 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ap_align_profiles test_inputs/d4proc1-A1.profile test_inputs/d4proc1-A2.profile"
./ap_align_profiles test_inputs/d4proc1-A1.profile test_inputs/d4proc1-A2.profile
|
2bdbd38f4476b0684849648997d939c88525b97169d1ffb123fb59662daa04f1 | Shell | 248 | 8 | #!/bin/bash
. /opt/venv/bin/activate
cd /groups/branson/home/kabram/PycharmProjects/poseTF
if nvidia-smi | grep -q 'No devices were found'; then
{ echo "No GPU devices were found. quitting"; exit 1; }
fi
numCores2use=1
python forSingularity.py
|
65db73ef161803df69f8dcbafb4b53397ecd8a77366fddd2c6c769dfb4a0891d | Shell | 248 | 16 | #!/bin/bash
if [ $# -ne 2 ]
then
echo "Please, give root for input and output fastq files"
exit
fi
fq=$1
outfq=$2
zcat ${fq}*R1* > ${outfq}_R1.fastq &
zcat ${fq}*R2* > ${outfq}_R2.fastq &
wait
gzip ${outfq}_R1.fastq &
gzip ${outfq}_R2.fastq
|
ccea50759bac90cb633390fb8a32e00b206cc92e199c8445ca840cfd77fb01ba | Shell | 248 | 7 | #!/bin/bash
echo -e "Running ./ap_WeightedOnlineStatistics"
./ap_WeightedOnlineStatistics
echo -e "Running ./ap_WeightedOnlineStatistics test_inputs/random_normal_weighted.txt"
./ap_WeightedOnlineStatistics test_inputs/random_normal_weighted.txt
|
9ce4897a9a90b7d5d3f48bec850101422b68bf0274adf763e88a88033a6bb210 | Shell | 249 | 17 | #!/usr/bin/env bash
set -euo pipefail
SRC="amd64/alpine:3.14"
TAG="cog-test-fixture:alpine"
echo "Creating test image fixtures"
docker pull $SRC
docker tag $SRC $TAG
docker save -o alpine.tar $TAG
docker rmi $TAG
echo "Test fixtures created"
|
08bca4af9eeb8318468593d44f9f071051f83bd3b1d18abc51cd868b6ecc557d | Shell | 251 | 6 | mkdir -p output/vis/Replica
cd output/vis/Replica
# you can also download the room1.zip manually through
# link: https://caiyun.139.com/m/i?1A5CwEM2ZjTNz password: Z2o7
wget https://cvg-data.inf.ethz.ch/nice-slam/vis/Replica/room1.zip
unzip room1.zip |
0e529eb9dbc65853baedc4a4bf0ca97ffa96b20ee68d339ac2399d9192c06e5d | Shell | 251 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
for i in 2gb1.pdb 2kwi.pdb 4mcb.pdb 5edw.pdb
do
echo -e "#Running python3 ./phi_psi.py test_inputs/"$i
python3 ./phi_psi.py test_inputs/$i
done
|
64863d0d2a18b1859b6ccebc6f5cd6fc71576482048d2428469a2c13bc3b3929 | Shell | 251 | 9 | #!/bin/bash
#SBATCH --time=2-01:00:00
#SBATCH --output=/home/intoumanis/sugar/code/logs/GLM1.out
#SBATCH --error=/home/intoumanis/sugar/code/logs/GLM1.err
module load Python/Anaconda_v11.2021
source activate expert_power
srun python glm_1st_level.py |
3f75cffab0dc6714df458ce21afb5268287d051e90cc0e4c92f77b25067d8516 | Shell | 253 | 5 | #!/bin/bash
# Written by Minh Nguyen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
ROOTDIR=`readlink -f $0 | xargs dirname`/../
python -m unittest discover --verbose --start-directory $ROOTDIR/cbig/Nguyen2020/
|
9ad9d30cd80256784c27c36d25693fc269f5f77fc33fcdd8a5cb4560ac5b4b05 | Shell | 253 | 10 | #!/usr/bin/env sh
export FLASK_APP=codex.main && \
export FLASK_SECRET_KEY=dev_dummy_key && \
export APP_ENVIRONMENT=DEV && \
BUILD_GIT_SHA=dummy_git_sha && \
export BUILD_GIT_SHA && \
BUILD_TIMESTAMP="$(date)" &&\
export BUILD_TIMESTAMP && \
flask run |
081049bb5f8fa70c0c1ed010b5d0d7f33aac63019c6acd741855e84c0b14a468 | Shell | 254 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo "#Running python3 fasta_subset.py 0.2 ./test_inputs/small500_95identical.fasta"
python3 fasta_subset.py 0.01 ./test_inputs/small500_95identical.fasta
|
bc4b654e433e249a1c1ac1ec16d37748f4fcb8f141013dc47b7aad429ec08e62 | Shell | 254 | 15 | #!/bin/bash
get_value_by_key() {
local key="$2"
local value=$(sed -ne "s/.*$key *: *\(.*\)$/\1/p" "$1")
echo $value
}
get_key_by_value() {
local value="$2"
local key=$(sed -ne "s/ *\([^ ]*\) *: *$value/\1/p" "$1")
echo $key
}
|
42e7f2b643ae628491e58a322b11e93b82bc44c492a5b56eca63a9f3d90ffe11 | Shell | 255 | 6 | git clone https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
module load cmake
cmake .. # if needed: "cmake .. -DUSE_STATIC_RUNTIME=OFF -DCMAKE_INSTALL_PREFIX=/scratch/PATHTOBINFOLDER"
make # and with option above "make install" |
36939d81559c274fec0e1f314e84b1e52950566f88c59109bb274fd06ae50045 | Shell | 256 | 9 | #!/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
module load matlab
matlab -nodisplay -r "maxNumCompThreads(1)" < SVD_forMSI_short.m ; exit; |
50a3705373cf705dc8f61423bbbcaacf717ad8d42764202d1c63357082d00100 | Shell | 257 | 13 | #!/bin/sh
juliapath=`which julia`
compiled_code="./SimplicialTS/Simplicial.so"
nthreads=$1
input_file=$2
output_file=$3
##Launching the code
time julia -J ${compiled_code} --threads ${nthreads} simplicial_multivariate.jl ${input_file} > ${output_file}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.