sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9c3b1c279f990fb2c9609ba550f26439248959f925916ada2a8daae722cc7881 | Shell | 176 | 10 | #!/bin/bash
set -e
set -x
pytest \
--cov-report=xml \
--cov-report=term \
--cov=rpy2.rlike \
--cov=rpy2.robjects \
./rpy2-robjects/src/rpy2/robjects/tests
|
ab73cb91977b2c96be19b76a1491f717083e1ee0b1f591373e1f42108731eba2 | Shell | 176 | 12 | #!/bin/bash
# Increases bin size from 50 to 150 to have the right length for DeepRiPe and Multi-resBind
FILE=$1
CHROMSIZES=$2
bedtools slop -i $FILE -g $CHROMSIZES -b 50 |
c6d49cd90bceaad8b2e8723f140412bba7ca2bcbb0af96d769653e42e8c98bd5 | Shell | 176 | 10 | #!/bin/bash -l
#$ -l h_rt=48:00:00
#$ -pe omp 2
#$ -N move_data
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; move_data; exit"
|
8b5937385f26f99f3be9463abf61393169d714d3cf1060bc44991a9734d7fcdf | Shell | 177 | 11 |
cd /data/users/jared/ENS/6mo_LMMP/preprocessing/bustools_required_files_10xv2_mm
kallisto index -i mm_cDNA_introns_mm_10xv2.idx -k 31 cDNA_introns.fa
echo "we got here"
|
9675cd156849d8b1705a3838ece730333c5550292ab46c6c425590e1347d9283 | Shell | 177 | 1 | rsync -Pav /projects/pfenninggroup/bloodAD/ldsc/IDR_optimal_peaks_hg38/All /projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq/data/tidy_data/ldsc_interferon_response |
43619905fe001644e7e6ed1988ad1f7fedcd82cf457e6c57bf0c15e93ae851b4 | Shell | 178 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 2
#$ -N fit_7694
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_7694; exit"
|
49b8ec597a705ee70ef913479c41b199008537a0530e326be32d1bb160b464e3 | Shell | 178 | 5 | python ./inference.py \
--num_designs 10 \
--out examples/out/design \
--pdb examples/pdbs/rsv5_5tpn.pdb \
--contigs 0-25,A163-181,25-30 --T 25 --save_best_plddt
|
68ef78c584c2da18bd63738fb902487e2465d20c94eb5ea8cd252e04481480f4 | Shell | 178 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 4
#$ -N fit_7688
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_7688; exit"
|
7b874f68e7852286dd52b78d9fccf149144e101e892a011f32362f4d7d2ec2d4 | Shell | 178 | 3 | # make the header bright green
find "${CELLXGENE_GATEWAY_DIR}/templates" -name index.html -exec sed -i -e 's/<head>/<head>\
> <style> header h3 {color: #0F0;} <\/style>/g' {} \;
|
b1618e3e3ee75229e140474db905d4fa6870c92bf2291a2d95badc47c18747ad | Shell | 178 | 4 | #!/usr/bin/env bash
source venv/bin/activate
source experiments/scripts/templates.sh
cat ${1} | parallel --gnu --lb -j 4 --tmpdir . eval {} --rank {= '$_ = $job->slot() - 1' =}
|
c562d7c3bfed4952f16f8cc9046b0f4611d54f71bf34d45a9ac0bdb041022dca | Shell | 178 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 2
#$ -N fit_8921
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_8921; exit"
|
e5cee6b9e217cffc64e26e4eab4892f5398cc4427bb9e3341527d8831eca3d11 | Shell | 178 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 4
#$ -N fit_6692
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_6692; exit"
|
92b982573a4b9a064a5d64252819d2b22d879c2969b3a813f80b90fd6a259eaa | Shell | 179 | 8 | for ppi in 0 1 2 3 4 5
do
python /home/yancui/ppimae/main_transductive.py --ppi=$ppi --lr_f=0.01 --weight_decay_f=0.001 --residual --inductive_ppi=-1 --expression
done
|
327833e1d558d20c2d4a81d23dde8108b35ad8c35d92818c7ad4ce6e9128bd23 | Shell | 180 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/mUCE.2186.background.chr.bed \
-b {file_pathway}/$bedfile \
-counts > mUCES.2186.background.snp.`basename $bedfile .bed`.counts
|
e80653f91c3dd8031434c9065a89282dc0b2ba848903403cdcb038aaa0c379ca | Shell | 180 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/aUCEs.5555.GRCg6a.without_chrZ.chr.bed \
-b {file_pathway}/$bedfile \
-mean > aUCEs.5555.snp.`basename $bedfile .bed`.corverage
|
063aae47c735a47370dd951e565b7a65541e61328010ae84ec5b4a4b49478171 | Shell | 181 | 8 | # merge 4D-labels for images in a folder
# $1: folder contains enquiry images
# $2: atlas folder "in_vivo" or "ex_vivo"
for G in `ls $1`
do
parcellation_merge_4D.sh $1/$G $2
done |
ba810b93d8b96f3046987acc17b0d8a5fbc69026e2d5e6267ef5a6fab170d628 | Shell | 181 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/mUCE.2186.background.chr.bed \
-b {file_pathway}/$bedfile \
-mean > mUCES.2186.background.snp.`basename $bedfile .bed`.corverage
|
c5ec8aee9f5d43b2564b960c4efa89b39d193ee0cfc1163f2bb957777c0cca2d | Shell | 181 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/GRCg6a.5555.background.without_chrZ.chr.bed \
-b $bedfile \
-mean > aUCEs.5555.background.snp.`basename $bedfile .bed`.corverage
|
012e71d9c36b2fa59d1b164d1a15d9ecc668c4972bdb82a91be8b72291253607 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_CLM_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
07dbd64056754a7f625effb8de19f4291a2d7cd0c937dc22153dc9bd9895b0ad | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_CLM_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
133d50655d293cfa896680d9fe829fe41580ae9e2c01e2676ebc04fa23effc96 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_ACB_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
3956f9535d6fb5545b0efd9309ce9011b72e4475b97eb56057367728631cdc62 | Shell | 182 | 10 | #!/bin/bash -l
#$ -l h_rt=12:00:00
#$ -pe omp 8
#$ -N HumanBrain
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; OCT_Scattering; exit"
|
518a9abbf25b0039d5b9b294fb08daae7a689cb620aae1a4fb1304d01bd8ca38 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_MXL_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
631dc1f812f15edc6fa94b74004f171a6a8a4704034b318db19da8df271e7f5c | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_ASW_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
78c62bbb494f2a815ee264785b65ba2549627f77595953bbcb36d7fe266dbde2 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_PEL_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
9f9d8ae2d8125d68fe78bf94cb58973405bcc230735334253e977c3d26ee9a7a | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_PUR_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
bec27f0857755f07bf4bff7e85a0a43a198b174ffeedc084b7b87b222d749fdd | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_MXL_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
c51431cdb7628b5b2cb0a40fa0bcf08a2cd5374d3aa65dcfcb6d7c124950c95c | Shell | 182 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N fit_PTSD1
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_PTSD1_1; exit"
|
cfae1a9d7211b79c08715b3685bd0ffa03a1fda3bdd8af8658989c1601e34acc | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_ACB_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
d569ca1044489b457b7a614129b2531c076574374568fa91b84a3ff19b9fd86e | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_PUR_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
d603a11239d807f6f826975265bd6682bb04a570138f719a1e2d6f03b6b3a8f8 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=8:mem=128gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_ASW_rfmix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
d83e35ccc7fe9f771730aaa05ca76d5aab36fd457dcd65c31a04ad7063e704c9 | Shell | 182 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N Hui_0505
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_Hui_0505; exit"
|
e4479e8d200565644f0e2a7686232c2b1f575521af1c4d9a195687908c3a2831 | Shell | 182 | 5 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=1:mem=16gb
#PBS -J 1-22
module load anaconda3/personal
python get_fragments_and_bootstrap_PEL_gnomix_0.1cM_maxanc.py $PBS_ARRAY_INDEX
|
e9fdb59db493af1d3f6c47ef4777c668a95bf877d937472dcb61eb2e29387765 | Shell | 183 | 9 | ROOT="."
ROOT+="/lsfm"
for i in {08..23}
do
nitorch crop $ROOT/align_channels/*${i}*.nii* --like $ROOT/slide/neun.${i}.slidecrop.nii.gz -o $ROOT/slide/{base}.slidecrop.nii.gz
done
|
2b5fa8684829cc14a6368c9bb22628be9e0e50d7284534767a24909a63c19847 | Shell | 184 | 10 | #!/bin/bash
union_peakset=$1
if [ ! -f ${union_peakset} ];then
echo "${union_peakset} does not exist."
exit 1
fi
sed -e "1d " ${union_peakset} | cut -f 1-3 > $2
echo "done."
|
2eca862a1fe498199fd728701ef655e5e11ee67f46dfd69479f169bca22c2fe7 | Shell | 184 | 13 | #!/bin/sh
GH_PAGES=gh_pages
rm -rf $GH_PAGES
git clone git@github.com:bbci/mushu $GH_PAGES
cd $GH_PAGES
git checkout gh-pages
rm -rf *
cp -r ../doc/_build/html/* .
touch .nojekyll
|
5cac0337958536d8fa7fdbce6a448d37198c3ef20273aedf2871a9f6f09f4934 | Shell | 184 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N fit_PTSD1_2
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_PTSD1_2; exit"
|
95fd47af56939f6077bee3914970f90e054775e28f2f86d5fde5634b89ee0d4f | Shell | 184 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N ret_depth
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; ret_depth_resolve; exit"
|
b0fa80d1f932492309e79f3dab4794e71fea34d500adb6feed18916f713ab93b | Shell | 184 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N fit_PTSD1_3
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_PTSD1_3; exit"
|
d9b43dcfb7e2528b85328de36488f837dbd9be5aef1321aa756966e5bdf27213 | Shell | 186 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 4
#$ -N fit_6692_tmp
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_6692_tmp; exit"
|
1cb36510302b70690412d6617229c2a19cf99ef11c6dfaf06b2bb8e1f7f3ce2d | Shell | 187 | 10 | #!/bin/bash -l
#$ -l h_rt=48:00:00
#$ -pe omp 4
#$ -N Hui_Sup
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_Hui_SupFrontal; exit"
|
4a4f671d97c1895d49b59a81f118c055bc283b1bfb277d04257732980b6b3666 | Shell | 187 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/aUCEs.5555.GRCg6a.without_chrZ.chr.bed \
-b {file_pathway}/maf_bed/$bedfile \
-counts > aUCEs.5555.snp.`basename $bedfile .bed`.counts
|
830495f160b7c088e63bad0c60bc1124c62400e4b19ded9946191a69f720d04b | Shell | 187 | 12 | #!/bin/bash
#PBS -q [QueueName]
#PBS -N [JobName]
#PBS -l nodes=1:ppn=2,walltime=24:00:00
#PBS -V
#PBS -M [Your-email]
#PBS -m a
#PBS -A ren-group
#PBS -j oe
[Your bash script content]
|
e0fac8b7071297f4e79937120667d4621c042cc35f89c42de484f5463333e00e | Shell | 187 | 9 | #!/bin/bash -l
#$ -l h_rt=100:00:00
#$ -pe omp 4
#$ -N fit_aft_rec
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_after_recon; exit" |
68bb2f63df418d248dce7eb4f4d178928fe2dad3d686f652313e2ec086e845b4 | Shell | 188 | 10 | #!/bin/bash -l
#$ -l h_rt=1:00:00
#$ -pe omp 4
#$ -N ret_vol_stitch
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; ret_volume_stitch; exit"
|
a6b5313887308cb400294884d9a8a98511cf716788c9292abc36df854bdf7312 | Shell | 188 | 6 | python ./inference.py \
--num_designs 10 \
--out examples/out/design \
--contigs 100 \
--T 25 --save_best_plddt \
--helix_bias 0.01 --strand_bias 0.01 --loop_bias 0.0
|
a953faa156db3a81e5f5c51b711ff44e719b81bde0d895df12b4754fc26c7012 | Shell | 188 | 5 | #!/usr/bin/env sh
./build/tools/caffe train \
--solver=models/bvlc_reference_caffenet/solver.prototxt \
--snapshot=models/bvlc_reference_caffenet/caffenet_train_10000.solverstate
|
9e773f320eceb772e5cff56209a064b696aaf44054d8707af47b9176889b3313 | Shell | 189 | 10 | #!/bin/bash -l
#$ -l h_rt=12:00:00
#$ -pe omp 4
#$ -N past_restitch
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; past_data_restitch; exit"
|
4907ff834550959afda4d27b70a96ec57cce4d386d7ddc43385b7657997599a1 | Shell | 190 | 9 | #!/bin/bash -ve
${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \
--seqType fq \
--max_memory 1G \
--output trinity_test_samples_SE
exit 0
|
7abb2935ea44647c670cb02add224923b3b5d332092d07ea107e551f98914d79 | Shell | 190 | 6 | #!/bin/bash
## upload to BU_Addiction_snRNA-seq/Striatum
rclone sync /projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq \
pfenninglab_gdrive:Data/Logan_OUD_Striatum_snRNA-seq
|
c9fbe5f2ac0f32e7a0e0316da4d7971e0b1ebb8775b4b8c6b2c88fe8f88f20ee | Shell | 190 | 9 | #!/bin/bash -ve
${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
--seqType fq \
--max_memory 1G \
--output trinity_test_samples_PE
exit 0
|
dcd33ed058761034982f85561514825b74700353f86a5e63ba8ac7b0b4b8d72c | Shell | 190 | 10 | #!/bin/bash -l
#$ -l h_rt=72:00:00
#$ -pe omp 4
#$ -N fit_aft_recon
#$ -j y
module load matlab/2019b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Fitting_after_recon; exit"
|
06c5745e9c3b9344fb06857ce152bb1715743de1e53414ce7d7741d6a1914234 | Shell | 191 | 7 | #!/bin/bash
set -ex
# Taken from https://www.tensorflow.org/install/source
# Only future is needed for our builds, as we don't build the Python package
pip install -U --user future==0.17.1
|
0e5e7ba1b2be0bacb367d04c72de8dda62a58bfecd55a148818accba0b1f6c9d | Shell | 192 | 9 | #!/bin/bash
python generate_data.py \
--hla_class HLA_I \
--label all_match \
--prop_train 0.6 \
--prop_valid 0.2 \
--n_fold 5 \
--rseed 1627
|
f4c59467a42ddd7819611c06e933a836786772be3860853a415b6b79c079bec7 | Shell | 192 | 10 | #!/bin/sh
S=2000000
N=256
LOG="`git rev-parse --short HEAD`.log"
rm -f $LOG
while [ $N -lt $S ] ; do
printf "%7d " $N | tee -a $LOG
./benchmark $S $N | tee -a $LOG
N=`expr 2 \* $N`
done
|
3c2989d463c3eeec0d840810b0f1cf87c0c25822273125d9d38483c25e596ba7 | Shell | 193 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 2
#$ -N double_check
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Double_check_tile_recon; exit"
|
a85a6f0bbfeaeba15f765eb5a350b7257e536ab794fc35e3342b8a33a40c70cf | Shell | 193 | 10 | #!/bin/bash
python generate_data.py \
--hla_class HLA_II \
--label all_match \
--prop_train 0.6 \
--prop_valid 0.2 \
--n_fold 5 \
--rseed 1627
|
403c63be4505ce9380273493850f212554d542eb8bec04997f61610a2700e4f1 | Shell | 194 | 2 | singularity exec -e /seq/RNASEQ/TOOLS/TRINITY/SINGULARITY/Trinity.simg Trinity --seqType fq --single `pwd`/reads.left.fq.gz --max_memory 1G --CPU 2 --output `pwd`/trinity_out_dir_singularity
|
e6a75b85ba51f8424a9696d2c81535a77789a95a393c74e9578b2f8a83b5831e | Shell | 194 | 8 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/../../" && pwd)
python3 "$SCRIPT_DIR/tools/ci/run_fa4_ci.py" \
--repo-root "$SCRIPT_DIR" \
"$@"
|
fc01e55fd08f3f99619b22b5c5074173311acd053105fa80e24dcf3e3884d32d | Shell | 194 | 10 | #!/bin/bash -l
#$ -l h_rt=48:00:00
#$ -pe omp 2
#$ -N ref_vol_stitch
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; ref_vol_stitch_from_AB; exit"
|
37feac805f7b458bace5a08f24c2bd225df3db12ea72fe1b35f1551c1c97ab82 | Shell | 195 | 3 | while read s;
do nohup bash /projects/ps-renlab2/y2xie/projects/44.colab/szu_mba/scripts/hic_balance_subtype.sh $s &
done </projects/ps-renlab2/y2xie/projects/44.colab/szu_mba/meta/subclass.txt
|
f41e340cb9ff8f7e3d3cee9913df143c4398759fad6d4502c8cc01ab530fc6c8 | Shell | 195 | 9 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 2
#$ -N Ori_aft_recon
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Ori_processing_after_recon; exit" |
10cf3524a03d98d13364292798c50ac391f3d2469dded92670fe2d8577f7a27b | Shell | 196 | 3 | #!/bin/sh
../../Trinity.pl --seqType fq --left ex9.reads.left.fq --right ex9.reads.right.fq --SS_lib_type RF --bfly_opts "--edge-thr=0.05 --stderr -V 18" --run_butterfly --output trinity_outdir
|
186c1c19d56547ab1165fb5bf6687a9f27e305368cdf16079abb66c5378a7068 | Shell | 196 | 7 | #!/usr/bin/bash
if [ ! -d "AURA_Human_data" ]; then
wget http://www.googledrive.com/host/0B9v5_ppcfmgWNTJzVjlkc0pCMVU
tar -xf 0B9v5_ppcfmgWNTJzVjlkc0pCMVU
rm 0B9v5_ppcfmgWNTJzVjlkc0pCMVU
fi |
7cf51be243e29408d0af42ab17e6c69b16cea90cdb0998dbcc1583a25cfd9ebe | Shell | 197 | 10 | #!/bin/bash -l
#$ -l h_rt=48:00:00
#$ -pe omp 4
#$ -N Ret_aft_recon
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Ret_processing_after_recon; exit"
|
019f46831fcfc88f1d141fe9328cf616ad3f8387a930f32a51cf12afdaa72a92 | Shell | 198 | 9 | #!/bin/bash
# Read name length test removed: max. name length in BAM is 254, replaced with test_5.sh
#bash test/test_1.sh
test/test_2.sh
test/test_3.sh
test/test_4.sh
test/test_5.sh
test/test_6.sh
|
b16d3a289d2e65c8076f4ee094a204f79dfa07b5b34e3e8d6c346f41effbce2c | Shell | 198 | 10 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 1
#$ -N ref_vol_stitch
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; OCT_ret_vol_stitch_from_AB; exit"
|
492559d60fb49a8d0e69a870f8ca1c3aa4c053e3072d9654b7fa993dfff5fc0c | Shell | 200 | 5 | sudo rm -rf ./trinity_out_dir
sudo rm -rf ./trinity_ext_sample_data_docker
sudo rm -rf ./trinity_ext_sample_data_singularity
sudo rm -rf ./trinity_ext_sample_data
sudo rm -rf ./trinity_out_dir_docker
|
8731e7b906461f2886811b8d3ee4bd89d48658c422ca570c94a136ab67fd0168 | Shell | 201 | 4 | #!/usr/bin/env bash
python device_server.py -g /home/quentin/comput/ethoscope-git/ -r -i /data/psv_misc/monitor_validation/monitor_validation_raw.mp4 -d -j ../../prototypes/json_config/config.json
|
89ad2c34f0065deaf12ada9e887e9f1eba76512a0add7b8f51045ff997506057 | Shell | 201 | 9 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cd $DS_ROOT_TASK/node-gyp-cache/ && tar -czf ${TASKCLUSTER_ARTIFACTS}/node-gyp-cache.tar.gz .
|
03f2d060291660d501546b8bfacdb4ebdd7b1e8037845e78c86788cdd50db1a5 | Shell | 202 | 5 | python ./inference.py \
--num_designs 10 \
--pdb examples/out/design_000000.pdb \
--out examples/out/partial_diffusion_design \
--contigs 38 --sampling_temp 0.3 --T 50 --save_best_plddt
|
3ad0b40abf38b86e7c7c3435c56eb2e40f4f32fd9a6cbf6b519a0cb339718954 | Shell | 202 | 11 | #!/bin/bash -l
#$ -l h_rt=48:00:00
#$ -pe omp 4
#$ -l mem_per_core=4G
#$ -N OCT_recon
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; OCT_recon_tmp; exit"
|
4e0edd32465fc372a33a653d5f834aac684cb1d7549be9b54375ac5fbeee6042 | Shell | 202 | 5 | bedfile=$1
bedtools coverage \
-a {file_pathway}/GRCg6a.5555.background.without_chrZ.chr.bed \
-b {file_pathway}maf_bed/$bedfile \
-counts > aUCEs.5555.background.snp.`basename $bedfile .bed`.counts
|
1bed2dcb7f799105dbe6ad340b61cc8cee26c8e53ca53fda860c345ef7b4a2d3 | Shell | 203 | 4 | #!/bin/bash
while read s;
do nohup bash /projects/ps-renlab2/y2xie/projects/44.colab/szu_mba/scripts/hic_APA_subtype.sh $s &
done</projects/ps-renlab2/y2xie/projects/44.colab/szu_mba/meta/subclass.txt
|
8156e451bfc276e4ddf1003fcad8f2cc624b6315fe999f87306bf9d33fdf0f28 | Shell | 203 | 11 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -l mem_per_core=8G
#$ -N ROI_stitch
#$ -j y
module load matlab/2018b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; Ref_ROI_recon; exit"
|
92d11f14a270cc7342741dee9ae176f4dc30dc613987b9da5cebb179c5499b46 | Shell | 203 | 6 | #!/bin/bash
DePTH predict --test_file data/Zheng_2021/zheng_2021_HLA_II_pairs.csv \
--hla_class HLA_II \
--output_dir results/ensemble_scores/HLA_II_all_match_zheng_default
|
a558b2265283f27fcaf68cbe6e3077d2d250ada8ee7023ab415e113e9a45e962 | Shell | 203 | 14 | #!/bin/bash
ROOT="."
ROOT+="/lsfm"
for i in {08..23}
do
nitorch reslice \
$ROOT/init_oct/vessels/vessels.${i}*.nii.gz \
-l calb2neun/$i/affine.lta \
-o $ROOT/align_channels/{base}.moved{ext}
done
|
da966f47308cbcbb6dfaa187f1dd0b0267ded15e902924cfc1eb623f509db4ef | Shell | 205 | 4 | #Mimic all the genomes to k-mers with length of 50bp and 10bp bootstraps
species=$1 #specify species genome
perl kmer_produce.pl {file_pathway}/${species}.fa 50 10 {file_pathway}/${species}_50bp_reads.fa
|
28d4aeea07fcd0fc055df98b3e278b27a11c5fc41df56a182810c3aebc2b932a | Shell | 206 | 7 | python ./inference.py \
--num_designs 10 \
--out examples/out/design \
--contigs 100 \
--T 25 --save_best_plddt \
--potentials aa_bias \
--aa_composition W0.2 --potential_scale 1.75
|
154da826ef457fb552de558c06b5eef060d6ec4c962da8cc942da63452574914 | Shell | 207 | 9 | #!/bin/bash
VERSION=`cat VERSION.txt`
singularity build trinityrnaseq.v${VERSION}.simg docker://trinityrnaseq/trinityrnaseq:$VERSION
singularity exec -e trinityrnaseq.v${VERSION}.simg Trinity --version
|
457469c5237689d0996e09b79f9ad8cb5103d19822e014d121997afd888a97e7 | Shell | 209 | 11 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -N BRM_ori_stitch
#$ -l mem_per_core=16G
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; BRM_ori_stitch; exit"
|
6da9a218e504fa01157419eba7b73832ae4128676eada1c249b7c9fd6d4d9fcb | Shell | 209 | 5 | python validate.py \
--model alpha_pose_resnet101_v1b --dataset coco --num-joints 17 \
--batch-size 128 --num-gpus 4 -j 60 \
--params-file duc_se_coco.params \
--input-size 320,256 --flip-test
|
7294535553234211b1176c8ac01be79c9d89f54bc5b2e6604aae20ffe98d5cbc | Shell | 209 | 13 | #!/bin/sh
cd "$(dirname "$0")"
. ./scripts/common_startup_functions.sh
setup_python
for file in $1/split_info*.json
do
# echo processing $file
python ./scripts/extract_dataset_part.py "$file"
done
|
8c8ae60a662e874c7ea4d620f955f63350ca1c62b6d1a7cd4bcb018906b89137 | Shell | 209 | 8 | #!/bin/bash
for logs in $(echo ../batch_logs/*.out ) ; do
failed_result=$(grep -r -1 "failed" $logs )
if [[ -n $failed_result ]]; then
base_log=$(basename $logs )
echo "failed: $base_log "
fi
done
|
a4d5ccc5f34a922c07259382a7aca810dce9329f5480ab1f20e7e9cb7124481d | Shell | 209 | 2 | #!/bin/bash
/usr/lib/trinityrnaseq/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300
|
df4fcd07eb6bf6121fa55a679f83ffc4758d02fa39542565e85bb0518d75fa76 | Shell | 209 | 8 | #!/bin/bash
num_bps=$(grep "SS_cons" $2 | awk '{print $3}' | tr -d '.' | tr -d '\n' | wc -c)
if [ $num_bps -gt 2 ]; then
R-scape --outdir $1 $2
else
echo "No consensus structure, R-scape skipped";
fi |
653049033c2b670b4e1a51d7f30f592759567e2a9597df9931593acbcd6f9300 | Shell | 211 | 9 | #!/bin/bash
MYPYPATH=src mypy \
--namespace-packages \
--explicit-package-bases \
--exclude src/rpy2/robjects/tests \
--exclude src/rpy2/ipython/tests \
--exclude build/ \
.
|
e62c89d381776d6d8ad0454f50f819c0587591a589544be20f14a4a5d57f18e3 | Shell | 211 | 11 | #!/bin/bash -l
#$ -l h_rt=24:00:00
#$ -pe omp 4
#$ -l mem_per_core=16G
#$ -N zoomin_stitch
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; ref_zoomin_stitch; exit"
|
37a7c6b217787c32a4f884dc1d927fc1db01825f7fef02007e6a8b57b7cd7e66 | Shell | 215 | 4 | #Build the ancestral sequences with high quality genomes from different branches
prequel --no-probs multiz_mammal.fa nonconserved-4d.cn.mod ancestor
# tree model called "nonconserved-4d.cn.mod" (built by phyloFit)
|
80e669e2ba06a77e5ef360bba7ee81fb9ee2d1f33762cd7abdd3c544fd7715ec | Shell | 216 | 2 | ../../Trinity --left `pwd`/reads.left.fq.gz --right `pwd`/reads.right.fq.gz --CPU 4 --max_memory 1G --singularity_img ../../Docker/trinityrnaseq.*.simg --seqType fq --output `pwd`/trinity_out_dir_singularity_intra
|
d6d67386bd5d557b569557802c8b88a01cc1eff4f355c7a30f69f1ab30c4c5d8 | Shell | 216 | 11 | #!/bin/bash -l
#$ -l h_rt=12:00:00
#$ -pe omp 4
#$ -N co_cross_stitch
#$ -l mem_per_core=32G
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "id='$SGE_TASK_ID'; co_cross_stitch_wrap; exit"
|
f92fcad684e5fb6589babbcfc592f33c9373f4f5bd4909dace5883fbc8bd2e60 | Shell | 216 | 13 | #!/bin/bash -l
#$ -P npbssmic
#$ -pe omp 28
#$ -l mem_per_core=13G
#$ -m ea
#$ -l h_rt=24:00:00
#$ -N vessel_segmentation
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "vesSeg_SCC; exit"
|
07674e7f43f7ed5d8adb59044a03f2d2243a12bda96777a424da8b9864c76cc8 | Shell | 218 | 5 | export DATA_FOLDER=./data
export MODEL_FOLDER=./output
python model_training/train_model.py --index 0 --data_folder $DATA_FOLDER --model_folder $MODEL_FOLDER --results_folder $MODEL_FOLDER --epochs_per_batch_step 10
|
2a92cd8181125f43bdb4e66dafb562e9af46ddfbc45df321e64f446e78d15cfd | Shell | 218 | 8 | #!/bin/bash
set -e
flake8 --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
# Apply stricter rules for the directories shared with Pulsar
flake8 --ignore=E203,D --max-line-length=150 lib/galaxy/jobs/runners/util/
|
b79023383b775917369f6ddede7a62e6b4b06671ea10c12032e2b38976455f5f | Shell | 219 | 10 | #!/bin/bash
IBM_CLOUD_FRONTEND_SPACE="covid-19-data-india"
ibmcloud target -s ${IBM_CLOUD_FRONTEND_SPACE} -o ${IBM_CLOUD_ORG}
cd ${TRAVIS_BUILD_DIR}/frontend
yarn install --ignore-engines
yarn build
ibmcloud cf push
|
f3a2a75099e2531bbedf68e5d6c03bceb3d4cb485b919777f5f4f3419a35a583 | Shell | 220 | 13 | #!/bin/bash -l
#$ -P npbssmic
#$ -pe omp 28
#$ -l mem_per_core=13G
#$ -m ea
#$ -l h_rt=24:00:00
#$ -N vessel_segmentation
#$ -j y
module load matlab/2020b
matlab -nodisplay -singleCompThread -r "SegtoGraph_SCC; exit"
|
04b74fd10d34319a51b6072e1b2a60d3e3d934a355533d851b18c3af24fc4007 | Shell | 221 | 9 | #!/bin/bash
flake8 \
--max-line-length 90 \
src/rpy2/rlike/functional.py \
src/rpy2/rlike/indexing.py \
src/rpy2/situation/__init__.py \
src/rpy2/rinterface/__init__.py \
src/rpy2/rinterface_lib/
|
191be718b3704b61d1ca9891a37cc034aed42a208386608c1a92385c48af6cd5 | Shell | 222 | 5 | python3 -m black bdd100k
python3 -m isort bdd100k
python3 -m pylint bdd100k
python3 -m flake8 --docstring-convention google bdd100k
python3 -m mypy --install-types --strict --allow-untyped-calls --show-error-codes bdd100k
|
6d03664845649ba9a9dbde570d04e2cd7f65c8ee62567319e45ab1131022002b | Shell | 222 | 2 | #Perform simulations of hub and non-hub bacteria removal, evaluate the robustness of GM networks, and repeat 10 times
perl robustness_evaluate.pl ../Stability evaluation/AD1M_MIS.xls AD1M.bacteria.info AD1M.robustness.xls
|
e4f7e807e878f7c173d04a617e9f4380714ba4d8a5bfc6b951f6d8aee52d8aea | Shell | 223 | 3 | docker build -f ./backend/Dockerfile . -t jsbroks/coco-annotator:python-env --no-cache
docker build . -t annotator_webclient_gpu --no-cache
docker build -f ./backend/workers/Dockerfile . -t annotator_workers_gpu --no-cache
|
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