sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b96f7362ca0fbc11387419a3d40ea88312619acb5227f6fee000a010127c8947 | Shell | 165 | 5 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_11_08_motifInPeaksRegression_nobackup/runMixedModelOnHeartRNA.R --cellType $1
|
c462595e328d086f282abba2262e409045c989f34a09a9ae90874cd6566ea250 | Shell | 165 | 6 | #!/bin/bash
cd /root/vsc/hnfc-dataset-agent/
source /root/miniconda3/bin/activate agent
python -m agent.launchers.hnfc_launch_10_item_fd_classifier
conda deactivate |
fbe7e84477ee51d5a8dc9a9baaecf9b81976a0d4366f3bd96549c51552d11b89 | Shell | 165 | 6 | #!/bin/bash
cd /root/vsc/hnfc-dataset-agent/
source /root/miniconda3/bin/activate agent
python -m agent.launchers.hnfc_launch_9_update_review_level
conda deactivate |
40fcb7725bd554f58a92f72dd21177d8624e9f6f2da0609aa33ee58da90c9ca8 | Shell | 166 | 5 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_19_largeScaleMixedModeling_nobackup/runMixedModelOnHeartRNA.R --cellType $1
|
6461f250e43d14d3159adb9dac2aa84a14ec2515d723202c7bbb938b2638ba40 | Shell | 166 | 6 | #!/bin/bash
cd /root/vsc/hnfc-dataset-agent/
source /root/miniconda3/bin/activate agent
python -m agent.launchers.hnfc_launch_0_twitter_refresher_1h
conda deactivate |
6fdd2b0406829373443daf8ad39c4e947d13c654d705107688c8d7f94c567f1d | Shell | 166 | 5 | #!/usr/bin/env bash
# This script installs horovod.
HOROVOD_WITH_GLOO=1 HOROVOD_WITHOUT_MPI=1 HOROVOD_WITHOUT_MXNET=1 pip install --no-cache-dir -U horovod==0.28.1
|
cc473abb3997ed5b024170607cd37b7258494c885391b321cd34859d36ef5937 | Shell | 166 | 11 | #!/bin/bash
set -Ceu
gpu="$1"
for SCRIPT in $(find examples_tests/ -type f -name '*.sh')
do
echo "Running example tests: ${SCRIPT}"
bash ${SCRIPT} ${gpu}
done
|
922b4434f2a2bb1dc4396321fbd2600d9cb42f6e0863ff13951761d0a27772db | Shell | 170 | 6 | for (( c=400; c<=12000; c+=400 ))
# for (( c=20; c<=100; c+=20 ))
do
echo python Step_6_N_SpliceAI_prediction.py $c
python Step_6_N_SpliceAI_prediction.py $c
done |
9e3767d5d0107f62dc7c3c00cfe221af59f64826d5724c2490abd1b96e8bc258 | Shell | 170 | 6 | #!/bin/bash
# 'KAS-Analyzer activate' was developed by Ruitu Lyu on 1-25-2022.
conda activate KAS-Analyzer
echo "KAS-Analyzer conda environment activate successfully!"
|
1bc5e537f38017740148c51f00a8bde5b9261aff0a0eabe736238417ab9d4936 | Shell | 171 | 6 | #!/bin/bash
# This makes the PDF manual then moves it and renames to the top directory.
# Barnett 12/6/17
make latexpdf
mv _build/latex/finufft.pdf ../finufft-manual.pdf
|
3ef8186efa14c1e137c51419e2e8b0ce85219fbc62a9904f3b828b198908051a | Shell | 172 | 6 | #!/usr/bin/bash
sbatch sbatch_synthetic_hourglass_wores.sh
sbatch sbatch_synthetic_hourglass_wres.sh
sbatch sbatch_synthetic_unet_fixed.sh
sbatch sbatch_synthetic_unet.sh
|
8bc436287d24e31ccd1a501b7930fdb23a37496ec027809da9ef788cf014aedd | Shell | 172 | 9 | #!/bin/bash
set -euo pipefail
pip install pyrefly==0.51.0
find python/ray/data -name '*.py' \
| grep -vFf ci/lint/pyrefly-excluded-files.txt \
| xargs pyrefly check
|
dfa734d5a516105497d411dc8005215a5da7d474dceb3a47506108faf9c88c7a | Shell | 174 | 2 | cd ..
CUDA_VISIBLE_DEVICES=4,5 python train.py --exp HED_fc64 --epochs 5000 --batch_size 10 --base_lr 0.0001 --workers 8 --net HED --backbone 'resnet18' --feature_channel 64
|
58db4d3f530ff5a09989793a2efa5581b38548ee0d295e9ed76fbe84e2bab202 | Shell | 176 | 11 | #!/bin/bash
set -e
prefix="data/demo/"
# download demo data
./download_demo.sh $prefix
# download pretrained models
./download_checkpoints.sh
# run pipeline
./run.sh $prefix
|
88baeffa6872827b5d5ccfcad8cbbd4d605fdb72c7ccc964ab91da5429d5513b | Shell | 178 | 6 | # for seq_len in 200 400 600 800
for seq_len in 40 100 200 400 600 800
do
# echo "Processing ${seq_len}bp sequences..."
echo "python splam_train_model.py $seq_len"
done |
a20f7a64362edb240a43cdba3d7e5962bc38e37a81d72b713d9dacda1a620d15 | Shell | 178 | 7 | rm -rf print_testres.txt
./int2-test-laprouts3d
./int2-test-lfmm3d
./int2-test-lfmm3d-scale
./int2-test-lfmm3d-vec
mv print_testres.txt ../../print_testreslap.txt
rm -rf fort.13
|
d04f9550e6508b37f951827ae6c7b7cf823acce7f57735ddb11b6aea51bf4362 | Shell | 179 | 10 | #
https://github.com/jhmaindonald/qra/blob/master/data/HawCon.rda
curl -o ./fileInputs/HawCon.rds https://github.com/jhmaindonald/qra/blob/master/data/HawCon.rda
|
b37d1614530113f2337c9b50551a394a0d73b88c58acf0282281264255e48f83 | Shell | 180 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_11_08_motifInPeaksRegression_nobackup/runMotifATACregression.R --cellType $1 --fixedEffects $2
|
5af30885b7ef79f44268a1a19771af4e749a0e17fbf64c1e631745d42e6f5b4a | Shell | 181 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_05_redoPeakMotifRegression_nobackup/runMotifATACregression.R --cellType $1 --fixedEffects $2
|
5677a54118e20ac369e36442b9418f35974f847c8712f4b0c6318569029d1228 | Shell | 182 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_19_largeScaleMixedModeling_nobackup/runMixedModelOnHeartRNA.R --cellType $1 --fixedEffects $2
|
abdcc619eaa86057d92fb6fd62ea986e698af8d57426d1df0177c48ff7d85eec | Shell | 182 | 5 | threshold=1
SEQ_LEN=800
mkdir BAM_junctions
awk -v bound="$threshold" '{if($5 == bound && $6 != "?") {print}}' ../ALL_JUNCS/junctions.bed > ./BAM_junctions/junctions_$threshold.bed
|
691a647f6b79f3664341f23e4c387544226dafe4b79918a40e21575ee8c7e6e6 | Shell | 183 | 10 | #!/bin/bash
set -euo pipefail
set -x
if [[ "${BUILDKITE_COMMIT}" != "$(git rev-parse HEAD)" ]]; then
echo "Commit hash mismatch"
exit 1
else echo "Commit hash matches"; fi
|
dc89e8332f91423068a4a0fa94e81a09513c15b9091318086fb2af65b9c3bfc6 | Shell | 183 | 8 | #!/usr/bin/env bash
set -e
set -x
pdm run coverage run --source=siapy -m pytest -m "not manual"
pdm run coverage report --show-missing
pdm run coverage html --title "${@-coverage}"
|
45ac8fe531b78471ed9928e7c405db907676187de7f7ccc83c37df3267a4e712 | Shell | 184 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_11_08_motifInPeaksRegression_nobackup/runMotifCelltypeRegression.R --cellType $1 --fixedEffects $2
|
aad0fa711927d7f3ba0a2e042fd681ceb62ee9bd0fbe8fe1daa7b6a96aa1ef31 | Shell | 185 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_05_redoPeakMotifRegression_nobackup/runMotifCelltypeRegression.R --cellType $1 --fixedEffects $2
|
4b80b0d1a7575638858dbcfeb68b7e8a4f1176a3b856f3084f2a5020a7aed96e | Shell | 186 | 12 | #!/bin/bash
if [ "${TRAVIS_BRANCH}" != "master" ]
then
echo "Not master branch. Skipping"
exit 0
fi
set -e
# Make sure changelog is updated
.travis/in_commit.sh CHANGELOG.rst
|
3a55cdad2d68105573e05cb1d15dba46aa16eafced686d78581915cba1630353 | Shell | 188 | 3 | #!/bin/bash
#-------------------------------------------------------------------------------
~/Documents/test-mr-QS-B/test-imputation.sh &>~/Documents/test-mr-QS-B/test-imputation-log.txt
|
2437a0d97fc3c18a15a364e76f737d47efd735f191029181c42952edbdbdd8f6 | Shell | 190 | 7 | #! /bin/bash
for ((i = 1; i < 23; i++))
do
bcftools filter -e 'INFO/SVTYPE="BND"' chrs_union/${i}.vcf -Oz -o chrs_union/${i}_no_BND.vcf.gz
bcftools index chrs_union/${i}_no_BND.vcf.gz
done
|
709db0a0428748675d9d2a438d5fe0ffb9b0ab52a4b44062d7c58a9c4f171d95 | Shell | 190 | 11 | #!/bin/bash
#SBATCH --mem 20GB
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --job-name NeuralNetwork
module load miniconda3
conda activate Tensorflow
python FRASE-bot-RDKit-NN.py
|
9b06ada897ff8255eaef584400c4338037918756ec2dde47254d1c090007ff00 | Shell | 190 | 5 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_12_scalableSubtyping_nobackup/runSubtypeAnalysis.R --name $1 --clusters $2 --markerFile $3 --kval $4
|
c9fe0904081bbc1f2a25271c8daf139dde34a8626aa0f9609757e1cf8db84d85 | Shell | 191 | 16 | #!/bin/bash
OutDir=./out_F1
cat ${OutDir}/*.txt > ./score_sum_F1.txt
OutDir=./out_F2
cat ${OutDir}/*.txt > ./score_sum_F2.txt
OutDir=./out_F3
cat ${OutDir}/*.txt > ./score_sum_F3.txt |
8ea167a354da6839115769973f732740f268e51466acc31c2cfeab4a76198f28 | Shell | 192 | 7 | for SPLICEAI_VERSION in 1 2 3 4 5
do
echo ./2_spliceai_prediction_all_seq_N.sh $SPLICEAI_VERSION &
./2_spliceai_prediction_all_seq_N.sh $SPLICEAI_VERSION &
echo -e "\n"
done
# done |
4f23b5ad596fd1603137e62f2e9dbaff86028be2b603c63c13dcafa719cb3519 | Shell | 193 | 9 | #!/bin/bash
set -exuo pipefail
if [[ "${RAY_INSTALL_JAVA}" == "1" ]]; then
if [[ "${BUILD_JAR-}" == "1" ]]; then
echo "--- Build JAR"
./java/build-jar-multiplatform.sh linux
fi
fi
|
8ecf6282b8525552c3e67e921c3b7f1d7a5e67543d620aabc021c5bf79f0b2fd | Shell | 193 | 9 |
Rscript estimateIntercellVariation.R --cellType Fibroblast
Rscript estimateIntercellVariation.R --cellType Vascular_Endothelium
Rscript estimateIntercellVariation.R --cellType Macrophage
|
7f3c1b64edfd67fc0aea0c73b03ec3014058a5288eecce244893eb596c1d4d42 | Shell | 194 | 10 | #!/usr/bin/env bash
set -e
set -x
docs_src="docs/examples/src"
# docs_src="docs/concepts/src"
pdm run ruff check siapy tests scripts $docs_src --fix
pdm run ruff format siapy tests $docs_src
|
b2756ea56393cb3adb2281b9d79a84638b686dafb5739463566cbaded9fd8f48 | Shell | 195 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_11_08_motifInPeaksRegression_nobackup/runMotifATACregression.R --cellType $1 --fixedEffects $2 --pvalToUse $3
|
ca3bc6f9c1f115f6a8ecb12afe34174c6c1e0917f045ab7eb5d6c438c7a37b8d | Shell | 196 | 7 | TARGET=$1
for (( c=200; c<=20400; c+=200 ))
# for (( c=20; c<=100; c+=20 ))
do
echo python Step_6_SpliceAI_prediction.py $c N $TARGET
python Step_6_SpliceAI_prediction.py $c N $TARGET
done |
22913194e68821360544e49dfc9cae212e1dc23e4c0b50b057203d0606773cda | Shell | 199 | 3 | cd ..
CUDA_VISIBLE_DEVICES=2,3 python train.py --exp Deeplab_rs18_os8 --epochs 5000 --batch_size 10 --base_lr 0.0001 --workers 8 --net Deeplabv3 --backbone 'resnet18OS8' --name_classifier 'deeplab'
|
7075fe42ded7c518f67cf8f96c8a9f4de908f1f168b0bdbcdb203f7473841b0e | Shell | 199 | 8 | #!/bin/sh
inputFile=$1
design=${inputFile}
datPath="/path/"
randomise -i ${datPath}${inputFile}_4D.nii.gz -o ${datPath}${inputFile} -d ${datPath}${design}.mat -t ${datPath}${design}.con -n 5000 -T |
52f85d6cdcca70f14500310ecf6037d5ff7603a78ff89b6ce7fcbc6367efdc73 | Shell | 200 | 7 | TARGET=$1
for (( c=200; c<=20400; c+=200 ))
# for (( c=20; c<=100; c+=20 ))
do
echo python Step_6_SpliceAI_prediction.py $c noN $TARGET
python Step_6_SpliceAI_prediction.py $c noN $TARGET
done |
6ce24da324a9050aa02120ec80bd94bcafa01f93f4754afe210434343e07f455 | Shell | 200 | 3 | #!/bin/bash
#-------------------------------------------------------------------------------
~/Documents/test-mr-QS-B/simulate-missing-data.sh &>~/Documents/test-mr-QS-B/simulate-missing-data-log.txt
|
716ead867ccb0881c528469023be8f2fb2e73afc8836e45f159c5838fa552d45 | Shell | 201 | 5 | #!/bin/bash
set -euo pipefail
python ci/nb2py.py README.ipynb README.py # convert notebook to py script
python README.py # run the converted python script
rm README.py # remove the generated script
|
a49270bcc716686c23b7c32c69245a4d2db982c5c0815cdd74d58017a47a2b96 | Shell | 201 | 2 | cd ..
CUDA_VISIBLE_DEVICES=0,1 python train.py --exp HED_fc64_multiLoss --epochs 5000 --batch_size 10 --base_lr 0.0001 --workers 8 --net HED --backbone 'resnet18' --feature_channel 64 --multiLoss True
|
5c20c21d335489698da69414cab702e60c0b91924f47e95b46632b58e6e40f70 | Shell | 202 | 2 | cd ..
CUDA_VISIBLE_DEVICES=4,5 python train.py --exp HED_fc64_fcn --epochs 5000 --batch_size 10 --base_lr 0.0001 --workers 8 --net HED --backbone 'resnet18' --feature_channel 64 --name_classifier 'FCN'
|
276dd7a93a55d82e0ddd93805aec67609a2b12b32228d17eae8d7c65fcd2bf03 | Shell | 203 | 5 | #!/usr/bin/env bash
wget https://articles.chymera.eu/neurohost_opfvta.pdf
wget https://articles.chymera.eu/typhon_opfvta.pdf
diff-pdf --output-diff=comparison.pdf neurohost_opfvta.pdf typhon_opfvta.pdf
|
284eb1f1a5882b078ac490fc5cf3ba73823df88e2e7f28ee59e7dd1b5886b57c | Shell | 203 | 15 | #!/bin/bash
#
# label.sh
#
set -e
bed=$1
name=$2
cut -f -3 $bed \
| sort -k1,1V -k2,2n \
| bedtools merge -i stdin \
| awk -v OFS="\t" -v name=$name '{print $0, name}' \
> cleaned/${name}.bed
|
8621c3f263081ce3737af5577572012edea569ae8cd5a4159fb880873b246363 | Shell | 203 | 8 | rm -rf print_testres.txt
./int2-test-helmrouts3d
./int2-test-hfmm3d
./int2-test-hfmm3d-scale
./int2-test-hfmm3d-vec
./int2-test-hfmm3d-mps
mv print_testres.txt ../../print_testreshelm.txt
rm -rf fort.13
|
43a45b580731084cde337bcfff0de33b0ce82636affd399776b02292ef202eb6 | Shell | 205 | 12 | #!/bin/bash
source 00_global_variables.sh
OUT=PRS
for idx in "${!Phenotypes[@]}"
do
outDIR="${OUT}/${Phenotypes[$idx]}"
cd ${outDIR}
echo ${outDIR}
cat ./out/*.txt > ./score_sum.txt
done
|
14132be8337ad104b3497cfad46b0605956e37c5a844d095dfafb33ac362ff65 | Shell | 206 | 7 | #!/bin/bash
dir=.
parentdir="$(dirname "$dir")"
perl wikifil.pl ../text_data/enwiki-20170301-pages-articles1.xml-p000000010p000030302 > ../text_data/text8.txt
truncate -s 250000000 ../text_data/text8.txt
|
6d6001e6ec04715376d09123e8acace7b92ceb046b4829e1f51d80c6c5642970 | Shell | 206 | 10 | #!/bin/bash
export PATH=$PATH:~/github/ProjectAPI/Bash
output_file_name=~/logs/viewoutput.csv
cd ~/outputs/
rm $output_file_name
ViewDateDirectory.sh /tigress/LEIFER/Mochi/APIData/ $1
ViewSortedStatus.sh |
b714d7c5f724fff58a540f6020e83b15b52d3b81195b0bdb21d7127f8cc002ae | Shell | 206 | 4 | #! /bin/bash
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_19_largeScaleMixedModeling_nobackup/runMixedModelOnHeartRNA.R --cellType $1 --fixedEffects $2 --minGeneExprPercent $3
|
e3307773bd34ee12295dd37e78033b7a7bc48192cb26d9a81223d405cff63eb2 | Shell | 207 | 3 | project_root=/ccb/cybertron/khchao/splam-analysis-results/
output_dir=${project_root}train/results/MANE/REF_junctions/
sort -k1,1 -k2,2n -k3,3n ${output_dir}ref_d_a.bed | uniq > ${output_dir}ref_d_a.sort.bed |
80dd9e4d00c6fa13d72cb08e5c013d7db268e78e98101391141f477acc447c29 | Shell | 208 | 9 | #!/bin/bash
# Fetch the latest available version
wget https://storage.googleapis.com/ml4cvd/ml4cvd-master.zip
unzip ml4cvd-master.zip
cd ml4cvd-master/pyukbb
tools/run-after-git-clone
pip install -e .[dev]
|
501d5c9daa77684ba4f324156471174ca4ec462e5bfb31d3cda90978679e938e | Shell | 209 | 5 | #! /bin/bash
Rscript runGlmnetOnMotifs.R --promoterUpstream $1 --promoterDownstream $2 --coaccessCutoff $3 --maxNdistalSites $4 --peakSize $5 --featureSelection $6 --predictionTask $7 --pValFIMOcutoff $8
|
137005e9b8e302ea11244d99bb89b4c80248a86dc8ffa4dc56831e2789b480ff | Shell | 211 | 9 | # Python version 3.9.6
# module load Python/3.9.6-GCCcore-11.2.0
cd ~/venvs/
virtualenv minicLSTM
source ~/venvs/minicLSTM/bin/activate
# requirement
requirements=requirements.txt
pip install -r $requirements
|
72051816aa5f38b5e5597ebee57acb0d54de5c8cf7c42eabb438df82479b5319 | Shell | 211 | 9 | #!/bin/bash
folder_name=$1
script_name=$2
cd ~/github/ProjectAPI
echo 'running '$script_name
/usr/licensed/bin/matlab-R2016a -nodisplay -nosplash -nojvm -r "call_function('$script_name;$folder_name'); exit;"
|
c9c3c475f99d078f9dae35f747cdb8e4606d994ed22afb5aeed24afb0d5d2559 | Shell | 211 | 3 | cd ..
CUDA_VISIBLE_DEVICES=0,1 python train.py --exp Deeplab_rs18_os8_mh --epochs 5000 --batch_size 10 --base_lr 0.0001 --workers 8 --net Deeplabv3 --backbone 'resnet18OS8' --name_classifier 'deeplab_modified'
|
6d86cfb5cad35e80d50d625027ebbecd01d3ed35cbcf29744d1a50dc8df41a51 | Shell | 212 | 11 | #!/bin/bash
data_dir=../data/datasets
out_dir=$data_dir/tp
for dataset in $data_dir/*.csv;
do
python run_permutation.py \
--dataset $dataset \
--outdir $out_dir \
--n-threads 24
done |
6c2fcafffb07fe02d072fe8b063b944b839e86ea8756b37901fb75faf30dcf95 | Shell | 213 | 4 | echo "Updating the drprobe_clt source archive"
rm "drprobe_clt_src.tar.gz"
tar cvzf "drprobe_clt_src.tar.gz" "BuildCell" "CellMuncher_v2.0" "common" "celslc" "msa" "wavimg" "test" "README.md" "LICENSE"
echo Done.
|
324220b48820e5b4129da6c75e52acc6639970fd3e7ef1d7e822ea3a986065be | Shell | 214 | 3 |
python ~/bin/bbi-sciatac-demux/samplesheet/sciatac_samplesheet.py -i dfr_samplesheet.csv -o dfr_samplesheet.json -r /net/shendure/vol9/seq/NOVASEQ/210111_Riza_sciATAC3/nobackup/210112_GRC46NS_0339_A_HTWVLDSXY
|
4fe2e76e46ef304eeefc0ac3565a9c6cf4127415ae0f8cc2b4ae92881480dc8f | Shell | 214 | 3 | project_root=/ccb/cybertron/khchao/splam-analysis-results/
output_dir=${project_root}train/results/RefSeq_ALTS/REF_junctions/
sort -k1,1 -k2,2n -k3,3n ${output_dir}ref_d_a.bed | uniq > ${output_dir}ref_d_a.sort.bed |
e996f40d702f1fba7c27ce95cdea25134847d62b4747e866aa1c2252ebb79cc0 | Shell | 214 | 8 | #! /bin/bash
# Rscript NB9_vary_UMAP_noteTransferredLabels.R --featureSet $1 --useMNN $2 --lowDimOne $3 --lowDimTwo $4
Rscript NB9_vary_UMAP_noteTransferredLabels.R --sampleRNAname $1 --useMNN $2 --fripMin $3
|
b7f818a2ffc1de9039992a43c08d04fbc96f55472e3bb12ec1a5bb58232b1bf5 | Shell | 216 | 6 | CONDA_PATH=$(dirname $(dirname $(which conda)))
conda create --name rmsf-net python=3.8
source $CONDA_PATH/bin/activate rmsf-net
pip install -r requirements.txt
conda install moleculekit -c acellera -c conda-forge
|
16768d05630d9c877829f975e3234615abbaef7604f33927528c626f9890ac63 | Shell | 217 | 9 | #!/usr/bin/env bash
# Stop backend processes
ray stop
# Kill Java workers
# shellcheck disable=SC2009
ps aux | grep DefaultWorker | grep -v grep | awk '{print $2}' | xargs kill -9
# Remove temp files
rm -rf /tmp/ray
|
8a95cf4734795569c38911b3e17a862a1ba0c778afa73cd5a4dbdfc057475bdb | Shell | 218 | 7 | # create local postgres instance with username postgres
initdb $HOME/postgres_nils -U postgres
# start postgres
pg_ctl -D /home/nhinrichs/postgres_nils -l logfile start
# follow eicu instructions
make initialize
# ...
|
56817ac83133099e5e2eb3a15572d374679935b00fc8943a3fc8b0bd03920e1d | Shell | 219 | 8 | SPLICEAI_VERSION=$2
for (( c=500; c<=25000; c+=500 ))
do
echo python 2_spliceai_prediction_all_seq.py $c N $SPLICEAI_VERSION
python 2_spliceai_prediction_all_seq.py $c N $SPLICEAI_VERSION
echo -e "\n"
done
|
9c286b00e01305090b59271c959521952044245787765732b796b04ca55f3947 | Shell | 220 | 5 | #! /bin/bash
Rscript runGlmnetClassification.R --promoterUpstream $1 --promoterDownstream $2 --coaccessCutoff $3 --maxNdistalSites $4 --peakSize $5 --featureSelection $6 --predictionTask $7 --pValFIMOcutoff $8
|
700f52d8a3c7af28e848a4dcf63e4af32845d17e9b048f8ad30fee9d9a087722 | Shell | 222 | 5 | #! /bin/bash
Rscript runGlmnetOnMotifs.R --promoterUpstream $1 --promoterDownstream $2 --coaccessCutoff $3 --maxNdistalSites $4 --peakSize $5 --featureSelection $6 --predictionTask $7 --pValFIMOcutoff $8 --linkSet $9
|
0de19332293f03e92db2f16aa26235eee3ce5be45b2cdafcae022ed59391b05c | Shell | 225 | 6 | echo start `date`
python scripts_stage1/run.py \
--train_valid_list data/stage1/fitness_samples_train_valid.csv \
--training_data data/stage1/mutation_data.pt \
--outdir output_stage1
echo end `date`
|
dcf86d6524f58d9ee343ddb6b1cbed7e38d399a51643f579501d9f7cb1855e59 | Shell | 225 | 15 | #!/bin/bash
#
# sum_SR.sh
#
set -e
cat $1 \
| fgrep -v -e "name" \
| awk '{print $1"@"$3 "\t" $2 "\t" $4}' \
| awk '{a[$1]+=$3;}END{for(i in a)print i"\t"a[i];}' \
| tr '@' '\t' \
| sort -k1,1 \
| gzip \
> $2
|
46c4e28b056ba79b446c12a14f2625309ee8747908553597773d29999a625fd1 | Shell | 227 | 7 |
Rscript plotCoefficients.R --cellType Neuron --covar Age --genes LINGO1,KDM2B,FUS,SLC22A15,RBM25,KCNIP4
Rscript plotCoefficients.R --cellType Ventricular_Cardiomyocytes --covar SexM --genes KCNJ3,GADD45G,KDM6A,DOK5
|
645e5e33561584b470f32e71971ca0dd3283ac6180b2306baef116a3c74ab3c9 | Shell | 227 | 18 | #!/bin/bash
cd ..
git clone git@gitlab.com:spinnaker2/s2-sim2lab-app.git
cd s2-sim2lab-app
make
cd chip/app-pe/s2-lib
make
cd -
cd host/experiment/app/
cmake CMakeLists.txt
make
cd -
cd host/experiment/
./make_all_apps.py
|
094edfd105dc5f4f520c9ba708723f8c2fb2efce9e15f6d48a085808eed297fd | Shell | 228 | 2 | python val.py --weight ./ignored/new_weights/ignored/newnet_resnet50_128/18112021_065815/best_model_epoch4940.pth --dataPath ./data/DM4/testing/ --output ./ignored/valOutput --net DeepLabv3_modified_addBN --feature_channel 128
|
884023abe1f77dfc86acd76a65ded24021e86214017d41c35bda39f446f33908 | Shell | 228 | 9 | rm -rf print_testres.txt
./int2-test-helmrouts3d
./int2-test-hfmm3d
./int2-test-hfmm3d-zkbig
./int2-test-hfmm3d-scale
./int2-test-hfmm3d-vec
./int2-test-hfmm3d-mps
mv print_testres.txt ../../print_testreshelm.txt
rm -rf fort.13
|
5d9c8c9ef8cb81bd64d528625c46da43df542fc244f561e1a090eb669691df43 | Shell | 229 | 9 | export FILEID='1fTHAV0yL19S6MxFfa_UN8-ug75T944OP'
export FILENAME='project_gene_connectivity_data.zip'
wget https://bootstrap.pypa.io/get-pip.py
python -m pip install gdown
gdown $FILEID
echo Download complete. Extracting ... |
d1a29ed85a95fd24f3cf6b22aee82fb2539536307156c4fe3dc1c527db5562a7 | Shell | 229 | 7 | for f in geneset/*.gs.batch; do
prefix="$(basename -- $f)"
prefix=${prefix::-9}
echo $prefix
n_batch=$(ls -l geneset/${prefix}.gs.batch | wc -l)
sbatch --array 0-$((n_batch-2)) compute_score.sh ${prefix}
done
|
8ebb109bc0a18bdc61cb067eb39d9e38956a2a9912ec7e93b0d8b582060de8ce | Shell | 231 | 11 | #!/usr/bin/env bash
set -e
set -x
docs_src="docs/examples/src"
# docs_src="docs/concepts/src"
pdm run mypy siapy tests $docs_src
pdm run ruff check siapy tests scripts $docs_src
pdm run ruff format siapy tests $docs_src --check
|
51fb14981f95b06cc6c506f2e977cd957fca028d9dce9dfaecd5561c1a625fc7 | Shell | 237 | 4 | #! /bin/bash
# Rscript fileHere indiv cells ngenes indivSD cellSD
Rscript /net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/2020_12_29_SymSim_Power_Work/runSimulations.R --indiv $1 --cells $2 --ngenes $3 --indSD $4 --cellSD $5
|
9aaf6f3e81d0bcd63a56d3811ee4ba015e7943f548c52cc22e30732bf9150849 | Shell | 237 | 1 | python inference.py --weight ./ignored/dm_new_net_addBN/04112021_053427/best_model_epoch3920.pth --dataPath ./data/DM4/testing/Image/ --output ./ignored/testOutput --net DeepLabv3_modified_addBN --feature_channel 128 --backbone resnet18
|
faf2824b08a6ddcf1c7c77effc979f74b7c42fd0f782c6e8f8df40b6c549c499 | Shell | 240 | 11 | #!/bin/bash
set -eu -o pipefail
for LIST in "$@"; do
if [[ -f $LIST ]]; then
sed 's/ /\n/g' $LIST
printf "\n"
else
echo "$LIST" | sed 's/ /\n/g'
fi
done | grep -v ^$ | sort -u | tr -s '\n' ' ' | sed 's/ *$//'
|
1142b01d8db2d6203e1785890232805faef4be1a83bd5c00f68b3cff869f0487 | Shell | 241 | 11 | #!/bin/bash
set -euxo pipefail
S3_BUCKET=anyscale-example-video-analysis-test-bucket
export S3_BUCKET
python ci/nb2py.py README.ipynb README.py # convert notebook to py script
python README.py
rm README.py # remove the generated script
|
e528fce17c0f8580b5ad369b860966b3b0f8e5602034c2beb4b98cbc22365951 | Shell | 242 | 6 | echo start `date`
CUDA_VISIBLE_DEVICES=0 python -u make_esm2_3B_embed.py \
--PDB_coords_seq_hdf5 fitness_samples_seq_xyz.h5 \
--gpu_esm 0 --train_list fitness_samples.xls \
--out_hdf5 fitness_samples_esm2_3B_embed.h5
echo end `date`
|
e990173de12c583c24ce400667f9e5e3c43002223ed0b91718fe9ec7c669c488 | Shell | 242 | 2 | python verify_correctness.py --path1 unittest/27998_vasprun.xml --path2 unittest/27998_faircluster_vasprun.xml --type xml
python verify_correctness.py --path1 unittest/27998_all.traj --path2 unittest/27998_faircluster_vasprun.xml --type traj
|
fd838d6dfe381dbc6cd5413d7132b6a0aa96faa08b586af34002356acef856ac | Shell | 245 | 9 | TARGET=$1
SPLICEAI_VERSION=$2
for (( c=500; c<=25000; c+=500 ))
do
echo python 5_spliceai_prediction_all_seq.py $c N $TARGET $SPLICEAI_VERSION
python 5_spliceai_prediction_all_seq.py $c N $TARGET $SPLICEAI_VERSION
echo -e "\n"
done
|
64bc650b235a01a0cfc11d0d8cdade307962378da0e1fca7c283ec90af9946f5 | Shell | 247 | 12 | #!/bin/bash
#
# make_bkpt_rmsk.sh
#
set -e
cat \
/data/talkowski/rlc47/src/GRCh37.*.RMSK.merged.bed \
/data/talkowski/rlc47/src/GRch37.segdups_gaps_abParts_heterochrom.lumpy.exclude.bed \
| sort -k1,1V -k2,2n \
> breakpoint.rmsk.bed
|
c11224efbb38cc95d18ae45dc1a546bfcb8da2a4a42ef107104616fe4a158ba2 | Shell | 247 | 11 | cd ..
echo "deleting existing release related files"
rm -rf dist/*
rm -rf build/*
echo "creating a package for current release - pypi compatible"
python setup.py sdist bdist_wheel
echo "pushing the release to pypi"
python -m twine upload dist/* |
346bf3311c40526b06517fbaeb42dc28e5ecd9bb690b815a5075ead8276a1bd1 | Shell | 248 | 8 | TARGET=$1
SPLICEAI_VERSION=$2
for (( c=500; c<=25000; c+=500 ))
do
echo python 5_spliceai_prediction_all_seq.py $c noN $TARGET $SPLICEAI_VERSION
python 5_spliceai_prediction_all_seq.py $c noN $TARGET $SPLICEAI_VERSION
echo -e "\n"
done
|
95ebd0719ff05462e151332fa3b7b1416d1713c6c1e06dde9b758a9b31dc77a0 | Shell | 249 | 6 | #! /bin/bash
qsub -P trapnelllab -l mfree=80G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_24_ciceroWork_nobackup /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_24_ciceroWork_nobackup/runCiceroShell.sh
|
e4e4f62497b75157305f2faf2cc80c43e1d25bec84fe0da26544839a250b3f2c | Shell | 250 | 10 | #!/bin/bash
jobname=${1}
jobid=${2}
jobtype=${3}
echo "Make list of python script for emission"
launch-emission configure ${jobname} ${jobid} ${jobtype}
chmod +w -R logs/${jobname}/${jobid}
echo 'Start job'
launch-emission start ${jobname} ${jobid}
|
a74af36c4d4c42a5100eaacfd5dc5bb5a6529448923de00697813aea9e04d183 | Shell | 254 | 14 | #!/usr/bin/env bash
set -e
set -x
# Install pdm
curl -sSL https://pdm-project.org/install-pdm.py | python3 -
# Install python libraries
pdm install
# Install pre-commit
pdm run pre-commit uninstall
pdm run pre-commit install # --hook-type commit-msg
|
c41bf4a4e6ffa8161f0564df2a6f81456564bafcd549a91f5be5290fba1ebabd | Shell | 256 | 20 |
for dir in ??;
do
pushd $dir
bash do.sh
popd
done
for dir in ??
do
echo -n "${dir} "
tail -1 $dir/rmse.dat
done | awk '{print $1, $4}' > rmses.dat
for dir in ??
do
echo -n "${dir} "
tail -1 $dir/learning*
done > learning-last.dat
|
508d19475eea081db6ee91d920e2bab4598450e5402ef5b1bea68996366214d5 | Shell | 257 | 6 | #! /bin/bash
qsub -P trapnelllab -l mfree=80G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_04_redoCiceroWork_nobackup /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_04_redoCiceroWork_nobackup/runCiceroShell.sh
|
16ad40bda9ea8b05203ef917a3890f01b95a955aa981861b0feb4521a71d1ff5 | Shell | 260 | 8 | TARGET=$1
SPLICEAI_VERSION=$2
for (( c=1000; c<=22000; c+=1000 ))
do
echo ">> python Step_6_spliceai_prediction_all_seq.py $c N $TARGET $SPLICEAI_VERSION"
python Step_6_spliceai_prediction_all_seq.py $c N $TARGET $SPLICEAI_VERSION
echo "\n\n"
done
|
288ad81bd7ef1d3457d275212a0d17ec8ede7416591a15a6c4fed53ed19579de | Shell | 261 | 2 | #!/bin/bash -ue
check_sample_sheet.py --sample_sheet /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_01_11_Dana_and_HM11_nobackup/Hm11_dana_test_samplesheet.csv --star_file star_file.txt --level 2 --rt_barcode_file default --max_wells_per_samp 20
|
657f81df148b8ff956870c5c026a6c8bd65f3d97c4513b20c7e05bd915e543f6 | Shell | 261 | 11 | #!/bin/bash
source 00_global_variables.sh
OUT=PRS
UKB_bim=ukb_eur_unrel_comb
for idx in "${!Phenotypes[@]}"
do
outDIR="${OUT}/${Phenotypes[$idx]}"
cd ${outDIR}
plink --bfile ${UKB_bim} --score ./score_sum.txt 2 4 6 sum --out ./score_sum_indiv
done
|
cf20e9c43edbf18a1b152fa083a37a5ac38a99b327acb7e616a7bcb2534da474 | Shell | 261 | 13 | #!/bin/bash
set -euo pipefail
if [[ "${USER:-}" =~ "@" ]]; then
echo "ERROR: \$USER ('${USER:-}') contains invalid char '@'" >&2
exit 1
fi
if [[ "${HOME:-}" =~ "@" ]]; then
echo "ERROR: \$HOME ('${HOME:-}') contains invalid char '@'" >&2
exit 1
fi
|
60ecfba7871eac995ce7807c074d5172b9af3754b76d81d53465242344881b66 | Shell | 262 | 12 | #!/bin/bash
#SBATCH -p general
#SBATCH -N 1
#SBATCH --mem=12g
#SBATCH -n 1
#SBATCH -t 10:00:00
module use /proj/mnhallqlab/sw/modules
module load r/4.0.3_depend
R CMD BATCH --no-save --no-restore rt_prediction_meta_analysis.R rt_prediction_meta_analysis.Rout
|
64c433b17fe1837797a5cc2f974427b08dbeb9092da97b1fe7ce814103db81e4 | Shell | 264 | 8 | TARGET=$1
SPLICEAI_VERSION=$2
for (( c=1000; c<=22000; c+=1000 ))
do
echo ">> python Step_6_spliceai_prediction_all_seq.py $c noN $TARGET $SPLICEAI_VERSION"
python Step_6_spliceai_prediction_all_seq.py $c noN $TARGET $SPLICEAI_VERSION
echo "\n\n"
done
|
734e623a045f0fd92f96628cbca8b941ec53ccfeb08219894282fca7c91d0f57 | Shell | 271 | 13 |
# 9-9-21
# Get a run where I don't use any distal sites
Rscript gatherInputFiles.R --maxNdistalSites 0
# Also run one where I get big peaks at low cutoff, and keep many of them
Rscript gatherInputFiles.R --maxNdistalSites 20 --coaccessCutoff .035 --peakSize 1000
|
4f996cb3f966cb1d9fbbf84b7c7d3996a88811395d3bfd3988e269c70efdd1b4 | Shell | 274 | 11 | #!/bin/bash
jobname=${1}
jobid=${2}
sampling_num=${3}
echo "Make list of python script for mc decoding"
launch-mc-decode configure ${jobname} ${jobid} ${sampling_num}
chmod +w -R logs/${jobname}/${jobid}
echo 'Start mc decoding'
launch-mc-decode start ${jobname} ${jobid}
|
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