Yet Another Pipeline System (YAPS) 2 (COSMOS2-based)
A work in progress. Not really ready for prime time. This is a pure idea experiment and code may be abandoned in the future.
yaps is based on ruffus. This repository, yaps2, is based on a tweaked COSMOS2.
Example execution
yaps2 postvqsr --workspace=/path/to/workspace/name/test-pipeline --input-vcfs=inputs.txt --project-name="test-pipeline" --timeout=300 --log-level=INFO
Deployment
pip install --no-cache-dir --process-dependency-links git+https://github.com/indraniel/yaps2.git
# pygraphviz needs some extra install help
pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/" --force-reinstall --upgrade
Development
git clone https://github.com/indraniel/yaps2.git
cd yaps2
virtualenv venv
source venv/bin/activate
pip install --no-cache-dir --process-dependency-links -e .
# pygraphviz needs some extra install help
pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/" --force-reinstall --upgrade
# < do development work >
# test
yaps2 postvqsr --workspace=/path/to/workspace/name/test-pipeline --input-vcfs=inputs.txt --project-name="test-pipeline" --timeout=300 --log-level=INFO
# clean up dev workspace
make clean
Misc. Notes
BIO-1984 is the "grandfather" issue for most of these pipelines. See yaps2 --help and/or yaps <pipeline> --help for more information on the available commands/pipelines and options.
postvqsr pipeline
--input-vcfsis a file containing a tab-separated list of*.vcf.gzfiles in<CHROM>\t<VCF.GZ FILE>format- Example Usage (see
BIO-1984--BIO-1984/bin/run-pipeline.sh)
Mendelian Error Rate mie pipeline
- Example Usage (see
BIO-2000--BIO-2000/bin/1-run-pipeline.sh)
Principal Component Analysis pca pipeline
- Example Usage (see
BIO-2020 --BIO-2020/bin/1-run-pipeline.sh`)
Build38 realignment b38 pipeline
- Example Usage (see
BIO-2078--BIO-2078/bin/19-run-speedseq-realign-pipeline.sh)
React
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Alibaba
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Tencent