Create Dockerfile #1343
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| FROM python:3.10.14-slim-bullseye | ||
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| LABEL software="spades" \ | ||
| author="Sebastian Bassi <[email protected]>" \ | ||
| base_image="python:3.10.14-slim-bullseye" \ | ||
| container="spades" \ | ||
| about.summary="genome assembler for single-cell and isolates data sets" \ | ||
| about.home="https://ablab.github.io/spades/" \ | ||
| software.version="4.0.0" \ | ||
| upstream.version="4.0.0" \ | ||
| version="1" \ | ||
| extra.identifiers.biotools="spades" \ | ||
| about.copyright="2011-2014 Saint-Petersburg Academic University" \ | ||
| about.license="GPL-2+" \ | ||
| about.license_file="/usr/share/doc/spades/copyright" \ | ||
| extra.binaries="/usr/bin/metaspades,/usr/bin/metaspades.py,/usr/bin/plasmidspades,/usr/bin/plasmidspades.py,/usr/bin/rnaspades,/usr/bin/rnaspades.py,/usr/bin/spades,/usr/bin/spades.py,/usr/bin/truspades,/usr/bin/truspades.py" \ | ||
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There was a problem hiding this comment. I do not think this is for
There was a problem hiding this comment. this was based in an older Dockerfile published by Biocontainers, will remove old lines |
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| about.tags="biology::nucleic-acids, field::biology, field::biology:bioinformatics,:c++,:python, interface::commandline,:program, scope::utility, works-with::biological-sequence,:file" | ||
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| USER root | ||
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| RUN apt-get update && apt-get install -y build-essential cmake wget libbz2-dev | ||
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| RUN wget https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0.tar.gz | ||
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| RUN tar xfz SPAdes-4.0.0.tar.gz && rm SPAdes-4.0.0.tar.gz && cd SPAdes-4.0.0/ && ./spades_compile.sh | ||
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| # ./SPAdes-4.0.0/bin/spades.py --test | ||
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This is not accurate.
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please check again, just made changes to address these issues
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I would probably suggest you to build in the same way as release snapshots are being built: https://github.com/ablab/spades/blob/main/.github/workflows/release.yml#L53
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I've just tried this method, got the binaries but the spades.py test does not end in bin directory.
Here is what I tried:
after this, binaries are in bin, but not spades.py
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You'd also need to to
cmake --install. Alternatively, just pass-DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=alltospades_compile.sh.There was a problem hiding this comment.
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will try it tomorrow
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done, updated the Dockerfile and tested it