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This is a docker for 4.0.0 |
asl
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asl
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Thanks for the PR!
Please see the comments inside.
Dockerfile
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| 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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I do not think this is for 4.0.0:
- There is no truspades anymore
- There are more binaries there
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this was based in an older Dockerfile published by Biocontainers, will remove old lines
Dockerfile
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| upstream.version="4.0.0" \ | ||
| version="1" \ | ||
| extra.identifiers.biotools="spades" \ | ||
| about.copyright="2011-2014 Saint-Petersburg Academic University" \ |
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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:
cmake -B build/ -S src/ -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all
cmake --build build/ -j16
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=all to spades_compile.sh.
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done, updated the Dockerfile and tested it
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