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[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data
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Authored by jwb on Dec 1 2017, 10:43 PM.

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Summary

[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data
Approved by: jrm (mentor) or wen (mentor)
Differential to be added to commit message

Note:
makeplist did not prefix bin/kallisto-test with %%PORTEXAMPLES%%. I had
to add this myself. Is this a bug in makeplist, or is something missing
from my Makefile?

Test Plan

portlint -C: looks fine
Passed poudriere on {10.3,11.1}-{amd64,i386}
Tested by researchers in production

Diff Detail

Repository
rP FreeBSD ports repository
Lint
Automatic diff as part of commit; lint not applicable.
Unit
Automatic diff as part of commit; unit tests not applicable.

Event Timeline

jwb created this revision.Dec 1 2017, 10:43 PM
jrm added a comment.EditedDec 2 2017, 4:12 AM
  • I believe PORTEXAMPLES are for files installed under EXAMPLESDIR. You could grep the ports tree to confirm, but my feeling is that something under /bin doesn't belong with PORTEXAMPLES.
  • For make makeplist behavior, you could check Mk/Scripts/check-stagedir.sh.
  • Optional: I think you could also do PORTEXAMPLES=* and not have to add the files under EXAMPLESDIR to pkg-plist.
  • README.md probably belongs with DOCS/DOCSDIR.
biology/kallisto/Makefile
6 ↗(On Diff #36078)

remove wip

jwb added a comment.Dec 2 2017, 2:57 PM

Already ran the grep, and there are examples of %%PORTEXAMPLES%%bin/*. Also if I don't add %%PORTEXAMPLES%%, install fails when the option is off. I think it has to prefix anything that's only installed when the EXAMPLES option is on. Maybe makeplist just doesn't recognize post-install-EXAMPLES-on. No big deal...

Good idea using PORTEXAMPLES=*. I can then eliminate pkg-plist and just use PLIST_FILES instead.

I see what you're saying about README.md, but there are copies of in both ${WRKSRC} and ${WRKSRC}/test, so I get the impression that the developers want it bundled with the test data to ensure that users will see it. Do you think it's worth also installing in ${DATADIR}?

jwb updated this revision to Diff 36111.Dec 2 2017, 3:11 PM

Clean up per mentor suggestions

jrm accepted this revision.Dec 2 2017, 7:05 PM

Oh, I see. There is a different README.md in test/ which belongs with the examples. I guess the README.md in $WRKSRC/ could be installed with a DOCS option. Your call.

biology/kallisto/files/kallisto-test.in
5 ↗(On Diff #36111)

Remove trailing whitespace?

7 ↗(On Diff #36111)

Remove trailing whitespace?

9 ↗(On Diff #36111)

Remove trailing whitespace?

This revision is now accepted and ready to land.Dec 2 2017, 7:05 PM
This revision was automatically updated to reflect the committed changes.