[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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jrm
wen
koobs

Commits

rP455384: Fill out block comment
rP455382: [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq…

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

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No Lint Coverage

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No Test Coverage

Build Status

Buildable 13277
Build 13514: arc lint + arc unit

Event Timeline

jwb created this revision.Dec 1 2017, 10:43 PM

Herald added a subscriber: mat. · View Herald TranscriptDec 1 2017, 10:43 PM

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
7	remove wip

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}?

Clean up per mentor suggestions

Harbormaster completed remote builds in B13277: Diff 36111.Dec 2 2017, 3:11 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.