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biology/unanimity: Pacific Biosciences consensus library and applications
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Authored by jwb on Apr 23 2018, 5:19 PM.

Details

Summary

biology/unanimity: Pacific Biosciences consensus library and applications
Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message

Upstream does not appear to support shared libs at this point.

Test Plan

portlint -AC: looks fine
Passed poudriere on {10.4,11.1}-{amd64,i386}
Tested 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.Apr 23 2018, 5:19 PM
jrm added inline comments.Apr 24 2018, 4:24 AM
biology/unanimity/Makefile
14–16 ↗(On Diff #41771)

I wasn't aware that the comparison sign could be anything other than '>=' or '>'. Could you confirm this does what we expect? If this does work, it could be quite useful.

jwb added a comment.Apr 24 2018, 4:35 AM

Yep, 'been using this for years, at least in my wip ports. Very handy for persnickety genomics ports.

<<<ROOT@cray.acadix>>> /usr/ports/wip/unanimity 1003 # make clean depends

> Cleaning for unanimity-g20180307

> unanimity-g20180307 depends on file: /usr/local/sbin/pkg - found

> unanimity-g20180307 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)

> unanimity-g20180307 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)

> unanimity-g20180307 depends on package: pbseqan==g20171002 - found

> unanimity-g20180307 depends on package: pbbam==g20180416 - found

> unanimity-g20180307 depends on package: pbcopper==g20180413 - found

> unanimity-g20180307 depends on file: /usr/local/bin/cmake - found

> unanimity-g20180307 depends on executable: ninja - found

> unanimity-g20180307 depends on package: pkgconf>=1.3.0_1 - found

> unanimity-g20180307 depends on file: /usr/local/bin/python2.7 - found

> unanimity-g20180307 depends on file: /usr/local/bin/python2.7 - found

[ change pbcopper version ]

<<<ROOT@cray.acadix>>> /usr/ports/wip/unanimity 1005 # make clean depends

> Cleaning for unanimity-g20180307

> unanimity-g20180307 depends on file: /usr/local/sbin/pkg - found

> unanimity-g20180307 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)

> unanimity-g20180307 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)

> unanimity-g20180307 depends on package: pbseqan==g20171002 - found

> unanimity-g20180307 depends on package: pbbam==g20180416 - found

> unanimity-g20180307 depends on package: pbcopper==g20180414 - not found

> License BSD3CLAUSE accepted by the user

> pbcopper-g20180413 depends on file: /usr/local/sbin/pkg - found

Same for g20180412.

jrm accepted this revision.Apr 24 2018, 4:38 AM

Nice.

This revision is now accepted and ready to land.Apr 24 2018, 4:38 AM
This revision was automatically updated to reflect the committed changes.