Bug 206926 - [NEW PORT] biology/vcftools: Tools for working with VCF genomics files
Summary: [NEW PORT] biology/vcftools: Tools for working with VCF genomics files
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Raphael Kubo da Costa
URL:
Keywords: feature, needs-patch, needs-qa, patch
Depends on:
Blocks:
 
Reported: 2016-02-04 16:16 UTC by Jason W. Bacon
Modified: 2016-02-26 17:10 UTC (History)
2 users (show)

See Also:
rakuco: maintainer-feedback+

Attachments
Shar archive (2.25 KB, text/plain)
2016-02-04 16:16 UTC, Jason W. Bacon 		no flags Details
Poudriere log (28.92 KB, text/plain)
2016-02-04 16:17 UTC, Jason W. Bacon 		no flags Details
Poudriere log (26.59 KB, text/plain)
2016-02-04 16:17 UTC, Jason W. Bacon 		no flags Details
Poudriere log (29.27 KB, text/plain)
2016-02-04 16:18 UTC, Jason W. Bacon 		no flags Details
Poudriere log (28.47 KB, text/plain)
2016-02-04 16:21 UTC, Jason W. Bacon 		no flags Details
Poudriere log (32.44 KB, text/plain)
2016-02-04 16:22 UTC, Jason W. Bacon 		no flags Details
Poudriere log (29.31 KB, text/plain)
2016-02-04 16:23 UTC, Jason W. Bacon 		no flags Details
Shar archive (2.20 KB, text/plain)
2016-02-26 16:54 UTC, Jason W. Bacon 		no flags Details
Show Obsolete (3) View All Add an attachment (proposed patch, testcase, etc.)

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Description Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:16:38 UTC 
Created attachment 166565 [details]
Shar archive

A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.

WWW: https://github.com/vcftools/vcftools

One of many prerequisites on the way for the dDocent genomics pipeline.
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:17:22 UTC 
Created attachment 166566 [details]
Poudriere log
Comment 2 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:17:51 UTC 
Created attachment 166567 [details]
Poudriere log
Comment 3 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:18:19 UTC 
Created attachment 166568 [details]
Poudriere log
Comment 4 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:21:13 UTC 
Created attachment 166569 [details]
Poudriere log
Comment 5 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:22:23 UTC 
Created attachment 166570 [details]
Poudriere log
Comment 6 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 16:23:18 UTC 
Created attachment 166571 [details]
Poudriere log
Comment 7 Raphael Kubo da Costa freebsd_committer freebsd_triage 2016-02-26 14:19:00 UTC 
> BUILD_DEPENDS+=	pkg-config:${PORTSDIR}/devel/pkgconf

This should be USES=pkgconfig.

> DISTNAME=	${PORTNAME}_${PORTVERSION}
> GH_TAGNAME=	v${PORTVERSION}

If you just set DISTVERSIONPREFIX=v instead it also works. The file name in distinfo changes, but that's not a problem.
Comment 8 Kubilay Kocak freebsd_committer freebsd_triage 2016-02-26 14:47:20 UTC 
Please use the following format for new ports:

[NEW PORT] category/port: <the value of the COMMENT field>
Comment 9 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-26 16:54:14 UTC 
Created attachment 167451 [details]
Shar archive


Thanks again for the tips.  I knew about USES=pkgconfig: That was an oversight.  I updated my checklist regarding DISTVERSIONPREFIX.
Comment 10 commit-hook freebsd_committer freebsd_triage 2016-02-26 17:08:31 UTC 
A commit references this bug:

Author: rakuco
Date: Fri Feb 26 17:07:59 UTC 2016
New revision: 409624
URL: https://svnweb.freebsd.org/changeset/ports/409624

Log:
  New port: biology/vcftools.

  A set of tools written in Perl and C++ for working with VCF files, such as
  those generated by the 1000 Genomes Project.

  WWW: https://github.com/vcftools/vcftools

  PR:		206926
  Submitted by:	Jason Bacon <bacon4000@gmail.com>

Changes:
  head/biology/Makefile
  head/biology/vcftools/
  head/biology/vcftools/Makefile
  head/biology/vcftools/distinfo
  head/biology/vcftools/pkg-descr
  head/biology/vcftools/pkg-plist
Comment 11 Raphael Kubo da Costa freebsd_committer freebsd_triage 2016-02-26 17:10:48 UTC 
Committed, thank you!