Bug 206939 - [NEW PORT] biology/bowtie: Ultrafast, memory-efficient short read aligner
Summary: [NEW PORT] biology/bowtie: Ultrafast, memory-efficient short read aligner
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, patch, patch-ready
Depends on:
Blocks:
 
Reported: 2016-02-05 03:52 UTC by Jason W. Bacon
Modified: 2016-03-05 14:00 UTC (History)
1 user (show)

See Also:


Attachments
Shar archive (7.13 KB, text/plain)
2016-02-05 03:52 UTC, Jason W. Bacon
no flags Details
Poudriere log (17.90 KB, text/plain)
2016-02-05 03:53 UTC, Jason W. Bacon
no flags Details
Poudriere log (328.73 KB, text/plain)
2016-02-05 03:53 UTC, Jason W. Bacon
no flags Details
Shar archive (7.50 KB, text/plain)
2016-03-04 15:38 UTC, Jason W. Bacon
no flags Details
Poudriere log (329.20 KB, text/plain)
2016-03-04 15:40 UTC, Jason W. Bacon
no flags Details
Poudriere log (329.78 KB, text/plain)
2016-03-04 15:41 UTC, Jason W. Bacon
no flags Details

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Description Jason W. Bacon freebsd_committer 2016-02-05 03:52:24 UTC
Created attachment 166589 [details]
Shar archive

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

WWW: http://bowtie-bio.sourceforge.net/index.shtml

Dependency for Trinity genomics pipeline.
Comment 1 Jason W. Bacon freebsd_committer 2016-02-05 03:53:09 UTC
Created attachment 166590 [details]
Poudriere log
Comment 2 Jason W. Bacon freebsd_committer 2016-02-05 03:53:44 UTC
Created attachment 166591 [details]
Poudriere log
Comment 3 Raphael Kubo da Costa freebsd_committer 2016-02-26 17:36:30 UTC
A few comments and suggestions:

* GH_TAGNAME can be replaced with DISTVERSIONPREFIX=v.
* WITH_DEBUG=yes should only be set by users, you're not supposed to force a debug version to be built by default.
* The bsd.port.{pre,post}.mk includes can be replaced by a single bsd.port.mk include at the end.
* The code in Mk/bsd.sites.mk handling USE_GITHUB already takes care of properly setting WRKSRC, so you don't need to set it in the Makefile.
* bowtie's Makefile already handles installing the *-l and *-s binaries, so you can drop that part of your do-install code (and make it a post-install target instead).
Comment 4 Jason W. Bacon freebsd_committer 2016-03-01 02:19:21 UTC
Hold off on this.

We're going to need both bowtie 1 and bowtie 2 for Trinity.  I'll send an altered shar and another PR for bowtie 2 shortly.
Comment 5 Jason W. Bacon freebsd_committer 2016-03-04 15:38:45 UTC
Created attachment 167715 [details]
Shar archive

Modified port to coexist with bowtie2.  It will be necessary to maintain both bowtie1 and bowtie2 for a while.  E.g., both are currently required by the Trinity genomics pipeline.
Comment 6 Jason W. Bacon freebsd_committer 2016-03-04 15:40:29 UTC
Created attachment 167716 [details]
Poudriere log
Comment 7 Jason W. Bacon freebsd_committer 2016-03-04 15:41:09 UTC
Created attachment 167717 [details]
Poudriere log
Comment 8 Kubilay Kocak freebsd_committer freebsd_triage 2016-03-04 15:56:48 UTC
Thank you Jason

For future issues please use the format category/portname: ${COMMENT}

Also, poudriere logs are not required to be attached, but please confirm they have been tested in the issue description, something like:

portlint: OK (summary output)
testport: OK (poudriere: <versions>, <archs>, <options> tested)
unittest: OK (test suite summary output)
Comment 9 Raphael Kubo da Costa freebsd_committer 2016-03-05 13:21:14 UTC
portlint -AC looks OK in my tests, as well as poudriere testport with an 11amd64 jail, so I'm landing this one.
Comment 10 commit-hook freebsd_committer 2016-03-05 13:21:51 UTC
A commit references this bug:

Author: rakuco
Date: Sat Mar  5 13:21:27 UTC 2016
New revision: 410180
URL: https://svnweb.freebsd.org/changeset/ports/410180

Log:
  New port: biology/bowtie.

  Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
  DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
  reads per hour.

  WWW: http://bowtie-bio.sourceforge.net/index.shtml

  PR:		206939
  Submitted by:	Jason Bacon <bacon4000@gmail.com>

Changes:
  head/biology/Makefile
  head/biology/bowtie/
  head/biology/bowtie/Makefile
  head/biology/bowtie/distinfo
  head/biology/bowtie/files/
  head/biology/bowtie/files/patch-Makefile
  head/biology/bowtie/pkg-descr
  head/biology/bowtie/pkg-plist
Comment 11 Jason W. Bacon freebsd_committer 2016-03-05 14:00:32 UTC
Guys,

Thanks for the feedback and the quick commit!