Bug 207993

Summary: [NEW PORT] biology/p5-transdecoder: Identify candidate coding regions within transcript sequences
Product: Ports & Packages Reporter: Jason W. Bacon <jwb>
Component: Individual Port(s)Assignee: Kurt Jaeger <pi>
Status: Closed FIXED    
Severity: Affects Some People CC: pi
Priority: ---    
Version: Latest   
Hardware: Any   
OS: Any   
Attachments:
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Description Jason W. Bacon freebsd_committer freebsd_triage 2016-03-14 18:47:23 UTC 
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.

WWW: http://transdecoder.github.io/

Dependency for upcoming Trinity genomics pipeline.

portlint: OK (looks fine.)
testport: OK (poudriere: {10.1,9.3}-RELEASE {amd64,i386})
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2016-03-15 21:16:10 UTC 
Created attachment 168259 [details]
Shar archive
Comment 2 Kurt Jaeger freebsd_committer freebsd_triage 2016-03-16 19:24:05 UTC 
testbuild@work
Comment 3 commit-hook freebsd_committer freebsd_triage 2016-03-16 20:12:46 UTC 
A commit references this bug:

Author: pi
Date: Wed Mar 16 20:12:33 UTC 2016
New revision: 411246
URL: https://svnweb.freebsd.org/changeset/ports/411246

Log:
  New port: biology/p5-transdecoder

  TransDecoder identifies candidate coding regions within transcript
  sequences, such as those generated by de novo RNA-Seq transcript
  assembly using Trinity, or constructed based on RNA-Seq alignments
  to the genome using Tophat and Cufflinks.

  WWW: http://transdecoder.github.io/

  PR:		207993
  Submitted by:	Jason Bacon <bacon4000@gmail.com>

Changes:
  head/biology/Makefile
  head/biology/p5-transdecoder/
  head/biology/p5-transdecoder/Makefile
  head/biology/p5-transdecoder/distinfo
  head/biology/p5-transdecoder/pkg-descr
  head/biology/p5-transdecoder/pkg-plist
Comment 4 Kurt Jaeger freebsd_committer freebsd_triage 2016-03-16 20:40:51 UTC 
Committed, thanks! Please note that I updated to 2.1.0.
Comment 5 Jason W. Bacon freebsd_committer freebsd_triage 2016-03-17 14:36:03 UTC 
Thanks, Kurt!  The upgrade should be OK in this case.  It would be better to ask before upgrading ports, though.  Many of the genomics apps we use are very sensitive to specific versions of dependencies, since they depend on specific algorithms and command line flags that can change.  They often bundle dependencies as a defensive move for that reason, but I unbundle them wherever it seems reasonable.

Cheers,

    Jason
Comment 6 Kurt Jaeger freebsd_committer freebsd_triage 2016-03-17 14:41:10 UTC 
As this was a new port, I assumed that upgrading it from the start would not be a big problem 8-}