Bug 195592 - [NEW PORT] biology/samtools
Summary: [NEW PORT] biology/samtools
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Pawel Pekala
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-12-02 23:53 UTC by cartwright
Modified: 2014-12-15 22:00 UTC (History)
1 user (show)

See Also:

Attachments
patch to add biology/samtools as new port (7.48 KB, patch)
2014-12-02 23:53 UTC, cartwright 		no flags Details | Diff
patch to add biology/samtools as new port (v2) (8.40 KB, patch)
2014-12-15 21:29 UTC, cartwright 		no flags Details | Diff
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Description cartwright 2014-12-02 23:53:40 UTC 
Created attachment 150113 [details]
patch to add biology/samtools as new port

samtools is a popular set of tools for manipulating next-generation sequencing data in biology.  I have created a port for it and am willing to maintain it.

It requires the biology/htslib port found in request 195591.
Comment 1 Pawel Pekala freebsd_committer freebsd_triage 2014-12-14 22:53:21 UTC 
Fails to build on FreeBSD 8.4 and 9.3 (same reason), please see log:

http://people.freebsd.org/~pawel/buildlogs/samtools-1.1.log
Comment 2 cartwright 2014-12-15 21:29:02 UTC 
Created attachment 150610 [details]
patch to add biology/samtools as new port (v2)
Comment 3 cartwright 2014-12-15 21:30:33 UTC 
(In reply to Pawel Pekala from comment #1)
> Fails to build on FreeBSD 8.4 and 9.3 (same reason), please see log:
> 
> http://people.freebsd.org/~pawel/buildlogs/samtools-1.1.log

I updated the patch to fix the logl expl missing on Freebsd 8 and 9.

Instead of placing a check inside the port's makefile, I decided to update the source file instead.
Comment 4 commit-hook freebsd_committer freebsd_triage 2014-12-15 21:59:30 UTC 
A commit references this bug:

Author: pawel
Date: Mon Dec 15 21:59:22 UTC 2014
New revision: 374767
URL: https://svnweb.freebsd.org/changeset/ports/374767

Log:
  Samtools implements various utilities for post-processing alignments in the
  SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
  with bcftools), and a simple alignment viewer.

  WWW: http://www.htslib.org/

  PR:		195592
  Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

Changes:
  head/biology/Makefile
  head/biology/samtools/
  head/biology/samtools/Makefile
  head/biology/samtools/distinfo
  head/biology/samtools/files/
  head/biology/samtools/files/patch-Makefile
  head/biology/samtools/files/patch-errmod.c
  head/biology/samtools/files/pkg-message.in
  head/biology/samtools/pkg-descr
  head/biology/samtools/pkg-plist