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Port details
samtools Tools for manipulating next-generation sequencing data
1.3.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Dec 2014 21:59:37
License: MIT
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/
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/samtools/ && make install clean
To add the package: pkg install samtools

PKGNAME: samtools

distinfo:

TIMESTAMP = 1463691050
SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768
SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. htslib>=1.3 : biology/htslib
  2. autoconf-2.69 : devel/autoconf
  3. autoheader-2.69 : devel/autoconf
  4. autoreconf-2.69 : devel/autoconf
  5. aclocal-1.15 : devel/automake
  6. automake-1.15 : devel/automake
  7. gmake : devel/gmake
Library dependencies:
  1. libhts.so : biology/htslib
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
autoreconf gmake ncurses perl5 shebangfix

Master Sites:
  1. https://codeload.github.com/samtools/samtools/tar.gz/1.3.1?dummy=/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 May 2016 20:28:55
Original commit files touched by this commit  1.3.1
Revision:415914
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
19 May 2016 11:09:14
Original commit files touched by this commit  1.3
Revision:415503
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
01 Feb 2016 21:59:15
Original commit files touched by this commit  1.3
Revision:407776
marino search for other commits by this committer
biology/samtools: document ncurses requirement (USES+=ncurses)

approved by:	infrastructure blanket
25 Dec 2015 01:31:09
Original commit files touched by this commit  1.3
Revision:404398
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
06 May 2015 15:16:54
Original commit files touched by this commit  1.2
Revision:385521
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
06 Mar 2015 12:53:59
Original commit files touched by this commit  1.2
Revision:380597
robak search for other commits by this committer
biology/samtools: update 1.1 -> 1.2

PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
15 Dec 2014 21:59:20
Original commit files touched by this commit  1.1
Revision:374767
pawel search for other commits by this committer
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>

Number of commits found: 8

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