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Port details
plinkseq Toolset for working with human genetic variation data
0.10_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: bacon4000@gmail.com search for ports maintained by this maintainer
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data. The specific focus is to provide a platform
for analytic tool development for variation data from large-scale
resequencing and genotyping projects, particularly whole-exome and
whole-genome studies. It is independent of (but designed to be
complementary to) the existing PLINK package.

WWW: http://atgu.mgh.harvard.edu/plinkseq/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (13 items)
  1. /usr/local/share/licenses/plinkseq-0.10_1/catalog.mk
  2. /usr/local/share/licenses/plinkseq-0.10_1/LICENSE
  3. /usr/local/share/licenses/plinkseq-0.10_1/GPLv2
  4. bin/behead
  5. bin/browser
  6. bin/gcol
  7. bin/mm
  8. bin/mongoose
  9. bin/pdas
  10. bin/pseq
  11. bin/smp
  12. bin/tab2vcf
  13. lib/libplinkseq.a
  14. Collapse this list.

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

PKGNAME: plinkseq

distinfo:

SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58
SIZE (plinkseq-src-0.10.tgz) = 6090698


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

Build dependencies:
  1. gmake : devel/gmake
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
libtool gmake

Master Sites:
  1. http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
13 May 2017 03:35:51
Original commit files touched by this commit  0.10_1
Revision:440746
linimon search for other commits by this committer
Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
27 Feb 2017 14:09:25
Original commit files touched by this commit  0.10_1
Revision:434941
jbeich search for other commits by this committer
biology/plinkseq: unbreak with clang 4.0

PR:		216618
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
11 Nov 2016 09:31:03
Original commit files touched by this commit  0.10
Revision:425879
linimon search for other commits by this committer
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
21 Apr 2016 16:43:15
Original commit files touched by this commit  0.10
Revision:413746
swills search for other commits by this committer
many ports: mark broken on powerpc64
11 Dec 2015 08:48:57
Original commit files touched by this commit  0.10
Revision:403506
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
12 Oct 2014 03:16:10
Original commit files touched by this commit  0.10
Revision:370680
wen search for other commits by this committer
- Update to 0.10

PR:		194309
Submitted by:	jwbacon@tds.net(maintainer)
04 Oct 2014 15:12:45
Original commit files touched by this commit  0.08_3
Revision:369969
sunpoet search for other commits by this committer
- Update to 2.6.0
- Update MASTER_SITES
- Add my LOCAL to MASTER_SITES
- Use USE_CSTD
- Use MAKE_CMD
- Reformat pkg-descr
- Update WWW
- Take maintainership
- Bump PORTREVISION for devel/protobuf shlib change

Changes:	https://code.google.com/p/protobuf/source/browse/trunk/CHANGES.txt
22 Jul 2014 22:12:15
Original commit files touched by this commit  0.08_2
Revision:362596
amdmi3 search for other commits by this committer
- Switch to USES=libtool, drop .la files
- Fix shebangs

Approved by:	portmgr blanket
07 Mar 2014 11:37:35
Original commit files touched by this commit  0.08_1
Revision:347367
bapt search for other commits by this committer
Convert to dos2unix
31 Jan 2014 12:33:12
Original commit files touched by this commit  0.08_1
Revision:341988
miwi search for other commits by this committer
- Stage support
11 Dec 2013 14:43:51
Original commit files touched by this commit  0.08_1
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
20 Sep 2013 15:55:44
Original commit files touched by this commit  0.08_1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
21 Mar 2013 14:09:23
Original commit files touched by this commit  0.08_1
Revision:314843
vanilla search for other commits by this committer
Fix build with protobuf-2.5.0

Obtained from:	miwi@
18 Mar 2013 15:14:28
Original commit files touched by this commit  0.08_1
Revision:314580
vanilla search for other commits by this committer
1: Upgrade protobuf to 2.5.0.
2: bump revision.
3: document UPDATING.
27 Sep 2012 09:59:25
Original commit files touched by this commit  0.08
Revision:304954
makc search for other commits by this committer
Add new ports biology/plink [1] and biology/plinkseq [2]:

PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>

Number of commits found: 15

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