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9 commits

Author SHA1 Message Date
Mathieu Arnold
6063af74e8 Add a USES=python:env, that will not add a dependency on Python. 
It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
 2017-12-04 15:27:29 +00:00
Luca Pizzamiglio
ecaa1024a6 biology/htslib biology/bcftools biology/samtools: Update to 1.6 
PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
 2017-10-25 10:19:50 +00:00
Tobias C. Berner
5da7ccc1fb Update math/gsl to 2.4 
Exp-Run by:	antoine
PR:		220408
 2017-07-03 20:38:11 +00:00
Tobias C. Berner
8c99ed5982 Update math/gsl to 2.3 
This release introduces some new features and fixes several bugs:
	http://savannah.gnu.org/forum/forum.php?forum_id=8751

* update to 2.3 and take maintainership
* update math/py-gsl to 2.2.0 for gsl2 support
* update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support

PR:		218952
Exp-run by:	antoine
Reviewed by:	mat, rakuco
Approved by:	rakuco (mentor)
Differential Revision:	https://reviews.freebsd.org/D10522
 2017-05-02 05:26:40 +00:00
Kurt Jaeger
04b3bb054f 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)
 2016-05-26 20:28:55 +00:00
Dmitry Marakasov
e87a8bd319 - Fix trailing whitespace in pkg-messages 
Approved by:	portmgr blanket
 2016-05-19 11:09:14 +00:00
Mathieu Arnold
7f4572eae4 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 
With hat:	portmgr
Sponsored by:	Absolight
 2016-04-01 13:29:15 +00:00
Jason Unovitch
d5dffd3623 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)
 2015-12-25 01:31:09 +00:00
Kurt Jaeger
def75b1a0f New port: biology/bcftools 
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.

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

PR:		199747
Submitted by:	cartwright@asu.edu
 2015-06-05 21:01:13 +00:00