| non port: biology/bcftools/Makefile |
|
SVNWeb
|
Number of commits found: 25 |
|
Fri, 24 Feb 2023
|
[ 23:30 Jason W. Bacon (jwb)  ]    65b8ab9
biology/bcftools: Update to 1.17
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/releases
Reported by: portscout
|
|
Thu, 5 Jan 2023
|
[ 23:19 Jason W. Bacon (jwb) ] adfc943
biology/bcftools: Update to 1.16
New plugin variant-distance to annotate records with distance to the
nearest variant
Numerous minor enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/releases
|
|
Wed, 7 Sep 2022
|
[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
|
|
Wed, 20 Jul 2022
|
[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above )
|
|
Sat, 26 Feb 2022
|
[ 15:04 Jason W. Bacon (jwb) ] 734d2c4
biology/bcftools: Update to 1.15
Several small enhancements
Changes: https://github.com/samtools/bcftools/releases
Reported by: portscout
|
|
Wed, 12 Jan 2022
|
[ 19:41 Tobias C. Berner (tcberner) ] 654acd8 (Only the first 10 of 66 ports in this commit are shown above. )
math/gsl: bump portrevision of consumers after update to 2.7.1
PR: 260201
|
|
Sat, 18 Dec 2021
|
[ 17:56 Jason W. Bacon (jwb) ] 9302b3e
biology/bcftools: Update to 1.14
A few minor enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/tags
|
|
Mon, 12 Jul 2021
|
[ 13:30 Jason W. Bacon (jwb) ] 94c639f
biology/bcftools: Update to 1.13
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/releases/tag/1.13
Reported by: portscout
|
|
Wed, 16 Jun 2021
|
[ 19:31 Tobias C. Berner (tcberner) ] 63e653a (Only the first 10 of 66 ports in this commit are shown above. )
math/gsl: update to 2.7
From [1]
* What is new in gsl-2.7:
* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
* fixed bug #60335 (spmatrix test failure, J. Lamb)
* fixed bug #36577
* clarified documentation on interpolation accelerators (V. Krishnan)
* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
* fixed doc bug #59758
* fixed bug #58202 (rstat median for n=5)
* added support for native C complex number types in gsl_complex
when using a C11 compiler
* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6 (Only the first 15 lines of the commit message are shown above )
|
|
Tue, 6 Apr 2021
|
[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
|
|
Sat, 20 Mar 2021
|
[ 17:14 jwb ]   (Only the first 10 of 17 ports in this commit are shown above. )
biology/htslib: Update to 1.12
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12
Numerous enhancements, performance improvements, and bug fixes since 1.11
Build-tested all other htslib dependents, no revbumps should be needed
Reported by: portscout
|
|
Thu, 5 Nov 2020
|
[ 20:34 jwb ]
biology/bcftools: Upgrade to 1.11
Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/bcftools/releases/tag/1.11
Reported by: portscout
|
|
Mon, 3 Aug 2020
|
[ 18:16 jwb ]
biology/bcftools: Upgrade to 1.10.2
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/bcftools/tags
Take maintainership per ports/248089.
PR: ports/248089
|
[ 17:40 jwb ] (Only the first 10 of 12 ports in this commit are shown above. )
biology/htslib: Upgrade to 1.10.2
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags
Bump PORTREVISION on dependents that don't require additional patching
PR: 248089
|
|
Fri, 25 Oct 2019
|
[ 23:41 tcberner ] (Only the first 10 of 64 ports in this commit are shown above. )
math/gsl: update to 2.6
- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
- this also breaks the two consumers of this port
- biology/gemma: has a conflict with cblas, and is makred broken.
PR: 241363
Exp-run by: antoine
|
|
Thu, 2 Aug 2018
|
[ 19:30 fernape ]
biology/bcftools: update to 1.9
While here:
* Update LICENSE handling
* Move all commands to bin/
PR: 230169
Submitted by: ndowens.fbsd@yandex.com
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D16543
|
|
Sat, 23 Jun 2018
|
[ 08:27 tcberner ] (Only the first 10 of 47 ports in this commit are shown above. )
Update math/gsl to 2.5
PR: 229067
|
|
Mon, 4 Dec 2017
|
[ 15:27 mat ]
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
|
|
Wed, 25 Oct 2017
|
[ 10:19 pizzamig ] (Only the first 10 of 25 ports in this commit are shown above. )
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
|
|
Mon, 3 Jul 2017
|
[ 20:38 tcberner ] (Only the first 10 of 42 ports in this commit are shown above. )
Update math/gsl to 2.4
Exp-Run by: antoine
PR: 220408
|
|
Tue, 2 May 2017
|
[ 05:26 tcberner ] (Only the first 10 of 46 ports in this commit are shown above. )
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
|
|
Thu, 26 May 2016
|
[ 20:28 pi ]
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)
|
|
Fri, 1 Apr 2016
|
[ 13:29 mat ] (Only the first 10 of 1009 ports in this commit are shown above. )
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
|
|
Fri, 25 Dec 2015
|
[ 01:31 junovitch ] (Only the first 10 of 27 ports in this commit are shown above. )
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)
|
|
Fri, 5 Jun 2015
|
[ 21:01 pi ] (Only the first 10 of 12 ports in this commit are shown above. )
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
|
Number of commits found: 25 |
As an Amazon Associate I earn from qualifying purchases.