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.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
biology/samtools: Update to 1.16.1
New "reference" subcommand to extract CRAM features (1.16)
Numerous minor enhancements and bug fixes
Changes: https://github.com/samtools/samtools/releases
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
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 )
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 )
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
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
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
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)
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>
