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3033 commits

Author SHA1 Message Date
Jason W. Bacon
2d3f4b8c54 biology/vcf2hap: Update to 0.1.3 
Updates for new biolibc API

Changes:        https://github.com/auerlab/vcf2hap/releases
 2021-06-11 10:05:19 -05:00
Jason W. Bacon
874cf7c259 biology/ad2vcf: Update to 0.1.3 
Updates for new biolibc API

Changes:        https://github.com/auerlab/ad2vcf/releases
 2021-06-11 10:05:18 -05:00
Jason W. Bacon
495634f580 biology/biolibc: Update to 0.1.3 
Changes:        https://github.com/auerlab/biolibc/releases
 2021-06-11 10:05:18 -05:00
Piotr Kubaj
0a618235c7 biology/fasttree: fix build on powerpc 
LLVM on powerpc doesn't have libomp.
Same issue happens on armv6 and armv7 but someone has to test whether doing the same for those architectures is enough.
 2021-06-10 12:25:31 +00:00
Piotr Kubaj
8aae744d04 biology/cd-hit: fix build on powerpc 
LLVM on powerpc doesn't have libomp:
cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
 2021-06-10 00:35:36 +00:00
Joseph Mingrone
c33cf04fe5
biology/hyphy: Update to 2.5.31 
https://github.com/veg/hyphy/releases/tag/2.5.31
 2021-06-05 20:00:24 -03:00
Yuri Victorovich
8b8c1272ea biology/jalview: Broken on 11 
Also fix number of lines in pkg-descr, and replace space with tab.

Reported by:	fallout
 2021-06-05 11:53:07 -07:00
Yuri Victorovich
8541c28c07 biology/seqan3: Update 3.0.2-1195 -> 3.0.3 
Reported by:	portscout
 2021-05-29 22:38:08 -07:00
Jason W. Bacon
da0bb00a74 biology/minimap2: Update to 2.20 
Add "extra" binaries to install

Changes:    https://github.com/lh3/minimap2/releases/tag/v2.20
 2021-05-29 16:06:34 -05:00
Yuri Victorovich
5b018ca962 biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit 2021-05-26 15:25:22 -07:00
Yuri Victorovich
be2fb2f290 biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers 2021-05-26 15:25:21 -07:00
Jason W. Bacon
4521502b9b biology/bowtie2: Update to 2.4.4 
Fix deadlock issue in multithreaded execution

Reported by:    portscout
 2021-05-24 11:35:43 -05:00
Yuri Victorovich
191694478f biology/py-resdk: Update 13.2.0 -> 13.3.0 
Reported by:	portscout
 2021-05-24 00:26:50 -07:00
Yuri Victorovich
635f49c9fd biology/seqkit: Update 0.16.0 -> 0.16.1 
Reported by:	portscout
 2021-05-19 23:02:26 -07:00
Danilo Egea Gondolfo
809338d451 biology/iolib: Drop maintainership 2021-05-19 20:56:24 +01:00
Alexey Dokuchaev
6464fe05fe - Update Unipro UGENE to version 38.1 and thus unbreak 
- CONFIG defaults to 64-bit mode now, adjust the check
 2021-05-18 15:24:55 +00:00
Jason W. Bacon
1effaacbaf biology/bowtie2: Update to 2.4.3 
Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64

Reported by:    portscout
Tested by:      pkubaj (powerpc64*)
 2021-05-17 18:40:15 -05:00
Jason W. Bacon
43397d188c biology/ucsc-userapps: Update to v414 
Update license message.  Confirmed via conversation with UCSC that some
proprietary code is used in the "free" tools build.  UCSC is working on it.
 2021-05-15 10:23:08 -05:00
Yasuhiro Kimura
9671981826
*: Remove unnecessary 'port' argument from USES=readline 
PR:		248459
Exp-run by:	antoine
 2021-05-15 09:14:04 +02:00
Dmitry Marakasov
463cdea856 biology/cytoscape: mark unconditionally BROKEN 
Approved by:	portmgr blanket
 2021-05-12 14:55:52 +03:00
Dmitry Marakasov
4b5a5c6d9c biology/ugene: mark BROKEN (does not fetch) 
Approved by:	portmgr blanket
 2021-05-12 14:55:32 +03:00
Yuri Victorovich
4235be6602 biology/seqan3: Correct dependencies 2021-05-11 22:46:21 -07:00
Yuri Victorovich
caced2ad00 biology/seqan3: Add dependency math/lemon 2021-05-11 19:51:37 -07:00
Yuri Victorovich
37be696536 New port: biology/seqan3: C++ header-only library for biological sequence analysis 2021-05-11 18:21:38 -07:00
Po-Chuan Hsieh
f747a647a1
biology/libsbml: Rename LIBXML option to LIBXML2 2021-05-12 05:46:56 +08:00
Thierry Thomas
1d44af5898 math/py-matplotlib: chase minimum Python version in dependent ports 
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.

PR:		255347
Reported by:	sunpoet
 2021-05-10 22:13:20 +02:00
Yuri Victorovich
4e8265c624 biology/mothur: Update 1.45.2 -> 1.45.3 
Reported by:	portscout
 2021-05-09 09:11:11 -07:00
Mathieu Arnold
3505159e72
Deorbit RESTRICTED && NO_CDROM, part two. 
Move ports to the licenses framework.

RESTRICTED → auto-accept (unless expressly stated otherwise)
NO_CDROM → dist-mirror pkg-mirror auto-accept

Differential Revision:  https://reviews.freebsd.org/D30010
 2021-05-06 13:47:48 +02:00
Mathieu Arnold
adb93122cb
Deorbit RESTRICTED && NO_CDROM, part one. 
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.

Approved by:	rene
Differential Revision:	https://reviews.freebsd.org/D30010
 2021-05-06 13:47:41 +02:00
Yuri Victorovich
4e9b2197ad biology/py-resdk: Update 13.1.0 -> 13.2.0 
Reported by:	portscout
 2021-05-05 12:56:26 -07:00
Jason W. Bacon
ba4a5525a2 biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 08:20:39 -05:00
Jason W. Bacon
d2a830e3bd biology/py-dnaio: Update to 0.5.1 
Add py.typed and distribute .pyi files
 2021-05-04 08:19:25 -05:00
Tobias Kortkamp
6707a3c942
Clean up some things 
- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
 2021-05-01 19:55:55 +02:00
Yuri Victorovich
ce04d9a5ee biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1 
Reported by:	portscout
 2021-04-27 01:56:19 -07:00
Jason W. Bacon
dd7bec7711 biology/ncbi-entrez-direct: Update to 14.9.20210423_1 
A few fixes to pass upstream test script
 2021-04-26 11:53:11 -05:00
Jan Beich
bc9e901a17 devel/libepoll-shim: update to 0.0.20210418 
Changes:	https://github.com/jiixyj/epoll-shim/compare/v0.0.20210322...v0.0.20210418
Reported by:	portscout
Approved by:	manu
Differential Revision:	https://reviews.freebsd.org/D29822
 2021-04-26 14:17:32 +00:00
Yuri Victorovich
af49fbec4f biology/jalview: Update 2.07 -> 2.11.1.4 
Take maintainership.
 2021-04-25 16:00:36 -07:00
Antoine Brodin
28164db7c5 Hook biology/ucsc-userapps to the build 2021-04-25 17:47:23 +00:00
Jason W. Bacon
6b63ef7436 biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project 
These are the command-line bioinformatics utilities associated with the UCSC
genome browser.  Care has been taken to install only the freely available
tools.  However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.

Contact UCSC if you are using this port for commercial purposes.
 2021-04-25 12:18:38 -05:00
Jason W. Bacon
ab50f8435a biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases 
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
 2021-04-24 18:40:16 -05:00
Yuri Victorovich
874e67eb5c biology/viennarna: Update 2.4.17 -> 2.4.18 2021-04-23 18:57:38 -07:00
Yuri Victorovich
0ccc5f2584 biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5 2021-04-23 14:57:50 -07:00
Yuri Victorovich
8ec7f5d3de biology/abyss: Update 2.3.0-3 -> 2.3.1 
Reported by:	portscout
 2021-04-22 10:18:02 -07:00
Jason W. Bacon
3c21e709e8 biology/py-crossmap: Update to 0.5.4 
Add viewchain command
Reported by:  portscout
 2021-04-21 08:31:13 -05:00
Kai Knoblich
256e9bc3b5 biology/py-crossmap: Fix build with Python 3.8+ 
* Add missing dependency devel/py-nose that is required to build.  With
  Python 3.6/3.7 there are no build issues because the sdist contains
  Python Eggs of "nose" for these versions.

While I'm here:

* Set NO_ARCH because the port has no architecture specific files.
* Make it concurrent safe, package installs a script and bump
  PORTREVISION due package change.

PR:		253815
Approved by:	portmgr (build fix)
MFH:		No (The port was added after the 2021Q1 branch)
 2021-04-21 09:44:44 +02:00
Kai Knoblich
aaa6b0fc85 biology/py-bigwig: Fix packaging with Python 3.8+ 
* Apply the same fix as in 9cb5898561 by
  stripping libraries by wildcard paths.

* Also use PYTHONPREFIX_SITELIBDIR instead PYTHON_SITELIBDIR to make
  the port PREFIX safe while I'm here.

PR:		253815
Approved by:	python (with hat)
 2021-04-21 09:41:29 +02:00
Yuri Victorovich
b9f16eadc9 New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics 2021-04-19 21:22:01 -07:00
Jason W. Bacon
3bc87a0f1a biology/snpeff: Improvements to Makefile and patches 
Reported by:    Omp
 2021-04-19 11:41:58 -05:00
Yuri Victorovich
8e65beb783 biology/abyss: Update 2.2.5 -> 2.3.0-3 2021-04-18 13:19:56 -07:00
Jason W. Bacon
5164d38ee5 biology/snpeff: Genetic variant annotation and effect prediction toolbox 
Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
 2021-04-18 13:46:29 -05:00