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2916 commits

Author SHA1 Message Date
Jason W. Bacon
2730cd269d biology/py-multiqc: Update to 1.9 
Fix runtime error due to incompatibility of 1.8 with latest matplotlib
Drop python2 support
Numerous new features and bug fixes
 2021-02-05 01:37:04 +00:00
Jason W. Bacon
3d92ad6430 biology/fastqc: Update to 0.11.9 
Minor bug fixes since 0.11.8
 2021-02-04 15:56:33 +00:00
Yuri Victorovich
796bc858a2 biology/bioparser: Update 3.0.12 -> 3.0.12-2 
Install target is added.
 2021-02-03 19:08:28 +00:00
Jason W. Bacon
b9a6bfa5fa biology/py-cutadapt: Update to 3.2 
biology/py-dnaio: Update to 0.5.0
archivers/py-xopen: Update to 1.0.0

Numerous bug fixes and enhancements since cutadapt 3.2

Document cutadapt dependency versions dnaio~=0.5.0 xopen~=1.0.0
Bump python dependency to 3.6+ to restrict package builds
 2021-02-02 20:39:09 +00:00
Jason W. Bacon
aad6ba1685 biology/bowtie2: Reverse switch to devel/onetbb 
Mistakenly believed onetbb was already committed

PR:             252683
 2021-01-30 17:43:56 +00:00
Jason W. Bacon
1daa1d9193 biology/bowtie2: Switch to devel/onetbb 
PR:             252683
Submitted by:   martymac
 2021-01-30 17:39:53 +00:00
Jason W. Bacon
d3b9bdbb62 biology/vsearch: Update to 2.15.2 
Code clean up and modernization

Reported by:    portscout
 2021-01-30 15:31:11 +00:00
Sunpoet Po-Chuan Hsieh
4aa27da231 Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+ 
PR:		250103
 2021-01-30 13:29:58 +00:00
Joseph Mingrone
059ebf3da7 biology/hyphy: Update to version 2.5.27 
https://github.com/veg/hyphy/releases/tag/2.5.27
 2021-01-27 11:33:53 +00:00
Jason W. Bacon
3c0ec18494 biology/kallisto: Add -lz for pending hdf5 upgrade 
PR:             252965
Submitted by:   thierry
 2021-01-26 01:34:20 +00:00
Jason W. Bacon
1be2189fb5 biology/bedtools: Upgrade to 2.30.0 
Several bug fixes and performance enhancements

Reported by:    portscout
 2021-01-24 18:25:39 +00:00
Jason W. Bacon
92b5f80904 biology/haplohseq: Fix example scripts for python 3 
Also clean up plist
 2021-01-23 19:31:49 +00:00
Jason W. Bacon
ed49d2418f biology/bedtools: License changed upstream 2021-01-22 14:55:02 +00:00
Yuri Victorovich
9607e839e2 biology/gatk: Add the WITH_LARGE_FILES option. 2021-01-22 02:50:38 +00:00
Yuri Victorovich
470760f412 biology/gatk: Update 4.1.8.1 -> 4.1.9.0 2021-01-21 23:15:40 +00:00
Mark Linimon
7b1d50abc2 Fix build on GCC-based systems by adding compiler:c++14-lang to USES: 
CMake Error in CMakeLists.txt:
  Target "runTests" requires the language dialect "CXX14" , but CMake does
  not know the compile flags to use to enable it.

Approved by:	portmgr (tier-2 blanket)
 2021-01-20 02:31:33 +00:00
Mark Linimon
2f70a05762 Add compiler:c++11-lang to USES to fix build on GCC-based systems: 
CMake Error in CMakeLists.txt:
  Target "rampler" requires the language dialect "CXX11" , but CMake does not
  know the compile flags to use to enable it.

Approved by:	portmgr (tier-2 blanket)
 2021-01-20 02:30:13 +00:00
Yuri Victorovich
dcbbedf21e biology/bioparser: Cosmetic changes 2021-01-19 09:56:15 +00:00
Yuri Victorovich
3f71b2e05d New port: biology/rampler: Standalone module for sampling genomic sequences 2021-01-19 09:49:53 +00:00
Yuri Victorovich
14a3d5e688 New port: biology/edlib: Fast C++ library for sequence alignment using edit distance 2021-01-19 09:41:54 +00:00
Yuri Victorovich
1446cc829c New port: biology/spoa: C++ implementation of the partial order alignment (POA) algorithm 2021-01-19 09:28:00 +00:00
Yuri Victorovich
f579f97eec New port: biology/biosoup: Collection of C++ header-only data structures for bioinformatics 2021-01-19 09:01:41 +00:00
Yuri Victorovich
352da80b91 New port: biology/bioparser: C++ header only parsing library for several formats in bioinformatics 2021-01-19 07:56:49 +00:00
Mark Linimon
c9edd6a5af Mark BROKEN on riscv64 the same as on aarch64. 
While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing
 2021-01-19 02:29:16 +00:00
Mark Linimon
58d53fb823 Mark BROKEN on riscv64 the same as armv*: 
# make[2]: cannot open makefile..

Note the filname reported is "Makefile." (e.g. probably empty suffix).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing
 2021-01-19 02:26:53 +00:00
Piotr Kubaj
652059e7b0 biology/vsearch: enable on powerpc64le 2021-01-16 17:51:56 +00:00
Joseph Mingrone
3d9e4abbe0 biology/hyphy: Update to version 2.5.26 
https://github.com/veg/hyphy/releases/tag/2.5.26
 2021-01-15 20:09:29 +00:00
Jason W. Bacon
d0029e3e01 biology/haplohseq: Restrict to python3 
Also remove extraneous @dir from plist

Reported by:    rene
 2021-01-15 00:08:06 +00:00
Antoine Brodin
29a9d959e5 Hook haplohseq to the build 2021-01-14 21:44:50 +00:00
Jason W. Bacon
eb0d9154a7 biology/haplohseq: Resurrect and fix python2 dependency 
Move upstream to Github fork
 2021-01-14 15:51:19 +00:00
Danilo G. Baio
b53abbd839 Remove PY_SPHINX from ports using Python 3 
Approved by:	 portmgr blanket
Differential Revision:	https://reviews.freebsd.org/D28093
 2021-01-14 14:34:38 +00:00
Joseph Mingrone
ed900cd58f biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build 
- USES=compiler:openmp still forces building with GCC.  This is no longer
  necessary on tier 1 platforms, which have openmp in base.

- Mark broken on i386, because base clang doesn't have 64 bit atomic
  functions for i386 (see bug 230888).

PR:		247753, 252379
Submitted by:	cmt (based on)
 2021-01-12 18:12:12 +00:00
Joseph Mingrone
56dac58885 biology/hyphy: Remove USES=compiler:openmp 
USES=compiler:openmp still forces building with GCC.  This is no longer
necessary on tier 1 platforms, which have openmp in the base system.

PR:		247753, 252379
 2021-01-11 17:54:42 +00:00
Jason W. Bacon
d139fe0bb6 biology/star: Drop dependency on gcc 
Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379
 2021-01-11 17:39:52 +00:00
Jason W. Bacon
bced63b1b3 biology/stacks: Drop dependency on gcc 
Replace compiler:openmp with compiler:c++11-lang and localbase
Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888)

PR:             port/247753, ports/252379
 2021-01-11 17:27:30 +00:00
Jason W. Bacon
ef66586163 biology/ncbi-blast+: Drop dependency on gcc 
Replace compiler:openmp with compiler:c++14-lang
Clang build also requires localbase:ldflags and a source patch to explicitly
set variables to shared
GCC-based platforms still require -latomic

PR:             port/247753, ports/252379
 2021-01-11 17:17:35 +00:00
Jason W. Bacon
426575b829 biology/gcta: Drop dependency on gcc 
Replace compiler:openmp with compiler:c++11-lang
Clang build also requires localbase:ldflags
Build tested on amd64, i386 and powerpc64 12.x-RELEASE

PR:             port/247753, ports/252379
 2021-01-11 17:09:37 +00:00
Jason W. Bacon
e1d8f0f9ca biology/fasttree: Drop dependency on gcc 
Simply remove compiler:openmp
Builds with base compiler on amd64, i386, and powerpc64 12.x-RELEASE

PR:             port/247753, ports/252379
 2021-01-11 16:58:13 +00:00
Jason W. Bacon
f5e841741a biology/cd-hit: Drop dependency on gcc 
Simply remove compiler:openmp
Builds with base compiler on amd64, i386, and powerpc64

PR:             port/247753, ports/252379
 2021-01-11 16:55:15 +00:00
Jason W. Bacon
1348c56403 biology/canu: Drop dependency on gcc 
Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379
 2021-01-11 16:51:15 +00:00
Joseph Mingrone
006187bc28 biology/py-biom-format: Update to version 2.1.10 
https://github.com/biocore/biom-format/releases/tag/2.1.10
 2021-01-11 05:28:11 +00:00
Joseph Mingrone
959aa35d1a biology/hyphy: Update to version 2.5.25 
https://github.com/veg/hyphy/releases/tag/2.5.25
 2021-01-11 02:51:29 +00:00
Jason W. Bacon
2a7a94c304 biology/pooler: Upgrade to 1.76 
Fixes race condition for make jobs in upstream Makefile

PR:             252352
Submitted by:   silas-freebsd@flatline.org.uk
 2021-01-08 22:44:13 +00:00
Jason W. Bacon
ad36c9cb17 biology/gemma: Upgrade to 0.98.3 
Minor bug fixes and enhancements

Reported by:    portscout
 2021-01-02 22:05:58 +00:00
Mark Linimon
f2fbf5a1ed For ports on riscv64 that fail the same (or similar ways) to aarch64, mark 
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
 2021-01-02 01:46:08 +00:00
Alexey Dokuchaev
8f46816990 - Update Unipro UGENE port to version 37.0 
- Drop no longer used WebEngine dependencies
- Force SSE2 on i386 (required for the build)
- Chase HTTP 301 redirection in the WWW line
 2020-12-31 13:43:09 +00:00
Antoine Brodin
aa7a6c429e Drop python 2.7 support from a few ports 
With hat:	portmgr
 2020-12-28 23:02:12 +00:00
Greg Lewis
05e1cc8a0a Restrict to Java 8, since this doesn't compile with Java 11 
PR:			251774
 2020-12-26 23:01:20 +00:00
Antoine Brodin
14be7bd191 scipy 1.5.4 is only compatible with python 3.6+ 
Reported by:	pkg-fallout
 2020-12-24 09:03:39 +00:00
Joseph Mingrone
a2869b87e2 biology/hyphy: Update to version 2.5.24 
https://github.com/veg/hyphy/releases/tag/2.5.24
 2020-12-20 20:21:52 +00:00