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2773 Commits

Author SHA1 Message Date
Antoine Brodin
05e7068032 Unbreak bulk -a 2020-07-14 07:59:28 +00:00
Fernando Apesteguía
eeb65f1dea biology/phyml: update to 3.3.20200621 
From ChangeLog: https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621

This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets

Reported by:	portscout
 2020-07-10 09:45:48 +00:00
Yuri Victorovich
7c58728f1a biology/gatk: Update 4.1.7.0 -> 4.1.8.0 2020-07-09 00:40:56 +00:00
Piotr Kubaj
c39c3cf66a biology/cufflinks: fix build on GCC architectures 
Using Boost requires modern compiler.

MFH:		2020Q3 (fix build blanket)
 2020-07-08 10:37:07 +00:00
Niclas Zeising
0e32330f15 Chanse update of devel/libffi 
Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.

PR:		247028 (for tracking)
 2020-07-04 18:11:42 +00:00
Tobias Kortkamp
815d0dd7cb biology/psi88: Unbreak build with GCC 10 
ctplot.f:69:29:

   69 |       CALL SYMBOL (XA,YA,.15,STRING,ANGLE,K)
      |                             1
Error: Rank mismatch in argument 'string' at (1) (scalar and rank-1)

http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/psi88-1.0_16.log

PR:		246700
 2020-07-04 12:15:58 +00:00
Tobias Kortkamp
4636ef2c1b biology/bowtie: Unbreak build with GCC 10 
In file included from ebwt.h:43,
                 from ebwt_build.cpp:11:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                      ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                                                                      ^

http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log

PR:		246700
 2020-07-04 10:46:08 +00:00
Joseph Mingrone
5848822bf5 biology/diamond: Update to version 0.9.36 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
 2020-07-03 11:22:49 +00:00
Tobias C. Berner
e2cd5999be Bump devel/jsoncpp consumers after r540853. 
Reported by:	Kevin Oberman <rkoberman@gmail.com>
 2020-06-30 17:46:18 +00:00
Joseph Mingrone
26bcffc642 biology/hyphy: Update to version 2.5.15 
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15
 2020-06-28 16:40:33 +00:00
Joseph Mingrone
bca3b9c7c6 biology/diamond: Update to version 0.9.35 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
 2020-06-27 16:26:54 +00:00
Sunpoet Po-Chuan Hsieh
aae33b1c39 Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113 
- Fix LICENSE_FILE
- Update pkg-descr
- Update WWW
- Bump PORTREVISION of dependent ports for dependency change

Changes:	https://metacpan.org/changes/distribution/IO-Stringy
 2020-06-26 11:55:23 +00:00
Yuri Victorovich
bfb73bae45 biology/py-bx-python: Update 0.8.8 -> 0.8.9 
Reported by:	portscout
 2020-06-26 04:17:11 +00:00
Muhammad Moinur Rahman
0f6a33fa25 biology/seaview: Update version 5.0.3=>5.0.4 
Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES
 2020-06-22 17:34:44 +00:00
Jason W. Bacon
364ffe7adb biology/vsearch: Update to 2.15.0 
Numerous minor enhancements
 2020-06-20 14:31:59 +00:00
Sunpoet Po-Chuan Hsieh
cb333cf1ec Move devel/swig30 to devel/swig and update to 4.0.1 
- Do not silence installation message
- Update dependent ports:
  - Fix build with swig 4.0.1
  - Update *_DEPENDS
  - Remove BINARY_ALIAS

Changes:	http://www.swig.org/news.php
PR:		246613
Exp-run by:	antoine
 2020-06-17 18:17:45 +00:00
Yuri Victorovich
40cd9173f1 biology/py-loompy: Update 2.0.17 -> 3.0.6 2020-06-16 02:26:08 +00:00
Yuri Victorovich
ebcf683eeb biology/py-gffutils: Update 0.10 -> 0.10.1 2020-06-16 02:10:08 +00:00
Muhammad Moinur Rahman
d1fc6f0742 biology/seaview: Update version 5.0.2=>5.0.3 
Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES
 2020-06-14 09:24:18 +00:00
Antoine Brodin
ae73d29444 Unbreak bulk -a 2020-06-13 15:05:44 +00:00
Jason W. Bacon
4a5b8a759b biology/picard-tools: CLI tools for manipulating sequencing data 
Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
 2020-06-13 13:54:47 +00:00
Jason W. Bacon
3fadea798f biology/py-biopython: Set python requirement to 3.6+ 
New requirement for v1.77 overlooked during upgrade
 2020-06-13 13:42:12 +00:00
Joseph Mingrone
f177208d8a biology/diamond: Update to version 0.9.34 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
 2020-06-12 12:12:12 +00:00
Yuri Victorovich
6be1f6208a biology/py-pysam: Update 0.15.4 -> 0.16.0 
Reported by:	potscout
 2020-06-09 05:03:48 +00:00
Mark Linimon
45b857df74 Add compiler:c++0x to USES to fix build on GCC-based systems: 
cc1plus: error: unrecognized command line option "-std=c++0x

Approved by:	portmgr (tier-2 blanket)
 2020-06-05 03:49:53 +00:00
Jason W. Bacon
c81fc00817 biology/bioawk: BWK awk modified for biological data 
Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
 2020-06-05 02:45:33 +00:00
Jason W. Bacon
a156fdcf52 biology/subread: Read alignment, quantification and mutation discovery 
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.
 2020-06-05 01:55:49 +00:00
Jason W. Bacon
c468c4c36e bioloty/vt: Discovers short variants from Next Generation Sequencing data 2020-06-04 18:28:13 +00:00
Joseph Mingrone
1337e0f38e biology/diamond: Update to version 0.9.33 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
 2020-06-03 21:44:36 +00:00
Joseph Mingrone
e677d43938 biology/hyphy: Update to version 2.5.14 
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
 2020-05-30 19:39:11 +00:00
Joseph Mingrone
b6ff694fa1 biology/iqtree: Update to version 2.0.6 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6
 2020-05-30 18:43:26 +00:00
Yuri Victorovich
9a1ae269a1 biology/abyss: Update 2.2.3 -> 2.2.4 2020-05-30 09:10:44 +00:00
Tobias Kortkamp
c7259fc4f0 Clean up some things 
Reported by:	portscan
 2020-05-30 00:57:02 +00:00
Jason W. Bacon
176e391e4b biology/py-biopython: Upgrade to 1.77 
Upstream support for python 3

PR:             ports/246763
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
 2020-05-29 02:03:29 +00:00
Yuri Victorovich
886c38f990 biology/gatk: Update 4.1.5.0 -> 4.1.7.0 2020-05-28 02:26:51 +00:00
Joseph Mingrone
f2eb31b436 biology/iqtree: Update to version 2.0.5 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5

While here, incorporate portfmt suggestions.
 2020-05-28 00:27:13 +00:00
Alexey Dokuchaev
907a4eb7ab Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1). 2020-05-27 11:59:13 +00:00
Mark Linimon
83bde94c5f Mark as BROKEN on powerpc64 12. It builds on -head. 
While here, pet portlint (remove extra blank line).

Approved by:	portmgr (tier-2 blanket)
 2020-05-26 03:37:48 +00:00
Jason W. Bacon
0a773a86c6 biology/py-dnaio: Upgrade to 0.4.2 
Reported by:    portscout
 2020-05-24 15:23:15 +00:00
Tobias C. Berner
90ba7116a9 biology/ugene: prepare for Qt5-5.15 2020-05-19 18:00:02 +00:00
Mark Linimon
f5d9ceebea Mark as BROKEN on powerpc64: 
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field

This may have something to do with compiler:openmp in USES.  However,
it has broken for more than 6 months at this point.

Approved by:	portmgr (tier-2 blanket)
 2020-05-17 02:25:16 +00:00
Sunpoet Po-Chuan Hsieh
7f5cbfeed4 Bump PORTREVISION for security/nettle shlib change 2020-05-16 10:51:32 +00:00
Yuri Victorovich
14a9e6c989 New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments 2020-05-16 03:11:05 +00:00
Yuri Victorovich
af1eacd3da biology/py-scikit-bio: Fix license 2020-05-16 02:29:20 +00:00
Yuri Victorovich
d7d9fbffcc biology/py-scikit-bio: Remove bogus lines 2020-05-16 02:28:14 +00:00
Yuri Victorovich
b1b7f59bd1 New port: biology/py-scikit-bio: Data structures, algorithms, educational resources for bioinformatics 2020-05-16 02:25:35 +00:00
Yuri Victorovich
634ce3b531 New port: biology/py-pandas-charm: Library for getting character matrices into and out of pandas 2020-05-16 00:14:16 +00:00
Yuri Victorovich
02a5c651ae New port: biology/py-ete3: Framework for the analysis and visualization of trees 2020-05-16 00:13:09 +00:00
Mark Linimon
8e6916844e Add compiler:c++11-lang to USES to fix build on GCC-based systems: 
configure: error: *** A compiler with support for C++11 language features is required.

Approved by:	portmgr (tier-2 blanket)
 2020-05-15 07:30:34 +00:00
Yuri Victorovich
04c132a637 New port: biology/scrm: Coalescent simulator for biological sequences 2020-05-15 04:58:27 +00:00