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* MFH: r549974Yuri Victorovich2020-09-251-1/+8
| | | | | | | | | | | biology/py-scikit-bio: Fix build on the i386 architecture Reported by: fallout Approved by: ports-secteam (fluffy) Notes: svn path=/branches/2020Q3/; revision=549979
* MFH: r547530Fernando Apesteguía2020-09-041-4/+14
| | | | | | | | | | | | | | | | | | | biology/mapm3: Fix build with llvm11, gcc10 Another instance of -fno-common issue. While here: * strip executables * add license PR: 249077 Submitted by: tphilipp@potion-studios.com (maintainer) Approved by: ports-secteam (blanket, build fix, -fno-common) Notes: svn path=/branches/2020Q3/; revision=547531
* MFH: r545542Kyle Evans2020-08-201-0/+14
| | | | | | | | | | | | | | | | | | | biology/paml: fix the build with LLVM 11 LLVM 11 switched from -fcommon to -fno-common by default. This revealed a slight misposition of names in paml.h, which caused one symbol per enum that's not used anywhere. The fix just moves the names back so that the enums are named that, rather than creating new unused symbols. Reviewed by: zeising Approved by: jrm (maintainer) Approved by: ports-secteam (joneum) Notes: svn path=/branches/2020Q3/; revision=545561
* MFH: r541482Piotr Kubaj2020-07-081-1/+1
| | | | | | | | | | | biology/cufflinks: fix build on GCC architectures Using Boost requires modern compiler. Approved by: portmgr (fix build blanket) Notes: svn path=/branches/2020Q3/; revision=541483
* Bump devel/jsoncpp consumers after r540853.Tobias C. Berner2020-06-301-1/+1
| | | | | | | Reported by: Kevin Oberman <rkoberman@gmail.com> Notes: svn path=/head/; revision=540909
* biology/hyphy: Update to version 2.5.15Joseph Mingrone2020-06-282-4/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15 Notes: svn path=/head/; revision=540728
* biology/diamond: Update to version 0.9.35Joseph Mingrone2020-06-272-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35 Notes: svn path=/head/; revision=540624
* Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113Sunpoet Po-Chuan Hsieh2020-06-261-1/+2
| | | | | | | | | | | | - Fix LICENSE_FILE - Update pkg-descr - Update WWW - Bump PORTREVISION of dependent ports for dependency change Changes: https://metacpan.org/changes/distribution/IO-Stringy Notes: svn path=/head/; revision=540492
* biology/py-bx-python: Update 0.8.8 -> 0.8.9Yuri Victorovich2020-06-262-4/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=540420
* biology/seaview: Update version 5.0.3=>5.0.4Muhammad Moinur Rahman2020-06-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=539893
* biology/vsearch: Update to 2.15.0Jason W. Bacon2020-06-202-4/+4
| | | | | | | Numerous minor enhancements Notes: svn path=/head/; revision=539742
* Move devel/swig30 to devel/swig and update to 4.0.1Sunpoet Po-Chuan Hsieh2020-06-171-4/+2
| | | | | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=539491
* biology/py-loompy: Update 2.0.17 -> 3.0.6Yuri Victorovich2020-06-162-5/+4
| | | | Notes: svn path=/head/; revision=539319
* biology/py-gffutils: Update 0.10 -> 0.10.1Yuri Victorovich2020-06-162-4/+4
| | | | Notes: svn path=/head/; revision=539317
* biology/seaview: Update version 5.0.2=>5.0.3Muhammad Moinur Rahman2020-06-142-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=538720
* Unbreak bulk -aAntoine Brodin2020-06-131-1/+1
| | | | Notes: svn path=/head/; revision=538676
* biology/picard-tools: CLI tools for manipulating sequencing dataJason W. Bacon2020-06-136-0/+170
| | | | | | | | | 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. Notes: svn path=/head/; revision=538672
* biology/py-biopython: Set python requirement to 3.6+Jason W. Bacon2020-06-131-1/+1
| | | | | | | New requirement for v1.77 overlooked during upgrade Notes: svn path=/head/; revision=538671
* biology/diamond: Update to version 0.9.34Joseph Mingrone2020-06-122-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34 Notes: svn path=/head/; revision=538606
* biology/py-pysam: Update 0.15.4 -> 0.16.0Yuri Victorovich2020-06-092-4/+4
| | | | | | | Reported by: potscout Notes: svn path=/head/; revision=538275
* Add compiler:c++0x to USES to fix build on GCC-based systems:Mark Linimon2020-06-051-1/+1
| | | | | | | | | cc1plus: error: unrecognized command line option "-std=c++0x Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=537984
* biology/bioawk: BWK awk modified for biological dataJason W. Bacon2020-06-055-0/+79
| | | | | | | | | | | | 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. Notes: svn path=/head/; revision=537983
* biology/subread: Read alignment, quantification and mutation discoveryJason W. Bacon2020-06-0518-0/+367
| | | | | | | | | | | | | | | 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. Notes: svn path=/head/; revision=537982
* bioloty/vt: Discovers short variants from Next Generation Sequencing dataJason W. Bacon2020-06-049-0/+147
| | | | Notes: svn path=/head/; revision=537926
* biology/diamond: Update to version 0.9.33Joseph Mingrone2020-06-032-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33 Notes: svn path=/head/; revision=537853
* biology/hyphy: Update to version 2.5.14Joseph Mingrone2020-05-303-438/+438
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14 Notes: svn path=/head/; revision=537106
* biology/iqtree: Update to version 2.0.6Joseph Mingrone2020-05-302-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6 Notes: svn path=/head/; revision=537101
* biology/abyss: Update 2.2.3 -> 2.2.4Yuri Victorovich2020-05-302-5/+4
| | | | Notes: svn path=/head/; revision=537064
* Clean up some thingsTobias Kortkamp2020-05-301-1/+2
| | | | | | | Reported by: portscan Notes: svn path=/head/; revision=537026
* biology/py-biopython: Upgrade to 1.77Jason W. Bacon2020-05-292-9/+11
| | | | | | | | | | Upstream support for python 3 PR: ports/246763 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=536875
* biology/gatk: Update 4.1.5.0 -> 4.1.7.0Yuri Victorovich2020-05-282-6/+6
| | | | Notes: svn path=/head/; revision=536734
* biology/iqtree: Update to version 2.0.5Joseph Mingrone2020-05-282-7/+7
| | | | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5 While here, incorporate portfmt suggestions. Notes: svn path=/head/; revision=536729
* Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).Alexey Dokuchaev2020-05-271-1/+1
| | | | Notes: svn path=/head/; revision=536688
* Mark as BROKEN on powerpc64 12. It builds on -head.Mark Linimon2020-05-261-1/+2
| | | | | | | | | While here, pet portlint (remove extra blank line). Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=536568
* biology/py-dnaio: Upgrade to 0.4.2Jason W. Bacon2020-05-242-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=536409
* biology/ugene: prepare for Qt5-5.15Tobias C. Berner2020-05-194-0/+40
| | | | Notes: svn path=/head/; revision=535875
* Mark as BROKEN on powerpc64:Mark Linimon2020-05-171-0/+2
| | | | | | | | | | | | 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) Notes: svn path=/head/; revision=535507
* Bump PORTREVISION for security/nettle shlib changeSunpoet Po-Chuan Hsieh2020-05-162-1/+2
| | | | Notes: svn path=/head/; revision=535391
* New port: biology/py-hits: Utilities for processing high-throughput ↵Yuri Victorovich2020-05-164-0/+27
| | | | | | | sequencing experiments Notes: svn path=/head/; revision=535347
* biology/py-scikit-bio: Fix licenseYuri Victorovich2020-05-161-1/+1
| | | | Notes: svn path=/head/; revision=535346
* biology/py-scikit-bio: Remove bogus linesYuri Victorovich2020-05-161-5/+0
| | | | Notes: svn path=/head/; revision=535345
* New port: biology/py-scikit-bio: Data structures, algorithms, educational ↵Yuri Victorovich2020-05-164-0/+44
| | | | | | | resources for bioinformatics Notes: svn path=/head/; revision=535344
* New port: biology/py-pandas-charm: Library for getting character matrices ↵Yuri Victorovich2020-05-164-0/+31
| | | | | | | into and out of pandas Notes: svn path=/head/; revision=535340
* New port: biology/py-ete3: Framework for the analysis and visualization of treesYuri Victorovich2020-05-164-0/+43
| | | | Notes: svn path=/head/; revision=535339
* Add compiler:c++11-lang to USES to fix build on GCC-based systems:Mark Linimon2020-05-151-1/+1
| | | | | | | | | configure: error: *** A compiler with support for C++11 language features is required. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=535275
* New port: biology/scrm: Coalescent simulator for biological sequencesYuri Victorovich2020-05-155-0/+45
| | | | Notes: svn path=/head/; revision=535266
* Update SphinxDanilo G. Baio2020-05-111-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Repocopy textproc/py-sphinx to textproc/py-sphinx18 Update it to 1.8.5 (latest version from 1.8.X). This version supports Python 2 and 3. Add test target. - textproc/py-sphinx: Update to 3.0.2 Python 3 only (3.5+). Add test target. - Mk/Uses/python.mk: Add PY_SPHINX Shared macro to use with flavors and not break ports with USES=python (all versions). Python >=3.5 --> textproc/py-sphinx (v3.0.2) Python < 3.5 --> textproc/py-sphinx18 (v1.8.5) All ports that uses sphinx were changed to use the new variable ${PY_SPHINX} in the dependency line, exceptions: * Ports that fails to build with sphinx 3.0.2 because of code. They are pointing to textproc/py-sphinx18 directly. There aren't many ports. * Ports that doesn't know Python flavors. - Add several patches to fix Sphinx consumers The most common issues are related with pkg-plist, the output files from Sphinx changes between versions, keep this dynamically is the better approach. This will save time in future sphinx updates. PR: 245629 Exp-run by: antoine Notes: svn path=/head/; revision=534966
* biology/hhsuite: fix build on powerpc64 elfv2Piotr Kubaj2020-05-111-1/+4
| | | | | | | | | Use GCC instead of Clang: /usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw' return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); Notes: svn path=/head/; revision=534934
* - Resurrect and unbreak by updating to version 34.0Alexey Dokuchaev2020-05-1012-0/+1774
| | | | | | | | - Stop providing outdated offline PDF documentation, users are advised to use the online files instead Notes: svn path=/head/; revision=534852
* Update devel/gmake to 4.3.Tijl Coosemans2020-05-091-0/+22
| | | | | | | | | | | | | Some changes have been made in this release that break backwards compatibility. Let USES=gmake force users to upgrade to this version so port maintainers don't have to support older versions. PR: 245725 Exp-run by: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=534792
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