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* 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
* Update to 7.6.13Mateusz Piotrowski2020-05-092-4/+4
| | | | | | | | Release announcement: https://foldingforum.org/viewtopic.php?f=108&t=34466 Notes: svn path=/head/; revision=534738
* Bump 37 ports depending on math/openblas through USES=blaslapack:openblas ↵Yuri Victorovich2020-05-062-1/+2
| | | | | | | because after the recent math/openblas update the library name changed in openblas Notes: svn path=/head/; revision=534190
* Bump 46 ports depending on math/openblas because the after the recent ↵Yuri Victorovich2020-05-062-1/+2
| | | | | | | math/openblas update the library name changed in openblas. Notes: svn path=/head/; revision=534185
* Preserve Gradle 6.2.2 for biology/gatkTobias Kortkamp2020-05-061-2/+2
| | | | | | | It fails to build with newer Gradle versions again. Notes: svn path=/head/; revision=534171
* Remove expired ports:Rene Ladan2020-05-0535-2475/+0
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x11-toolkits/slingshot: 64-bit unsupported 2020-05-05 x11-toolkits/xview-clients: 64-bit unsupported 2020-05-05 x11-wm/fluxconf: Broken for more than 6 months 2020-05-05 x11-wm/ion: Broken for more than 6 months 2020-05-05 x11-wm/matwm2: Broken for more than 6 months 2020-05-05 x11-wm/nickleby: Broken for more than 6 months 2020-05-05 x11-wm/olvwm: 64-bit unsupported 2020-05-05 x11-wm/ratmenu: Broken for more than 6 months Notes: svn path=/head/; revision=534093
* biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparserRene Ladan2020-05-051-3/+1
| | | | Notes: svn path=/head/; revision=534089
* biology/plink: Whole genome association analysis toolsetJason W. Bacon2020-05-046-0/+94
| | | | | | | | | | | Reversed removal, commit r471892 2018/06/07 Upgraded to 1.90 beta 6.17 PR: ports/243733 Submitted by: mzaki@e-mail.ne.jp Notes: svn path=/head/; revision=533993
* - update libgd to 2.3.0Dirk Meyer2020-05-042-1/+2
| | | | | | | | | - new option RAQM - resurrect deprecated gdlib-config - bump dependend ports Notes: svn path=/head/; revision=533989
* biology/hyphy: Update to version 2.5.12Joseph Mingrone2020-05-033-5/+5
| | | | | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.11 https://github.com/veg/hyphy/releases/tag/2.5.12 Notes: svn path=/head/; revision=533731
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