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* biology/fastx-toolkit: Fix build on FreeBSD 12Jason W. Bacon2018-05-162-2/+19
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15451 Notes: svn path=/head/; revision=470124
* Add upstream patch to fix the build with Qt 5.10.Raphael Kubo da Costa2018-05-152-1/+31
| | | | | | | | | | | _tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from 'QLatin1String' to 'const QKeySequence' gbarCheckBox->setShortcut(QLatin1String("")); ^~~~~~~~~~~~~~~~~ PR: 228213 Notes: svn path=/head/; revision=470045
* - Update to 3.3.20180214Wen Heping2018-05-152-5/+6
| | | | Notes: svn path=/head/; revision=469992
* biology/diamond: Update to version 0.9.22Joseph Mingrone2018-05-142-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22 Notes: svn path=/head/; revision=469925
* biology/hyphy: Bump PORTREVISION after upstream rerolled releaseJoseph Mingrone2018-05-143-14/+4
| | | | | | | | | Also, remove patch that upstream incorporated in new tarball. Upstream issue: https://github.com/veg/hyphy/issues/796 Notes: svn path=/head/; revision=469922
* biology/py-biopython: Unbreak on python3; Add licenseYuri Victorovich2018-05-131-2/+9
| | | | | | | | | | | | | | | | | | | | | | Two items prevented python3 compatibility: * Breakage of ASCII codec due to non-ascii characters in README: https://github.com/biopython/biopython/issues/1649 * The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab Port changes: * USES=python:2.7 -> USES=python * Add pre-configure that clears the README file * Add LICENSE/LICENSE_FILE Testing: * Ran the tutorial testcase http://biopython.org/DIST/docs/tutorial/Tutorial.html, particularly pdf writing through print/py-reportlab worked fine. Asked the upstream to clarify the acceptable dependency version: https://github.com/biopython/biopython/issues/1650 Approved by: portmgr blanket (unbreak for python3; add license) Notes: svn path=/head/; revision=469835
* biology/iqtree: Update to version 1.6.5Joseph Mingrone2018-05-112-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5 Notes: svn path=/head/; revision=469673
* New port, biology/hyphy: Hypothesis testing using PhylogeniesJoseph Mingrone2018-05-117-0/+645
| | | | | | | WWW: http://www.hyphy.org/ Notes: svn path=/head/; revision=469604
* Mark BROKEN: checksum and size mismatchAntoine Brodin2018-05-071-0/+2
| | | | | | | | Reported by: pkg-fallout MFH: 2018Q2 Notes: svn path=/head/; revision=469265
* Deprecate ports broken for more than 6 monthsAntoine Brodin2018-05-055-0/+10
| | | | Notes: svn path=/head/; revision=469100
* biology/iqtree: Update to version 1.6.4Joseph Mingrone2018-04-302-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4 Notes: svn path=/head/; revision=468714
* biology/paml: Set PORTVERSION directlyJoseph Mingrone2018-04-261-1/+1
| | | | | | | | | | Setting DISTVERSION= 4.9h in the last commit caused PORTVERSION to be translated to 4.9.h, which was not correct. Pointy-hat: jrm Notes: svn path=/head/; revision=468355
* biology/canu: Upgrade to 1.7 releaseJason W. Bacon2018-04-265-37/+51
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15201 Notes: svn path=/head/; revision=468321
* biology/paml: Update to version 4.9hJoseph Mingrone2018-04-253-27/+181
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Port Changes: - Add EXAMPLES option and install most files under EXAMPLESDIR - Add USES=dos2unix to fix DOS line endings Upstream Changes: Version 4.9h, March 2018 (*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for rates for loci. Since 4.9d, the program and the documentation are inconsistent about the two priors, and which value (0 or 1) means which prior. I have now checked the program and the documentation to make sure that they are consistent: prior = 0: gamma-Dirichlet (dos Reis 2014). This is the default. prior = 1: conditional i.i.d. prior (Zhu et al. 2015). I believe these two are similar especially if the number of loci (partitions) is large, but no serious comparisons between the two priors have been published. Thanks to Adnan Moussalli for pointing out the errors. (*) codeml. It was discovered that the mechanistic amino acid substitution model implemented in Yang et al. (1998; see table 3), specified by seqtype = 2 model = 6, has been broken for a long time, since version 3.0 (2000) at least. Version 2.0 (1999) seems to be correct. This means that the model become broken soon since it was published. I have now fixed this. This model of amino acid substitution starts from a Markov chain for codons and then aggregate the states and merge the synonymous codons into one state (the coded amino acid). This is an approximate formulation since the process after state aggregation is not Markovian anymore. I have now added another codon-based amino acid substitution model that treats amino acids as ambiguities codons. The model is specified by seqtype = 2 model = 5. This is an exact formulation. (*) codeml. The number of categories in the BEB calculation under M2 and M8 is unintentionally set to 4 rather than 10. I have changed this back to 10. The details of this calculation are in Yang et al. 2005 MBE. Version 4.9g, December 2017 (*) codeml. A bug caused the BEB calculation under the site model M8 (NSsites = 8) to be incorrect, with the program printing out warming messages like "strange: f[ 5] = -0.0587063 very small." This bug was introduced in version 4.9b and affects versions 4.9b-f. A different bug was introduced in version 4.9f that causes the log likelihood function under the site model M8 (NSsites = 8) to be calculated incorrectly. These are now fixed. Version 4.9f, October 2017 (*) baseml, nonhomogeneous models (nhomo & fix_kappa). Those models allow different branches on the tree to have different Q matrices. Roughly nhomo controls the base frequency parameters while gix_kappa controls kappa or the exchangeability parameters (a b c d e in GTR/REV, for example). I added the option (nhomo = 5, fix_kappa = 2), which lets the user to define branch types, so that branches of the same type have the same exchangeability parameters (a b c d e for GTR) and base composition parameters, while branches of different types have different parameters. Branch types are labeled (using # and $), 0, 1, 2, .... The labels should be consecutive positive integers. The old options nhomo = 3 or 4 work for some models like GTR, but not some other models which also have base composition parameters. In this update, I think those options should work with all those models. I have also edited the documentation (look for option variable nhomo for baseml). (*) baseml & codeml. i added an option fix_blength = 3 (proportional), which means that branch lengths will be proporational to those given in the tree file, and the proportionality factor is estimated by ML. (*) codeml. The program does not count the parameters correctly for model M0 when fix_kappa = 1. The bug was introduced in version 4.9c and affects versions 4.9c-e. This is now fixed. (*) codeml (seqtype = 2 model = 2). If you are analyzing multiple protein data sets (ndata > 1) under the empirical models such as wag, jtt, dayhoff. The results for the first data set are correct, but all later data sets are analyzed incorrectly under the corresponding +F models, that is, wag+F, jtt+F, dayhoff+F, etc. A bug in the program means that for the second and later data sets, the equilibrium amino acid frequencies are taken from the real data and not correctly set to those specified by the empirical models. I note that this bug was recorded in the update Version 3.14b, April 2005, but it was somehow not fixed, even in that version. This is now fixed. Thanks to Nick Goldman for reporting this again. (*) evolver (options 5, 6, 7 for simulating nucleotide, codon and amino acid alignments). If you choose the option of printing out the site pattern counts instead of the sequences (specified at the beginning of the control file such as MCbase.dat), and if you are simulating two or more alignments, the program crashes after finishing the first alignment. This is now fixed. (*) mcmctree. The program crashes if you have a mixture of morphological loci and molecular loci, if not all the morphological loci are before the molecular loci. I have now fixed this. I think this was never described anyway. Version 4.9e, March 2017 (*) Edited the readme files to change the license to GPL. (*) mcmctree. A bug was introduced in version 4.9b which causes the program to read the fossil calibration information in the tree file incorrectly, if joint (minimum and maximum) bounds are specified using the symbol '<' and '>'. If you use the notation "B()", "L()", and 'U()', the information is read correctly. This bug was introduced in version 4.9b and exists in 4.9c and 4.9d. Versions 4.9a and earlier were correct. Version 4.9d, February 2017 (*) mcmctree. Changed the default prior for rates for loci to gamma-Dirichlet (dos Reis 2014), and updated the documentation as well. It was set to the conditional i.i.d. prior (Zhu et al. 2015). (*) mcmctree. Added Bayes factor calculation. A program called BFdriver is included in the release, as well as a pdf document in the folder examples/DatingSoftBound/BFdriverDOC.pdf. We suggest that you use the exact likelihood calculation when you use this option, since the normal approximation is unreliable when the power posterior is close to the prior (when beta is small). Notes: svn path=/head/; revision=468297
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereDmitry Marakasov2018-04-252-2/+2
| | | | | | | | | | they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process. Approved by: portmgr blanket, mat Notes: svn path=/head/; revision=468282
* biology/unanimity: Pacific Biosciences consensus library and applicationsJason W. Bacon2018-04-2411-0/+146
| | | | | | | | Reviewed by: jrm Differential Revision: https://reviews.freebsd.org/D15172 Notes: svn path=/head/; revision=468214
* biology/seaview: Update version 4.6.3=>4.6.5Muhammad Moinur Rahman2018-04-242-6/+8
| | | | | | | - Pet portlint Notes: svn path=/head/; revision=468198
* biology/pbcopper: Core C++ library for Pacific Biosciences toolsJason W. Bacon2018-04-236-0/+133
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15171 Notes: svn path=/head/; revision=468101
* biology/pbbam: PacBio BAM C++ library, with SWIG bindingsJason W. Bacon2018-04-235-0/+182
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15154 Notes: svn path=/head/; revision=468100
* biology/pbseqan: Pacific Biosciences patched and stripped down SeqAnJason W. Bacon2018-04-215-0/+698
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15152 Notes: svn path=/head/; revision=467901
* biology/diamond: Update to version 0.9.21Joseph Mingrone2018-04-202-5/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Notes: svn path=/head/; revision=467847
* biology/ddocent: Bash pipeline for RAD sequencingJason W. Bacon2018-04-208-0/+617
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15139 Notes: svn path=/head/; revision=467808
* biology/freebayes: Bayesian haplotype-based polymorphism discovery and ↵Jason W. Bacon2018-04-2014-0/+293
| | | | | | | | | | genotyping Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15116 Notes: svn path=/head/; revision=467806
* biology/bedtools: Upgrade to 2.27.1Jason W. Bacon2018-04-196-54/+36
| | | | | | | | | | PR: 227272 Submitted by: jwb Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15137 Notes: svn path=/head/; revision=467783
* devel/boost-*: update to 1.67.0Jan Beich2018-04-182-1/+2
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_67_0.html PR: 227427 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D15030 Notes: svn path=/head/; revision=467711
* biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF filesJason W. Bacon2018-04-178-0/+511
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15109 Notes: svn path=/head/; revision=467553
* biology/fastahack: Utility for indexing and sequence extraction from FASTA filesJason W. Bacon2018-04-166-0/+99
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15080 Notes: svn path=/head/; revision=467485
* biology/smithwaterman: Smith-waterman-gotoh alignment algorithmJason W. Bacon2018-04-156-0/+149
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15072 Notes: svn path=/head/; revision=467402
* biology/tabixpp: C++ wrapper to tabix indexerJason W. Bacon2018-04-145-0/+131
| | | | | | | | | Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14977 Notes: svn path=/head/; revision=467343
* - Update to 1.71Wen Heping2018-04-092-5/+4
| | | | | | | Approved by: mauricio@arareko.net(maintainer, via email) Notes: svn path=/head/; revision=466835
* biology/pear-merger: Memory-efficient and accurate paired-end read mergerJason W. Bacon2018-04-044-0/+37
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14959 Notes: svn path=/head/; revision=466449
* biology/seqtk: Tool for processing sequences in FASTA/FASTQ formatJason W. Bacon2018-04-035-0/+51
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14954 Notes: svn path=/head/; revision=466379
* biology/trimadap: Trim adapter sequences from Illumina dataJason W. Bacon2018-04-036-0/+65
| | | | | | | | | Reviewed by: mat Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14935 Notes: svn path=/head/; revision=466367
* biology/rainbow: Efficient clustering and assembling of short readsJason W. Bacon2018-04-025-0/+50
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14924 Notes: svn path=/head/; revision=466235
* - Update to 1.61Wen Heping2018-04-012-6/+7
| | | | Notes: svn path=/head/; revision=466142
* biology/stacks: Software pipeline for building loci from short-read sequencesJason W. Bacon2018-03-317-0/+136
| | | | | | | | | Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14885 Notes: svn path=/head/; revision=466048
* biology/libgtextutils: Unbreak for FreeBSD 12Jason W. Bacon2018-03-292-1/+12
| | | | | | | | | Reported by: pkg-fallout Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14892 Notes: svn path=/head/; revision=465904
* biology/bamtools: API and toolkit for handling BAM filesJason W. Bacon2018-03-287-0/+76
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14877 Notes: svn path=/head/; revision=465808
* biology/ncbi-blast+: Upgrade to 2.7.1Jason W. Bacon2018-03-276-377/+409
| | | | | | | | | | | | | | | Patch Makefile.in.top to cleanly support DESTDIR Also resolves 225002, conflict with libproj PR: 226037 Reported by: wen Reviewed by: mat rene Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14854 Notes: svn path=/head/; revision=465726
* biology/iqtree: Update to version 1.6.3Joseph Mingrone2018-03-232-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3 Notes: svn path=/head/; revision=465330
* biology/py-pysam: Update to 0.14.1Yuri Victorovich2018-03-212-5/+5
| | | | | | | | | Also silenced STRIP_CMD. Reported by: portscout Notes: svn path=/head/; revision=465157
* Mark broken on armvX and mips.Mark Linimon2018-03-181-0/+4
| | | | Notes: svn path=/head/; revision=464909
* Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.Mark Linimon2018-03-181-0/+3
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=464907
* biology/diamond: Update to version 0.9.19Joseph Mingrone2018-03-172-5/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19 Notes: svn path=/head/; revision=464826
* biology/diamond: Update to version 0.9.18-49Joseph Mingrone2018-03-152-4/+5
| | | | | | | | | Pull in commits after the 0.9.18 release for build fixes. Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.18 Notes: svn path=/head/; revision=464549
* Return maho@'s ports to the pool after his commit bit expired.Rene Ladan2018-03-111-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=464164
* Remove now-useless, commented-out lines.Mark Linimon2018-03-101-4/+0
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=464132
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-1021-15/+21
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* biology/seqan-apps, biology/seqan: Update to 2.4.0Yuri Victorovich2018-03-107-1269/+90
| | | | | | | | | | | | | | | | | | | | | | | Port changes for biology/seqan-apps: * Changed to DISTVERSION * Updated COMMENT * Added USES=compiler:openmp * Removed BROKEN_xx (upstream now claims support for these architectures) * Removed USE_GCC * Added SSE4/AVX2/NATIVE SIMD options Port changes for biology/seqan: * Changed to DISTVERSION * Added NO_ARCH * Added PORTDOCS=* * Updated do-install PR: 225682 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Approved by: tcberner (mentor, implicit) Notes: svn path=/head/; revision=464043
* biology/iqtree: Update to version 1.6.2Joseph Mingrone2018-03-032-5/+4
| | | | | | | Upstream changes: http://www.iqtree.org/release/v1.6.2 Notes: svn path=/head/; revision=463462
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