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* 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
* Reduce dependency on the python2 metaportAntoine Brodin2018-02-191-1/+2
| | | | | | | | PR: 225752 Submitted by: Yasuhiro KIMURA Notes: svn path=/head/; revision=462307
* biology/py-pysam: Update to 0.14Yuri Victorovich2018-02-102-4/+4
| | | | | | | | | | | Changelog: https://github.com/pysam-developers/pysam/releases/tag/v0.14 Reported by: portscout Approved by: tcberner (mentor, implicit) Notes: svn path=/head/; revision=461449
* biology/py-bx-python: Update to 0.8.1Yuri Victorovich2018-02-102-8/+9
| | | | | | | | | | | | | | | | | Additional port changes: * Changed to DISTVERSION. * Added USE_PYTHON=cython. * Added stripping. * Updated maintainer e-mail. Reported compiler warnings to the upstream. Reported by: portscout Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D14283 Notes: svn path=/head/; revision=461348
* Canonicalize PyPi WWWs:Dmitry Marakasov2018-02-081-1/+1
| | | | | | | | | | - Switch to https:// - Remove trailing slashes Approved by: portmgr blanket Notes: svn path=/head/; revision=461265
* biology/diamond: Update to version 0.9.17Joseph Mingrone2018-02-012-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17 Notes: svn path=/head/; revision=460624
* - Update to 3.3.20180129Wen Heping2018-02-012-5/+4
| | | | Notes: svn path=/head/; revision=460569
* Multiple ports:Jason W. Bacon2018-01-3116-29/+16
| | | | | | | | | | | Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128 Notes: svn path=/head/; revision=460452
* devel/boost-*: update to 1.66.0Jan Beich2018-01-182-1/+2
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_66_0.html PR: 223922 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D13279 Notes: svn path=/head/; revision=459315
* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSAlexey Dokuchaev2018-01-111-2/+4
| | | | | | | | | when it was missing) - Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN - Fix some whitespace and formatting bugs along the way Notes: svn path=/head/; revision=458761
* Update Qt5 ports to 5.9.3.Raphael Kubo da Costa2018-01-061-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This took quite a lot of time because Qt's own build system underwent several changes in 5.8.0 that took a while to adapt to. And, of course, qt5-webengine is a behemoth that we need to patch like crazy due to its bundling of Chromium. In fact, most of the Chromium patches in qt5-webengine have been imported with no changes from www/chromium@433510 ("www/chromium: update to 56.0.2924.87"). New port: accessibility/qt5-speech Bigger changes to Qt5 ports we had to make: - Qt now allows using a configure.json file to define configuration options and specify configuration checks that can be done when qmake is invoked. However, configure.json checks done in a subdirectory only propagates to subdirectories, and checks elsewhere will fail if all .pro files are being parsed at once (i.e. qmake -recursive), so several ports had to switch to USES=qmake:norecursive along with manual additional qmake invocations in subdirectories in order to work. It's been mentioned in a few places such as Qt's bug tracker that qmake's recursive mode is pretty much deprecated, so we might switch to non-recursive mode by default in the future. - Uses/qmake.mk: Introduce QMAKE_CONFIGURE_ARGS. qmake now accepts arbitrary options such as '-foo' and '-no-bar' at the end of the command-line. They can be specified in QMAKE_CONFIGURE_ARGS. - graphics/qt5-wayland: The port can only be built if graphics/mesa-libs is built with the WAYLAND option, so a corresponding option (off by default) was added to the port. - misc/qt5-doc: Switch to a pre-built documentation tarball. The existing port was not working with Qt 5.9. Instead of trying to fix it, switch to what Gentoo does and fetch a tarball that already contains all documentation so that we do not have to build anything at all. The tarball's name and location in download.qt.io look a bit weird, but it seems to work fine. - www/qt5-webengine: Use binutils from ports, Chromium's GN build system generates a build.ninja that uses ar(1) with the @file syntax that is not supported by BSD ar, so we need to use GNU ar from binutils. - x11-toolkits/qt5-declarative-render2d: This port was merged into the main Qt Declarative repository upstream, and into x11-toolkits/qt5-quick in the ports tree. Changes to other ports we had to make: - biology/ugene: Drop a '#define point "."' that is not present in more recent versions of the port. Defining a macro with such a common name causes build issues with Qt 5.9, which uses |point| as an argument name in methods. - cad/qelectrotech: Fix plist with Qt 5.9. Directories are no longer installed with `cp -f -R', but rather `qmake install qinstall', which does not install %%DATADIR%%/elements/10_electric/20_manufacturers_articles/bosch_rexroth/.directory That's a local file that should not even have been part of the tarball anyway. - chinese/gcin-qt5: Add additional private Qt directories (which should not be used in the first place) to get the port to build with Qt 5.9. - devel/qtcreator: Fix plist with Qt 5.9. Something changed in qdoc and some test classes no longer generate documentation files. - security/keepassx-devel: Import a patch sent upstream almost a year ago to fix the build with Qt 5.9. Thanks to antoine for the exp-run, and tcberner and Laurent Cimon <laurent@nuxi.ca> for landing changes in our qt-5.9 branch. PR: 224849 Notes: svn path=/head/; revision=458293
* biology/seaview: Update version 4.6.2=>4.6.3Muhammad Moinur Rahman2018-01-053-7/+8
| | | | | | | | | - Added pkg-plist to pet portlint Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=458157
* New USES=eigenTobias C. Berner2018-01-021-5/+2
| | | | | | | | | | | | | | | | | | | | | | | | | Usage: USES=eigen:<version>[,<type>] version: 2 or 3 (required) type: build (default), run For example: USES=eigen:2,build,run will add a BUILD- and RUN_DEPENDS on math/eigen2, and USES=eigen:3 will add a BUILD_DEPENDS on math/eigen3. * Convert the existing ports to use it - biology/iqtree: remove run time dependency (seemed not to be needed) - graphics/movit: remove run time dependency (seemed not to be needed) - science/avogadro: add run time dependeny (installed cmake file requires it to be present) Reviewed by: rakuco, mat Differential Revision: https://reviews.freebsd.org/D13702 Notes: svn path=/head/; revision=457914
* - Update to 3.697Wen Heping2018-01-012-3/+4
| | | | Notes: svn path=/head/; revision=457755
* - Update to 5.16.0Wen Heping2018-01-013-4/+9
| | | | Notes: svn path=/head/; revision=457754
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1Joseph Mingrone2017-12-292-3/+4
| | | | Notes: svn path=/head/; revision=457516
* biology/iqtree: Update to version 1.6.1Joseph Mingrone2017-12-282-9/+8
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases Notes: svn path=/head/; revision=457467
* Disable the extra flag "-march=native" on arm to fix builds.Mark Linimon2017-12-271-3/+6
| | | | | | | | Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run Notes: svn path=/head/; revision=457351
* Update to 2.0.1Sunpoet Po-Chuan Hsieh2017-12-263-5/+31
| | | | | | | Changes: https://github.com/rvosa/bio-phylo/releases Notes: svn path=/head/; revision=457333
* biology/canu: Replace += with = for dependsJason W. Bacon2017-12-221-2/+2
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13574 Notes: svn path=/head/; revision=456982
* - Fix build on 11+Dmitry Marakasov2017-12-222-4/+11
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=456976
* [new port] biology/canu: Single molecule sequence assemblerJason W. Bacon2017-12-226-0/+167
| | | | | | | | Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574 Notes: svn path=/head/; revision=456950
* Try to bring some consistency to ports that have x86-specific pieces.Mark Linimon2017-12-212-12/+12
| | | | | | | | | | | | | | | | | - in general, if we think that the code is not architecture-specific, and instead just enables x86 assembler by default, those should use BROKEN rather than IGNORE. This will allow them to be attempted with TRYBROKEN. - spell i386 as x86. - spell asm as assembler. - pet portlint. These changes should have no effect on tier-1 builds. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456901
* Switch from swig 2.0 to swig 3.0Baptiste Daroussin2017-12-201-2/+4
| | | | Notes: svn path=/head/; revision=456845
* Mark more recently failing ports broken on aarch64.Mark Linimon2017-12-191-2/+3
| | | | | | | | | While here, pet portlint and reformat some other BROKEN statements. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456719
* Back out previous commits by jbeich demand.Mark Linimon2017-12-182-10/+2
| | | | Notes: svn path=/head/; revision=456588
* Bah. Remove spare line from cut-and-paste.Mark Linimon2017-12-181-1/+0
| | | | Notes: svn path=/head/; revision=456579
* Attempt to fix build on non-x86 archs. Untested, but does no harmMark Linimon2017-12-182-2/+11
| | | | | | | | | on x86. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456578
* biology/diamond: Update to version 0.9.14Joseph Mingrone2017-12-132-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14 Notes: svn path=/head/; revision=456220
* biology/seqtools: re-try on powerpc* after r449590Jan Beich2017-12-121-2/+0
| | | | Notes: svn path=/head/; revision=456096
* - Those ports fail to build with python3Antoine Brodin2017-12-111-1/+1
| | | | | | | - Add some explicit FLAVOR to dependencies where needed Notes: svn path=/head/; revision=456050
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