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* biology/cd-hit: Upgrade to 4.8.1Jason W. Bacon2019-03-144-14/+106
| | | | | | | Convert Makefile REINPLACE to patch for sending upstream Notes: svn path=/head/; revision=495746
* biology/bedtools: unbreak with libc++ 8Jan Beich2019-03-041-0/+5
| | | | | | | | | | | | | | | | | | | | | | In file included from FileReader.cpp:1: In file included from /usr/include/c++/v1/iostream:38: In file included from /usr/include/c++/v1/ios:216: In file included from /usr/include/c++/v1/__locale:15: In file included from /usr/include/c++/v1/string:505: In file included from /usr/include/c++/v1/string_view:176: In file included from /usr/include/c++/v1/__string:57: In file included from /usr/include/c++/v1/algorithm:640: In file included from /usr/include/c++/v1/initializer_list:47: In file included from /usr/include/c++/v1/cstddef:38: ../../../utils//gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ PR: 236192 Approved by: portmgr blanket Notes: svn path=/head/; revision=494554
* biology/paml: Update to version 4.9iJoseph Mingrone2019-02-263-4/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Upstream changes as described by the author: - mcmctree: I have added an option (duplication = 1) for dating a tree with both speciations and gene duplications, so that some nodes on the tree share divergence times. Nodes sharing ages are identified using labels in the tree file: #1, #2, .... I have yet to update the document about specification of the model. - mcmctree: The TipDate option was written for one locus or partition and never worked for more than two loci/partitions. I have edited the code so that it works for multiple partitions, some of which may be molecular and the others morphological. - codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7 (FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This option uses the observed codon or amino acid frequencies for the mutation-selection models of codon usage. Instead the program estimates the frequencies using maximum likeihood, which is what the option estFreq = 1 does. Look at the README file in the examples/mtCDNAape/ folder. - codeml clade model D: The bounds for the w (dN/dS) ratios in the first site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model D in 4.9b. The motivation for the bounds is that site class 0 represents strong purifying selection with a small w0, while site class 1 should include sites under weak purifying selection with a larger w1. However the bounds are arbitrary. In some datasets, the MLEs are found to be at the bounds, making the interpretation awkward. I have changed the bounds to the following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user should swap the estimates of w0 and w2 if w0 > w1. Notes: svn path=/head/; revision=493971
* New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end ↵Yuri Victorovich2019-02-256-0/+116
| | | | | | | sequence assembler Notes: svn path=/head/; revision=493842
* kallisto: Upgrade to 0.45.1, unbundle hstlibJason W. Bacon2019-02-245-16/+65
| | | | Notes: svn path=/head/; revision=493810
* biology/unanimity: Upgrade to 3.4.1Jason W. Bacon2019-02-243-5/+5
| | | | | | | Minor fixes and enhancements upstream. Notes: svn path=/head/; revision=493769
* biology/ngs-sdk: Update 2.9.3 -> 2.9.4Yuri Victorovich2019-02-233-5/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=493731
* biology/igv: Update 2.4.16 -> 2.4.19Yuri Victorovich2019-02-232-6/+6
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=493730
* biology/unanimity is not compatible with python 3.xAntoine Brodin2019-02-222-2/+2
| | | | | | | PR: 234633 Notes: svn path=/head/; revision=493621
* Update to 1.007005 (1.7.5)Sunpoet Po-Chuan Hsieh2019-02-223-17/+2
| | | | | | | Changes: https://metacpan.org/changes/distribution/BioPerl Notes: svn path=/head/; revision=493589
* biology/iqtree: Update to version 1.6.10Joseph Mingrone2019-02-212-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10 Notes: svn path=/head/; revision=493504
* Update to 1.007003Sunpoet Po-Chuan Hsieh2019-02-204-67/+16
| | | | | | | | | - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl-Run Notes: svn path=/head/; revision=493448
* Update to 1.007004 (1.7.4)Sunpoet Po-Chuan Hsieh2019-02-205-998/+189
| | | | | | | | | | | | - Add LICENSE_FILE - Use USES=shebangfix - Use COPYTREE_SHARE instead of CP -R - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl Notes: svn path=/head/; revision=493447
* Add p5-Bio-Cluster 1.7.3Sunpoet Po-Chuan Hsieh2019-02-205-0/+55
| | | | | | | | | | Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe the basic structure for a cluster of BioPerl objects. WWW: https://metacpan.org/release/Bio-Cluster Notes: svn path=/head/; revision=493444
* biology/pbseqan: Mark deprecatedJason W. Bacon2019-02-201-0/+2
| | | | | | | Upstream was merged into the SeqAn project represented by biology/seqan. Notes: svn path=/head/; revision=493403
* biology/unanimity: Upgrade to 3.4.0Jason W. Bacon2019-02-2010-70/+133
| | | | | | | | Switch from cmake to new meson build system Tests disabled for now pending work on unbundling googletest Notes: svn path=/head/; revision=493402
* biology/pbbam: Upgrade to 0.18.0 releaseJason W. Bacon2019-02-194-23/+47
| | | | | | | In preparation for unanimity upgrade Notes: svn path=/head/; revision=493399
* biology/pbcopper: Upgrade to 0.4.1 releaseJason W. Bacon2019-02-195-38/+26
| | | | | | | In preparation for biology/unanimity upgrade Notes: svn path=/head/; revision=493397
* vec_splats function is not supported by base GCC. Add USES=compiler:c11Mark Linimon2019-02-181-2/+2
| | | | | | | | | | | to fix build on powerpc platforms. PR: 235514 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=493230
* biology/pbseqan: Minor upgrade to latest commitJason W. Bacon2019-02-172-6/+6
| | | | | | | In preparation for biology/unanimity upgrade Notes: svn path=/head/; revision=493182
* Update dns/libidn2 to 2.1.1Sunpoet Po-Chuan Hsieh2019-02-092-2/+2
| | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS Notes: svn path=/head/; revision=492534
* biology/checkm: Update 1.0.12 -> 1.0.13Yuri Victorovich2019-02-092-5/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=492531
* - Update WWWDmitry Marakasov2019-02-071-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=492353
* biology/dsr-pdb: Correct typoYuri Victorovich2019-02-051-1/+1
| | | | Notes: svn path=/head/; revision=492270
* biology/dsr-pdb: Add c++11 flags because boost isn't found without itYuri Victorovich2019-02-053-2/+25
| | | | | | | | | | Also add patches for missing includes that only gcc complains about. PR: 235519 Reported by: Piotr Kubaj <pkubaj@anongoth.pl> Notes: svn path=/head/; revision=492269
* New port: biology/figtree: Graphical viewer of phylogenetic treesYuri Victorovich2019-02-034-0/+49
| | | | Notes: svn path=/head/; revision=492079
* New port: biology/graphlan: High-quality circular representations of ↵Yuri Victorovich2019-02-035-0/+127
| | | | | | | taxonomic, phylogenetic trees Notes: svn path=/head/; revision=492071
* New port: biology/prodigy-lig: Prediction of protein-small molecule binding ↵Yuri Victorovich2019-02-034-0/+34
| | | | | | | affinities Notes: svn path=/head/; revision=492059
* New port: biology/prodigal: Protein-coding gene prediction for prokaryotic ↵Yuri Victorovich2019-02-034-0/+51
| | | | | | | genomes Notes: svn path=/head/; revision=492058
* Move Objective-C ports to the v2 GNUstep ABI.David Chisnall2019-02-031-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | * Bump the LLVM revision used for GNUstep to 7, the minimum to support the new ABI. * GNUstep-back does not work with lld, so mark it to use Gold (BFD LD doesn't seem able to link Objective-C things). * Turn off some annoying debug logs in GNUstep back, which generate several messages per second when you move the mouse. These should never have been enabled in a release build anyway. * Downgrade Cenon to 4.0.2. This was the last version to actually work with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep can't parse). * Update gorm to git head. The current release doesn't work with the new Objective-C ABI, but -head has the patches to fix it. * Update PikoPixel and add it to the gnustep-app meta-package. * Update the three core GNUstep packages to the latest release. * Update gnumail and pantomime to the latest release and fix a linking error with the new ABI. * Update GNUstep FTP to the latest version. Reviewed by: bapt (previous version) Notes: svn path=/head/; revision=492056
* biology/py-loompy: Update 2.0.16 -> 2.0.17Yuri Victorovich2019-02-022-5/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=491995
* New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein ↵Yuri Victorovich2019-01-299-0/+122
| | | | | | | description format) Notes: svn path=/head/; revision=491546
* biology/py-pysam: Update 0.15.1 -> 0.15.2Yuri Victorovich2019-01-262-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=491232
* Sort categories Makefiles.Mathieu Arnold2019-01-221-1/+1
| | | | Notes: svn path=/head/; revision=490961
* Fix Qt5 symbol version scripts to put the catch-all clause first. WhenTijl Coosemans2019-01-163-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | a symbol matches multiple clauses the last one takes precedence. If the catch-all is last it captures everything. In the case of Qt5 libraries this caused all symbols to have a Qt_5 label while some should have Qt_5_PRIVATE_API. This only affects lld because GNU ld always gives the catch-all lowest priority. Older versions of Qt5Webengine exported some memory allocation symbols from the bundled Chromium. Version 5.9 stopped exporting these [1] but the symbols were kept as weak wrappers for the standard allocation functions to maintain binary compatibility. [2][3] The problem is that the call to the standard function in these weak wrappers is only resolved to the standard function if there's a call to this standard function in other parts of Qt5Webengine, because only then is there a non-weak symbol that takes precedence over the weak one. If there's no such non-weak symbol the call in the weak wrapper resolves to the weak wrapper itself creating an infinite call loop that overflows the stack and causes a crash. Some of the allocation functions are variants of C++ new and delete and it probably depends on the compiler whether these variants are used in other parts of Qt5Webengine. Remove the weak wrappers (make them Linux specific). This isn't binary compatible but we are already breaking that with the changes to the symbol versions. [1] https://github.com/qt/qtwebengine/commit/5c2cbfccf9aafb547b0b30914c4056abd25942a4 [2] https://github.com/qt/qtwebengine/commit/2ed5054e3a800fa97c2c9e920ba1e6ea4b6ef2a5 [3] https://github.com/qt/qtwebengine/commit/009f5ebb4bd6e50188671e0815a5dae6afe39db5 Bump all ports that depend on Qt5. PR: 234070 Exp-run by: antoine Approved by: kde (adridg) Notes: svn path=/head/; revision=490472
* biology/stacks: Upgrade to 2.3Jason W. Bacon2019-01-124-38/+14
| | | | | | | Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=490062
* New port: biology/hisat2: Program for mapping next-generation sequencing readsJason W. Bacon2019-01-117-0/+577
| | | | | | | Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=489981
* Fixup bulk -a errors with BUILD_ALL_PYTHON_FLAVORS=yes.Mathieu Arnold2019-01-111-1/+2
| | | | Notes: svn path=/head/; revision=489980
* biology/seqtools: fix build on current, if lld is lld7Kurt Jaeger2019-01-071-0/+1
| | | | | | | | | | - fixed by LLD_UNSAFE=yes PR: 230609 Submitted by: jbeich Notes: svn path=/head/; revision=489613
* biology/groopm fails to build with python3Antoine Brodin2019-01-071-1/+1
| | | | | | | PR: 234633 Notes: svn path=/head/; revision=489569
* Update dns/libidn2 to 2.1.0Sunpoet Po-Chuan Hsieh2019-01-062-0/+2
| | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS Notes: svn path=/head/; revision=489529
* Update science/hdf5 to 1.10.4Sunpoet Po-Chuan Hsieh2019-01-051-1/+1
| | | | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes PR: 233070 Submitted by: wen Notes: svn path=/head/; revision=489412
* biology/ncbi-blast+: Upgrade to 2.8.1Jason W. Bacon2019-01-014-32/+244
| | | | | | | | | | Remove hacks that are no longer needed New patch for endian.h location Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=488931
* biology/diamond: Update to version 0.9.24Joseph Mingrone2018-12-314-27/+12
| | | | | | | | | | Port changes: Tune for package building based on the author's recommendation. Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24 Notes: svn path=/head/; revision=488819
* biology/iqtree: switch to outsource cmake buildJoseph Mingrone2018-12-271-2/+2
| | | | Notes: svn path=/head/; revision=488558
* Update math/eigen3 to 3.3.7Tobias C. Berner2018-12-261-0/+1
| | | | | | | | - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6 - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7 Notes: svn path=/head/; revision=488363
* Change cmake default behaviour to outsource.Tobias C. Berner2018-12-258-8/+8
| | | | | | | | | | | | | | Ports that build out of source now simply can use "USES=cmake" instead of "USES=cmake:outsource". Ports that fail to build out of source now need to specify "USES=cmake:insource". I tried to only set insource where explictely needed. PR: 232038 Exp-run by: antoine Notes: svn path=/head/; revision=488341
* biology/iqtree: Update to version 1.6.9Joseph Mingrone2018-12-232-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9 Notes: svn path=/head/; revision=488217
* - Update to 1.73Wen Heping2018-12-222-5/+4
| | | | | | | | | PR: 234154 Submitted by: wenheping2000@hotmail.com(myself) Approved by: maintainer Notes: svn path=/head/; revision=488064
* Remove expired ports:Rene Ladan2018-12-214-57/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-12-19 net/py-libstorj: Broken for more than 6 months 2018-12-20 net/xferstats: Uses obsolete glib12 2018-12-20 net/wmlj: Uses obsolete glib12 2018-12-20 net/ipsorc: Uses obsolete glib12 2018-12-20 net/bsdproxy: Uses obsolete glib12 2018-12-20 net/gini: Uses obsolete glib12 2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead 2018-12-20 net/nocatsplash: Uses obsolete glib12 2018-12-20 net/jags: Uses obsolete glib12 2018-12-19 net/scribe: Broken for more than 6 months 2018-12-20 net/libnetdude: Uses obsolete glib12 2018-12-20 net/nepim: Uses obsolete glib12 2018-12-20 emulators/generator: Uses obsolete glib12 2018-12-19 emulators/py-nova: Broken for more than 6 months 2018-12-20 emulators/generator-cbiere: Uses obsolete glib12 2018-12-20 x11-toolkits/p5-Gtk-Perl: Uses obsolete glib12 2018-12-20 deskutils/ithought: Uses obsolete glib12 2018-12-20 deskutils/gaddr: Uses obsolete glib12 2018-12-20 x11-fonts/gfe: Uses obsolete glib12 2018-12-20 graphics/graphopt: Uses obsolete glib12 2018-12-19 graphics/fotoxx: Broken for more than 6 months 2018-12-20 graphics/gcolor: Uses obsolete glib12 2018-12-20 graphics/danpei: Uses obsolete glib12 2018-12-20 graphics/chbg: Uses obsolete glib12 2018-12-20 mail/pop3lite: Uses obsolete glib12 2018-12-20 mail/gbuffy: Uses obsolete glib12 2018-12-20 security/gtk-knocker: Uses obsolete glib12 2018-12-20 security/gpasman: Uses obsolete glib12 2018-12-20 security/crank: Uses obsolete glib12 2018-12-20 security/stegdetect: Uses obsolete glib12 2018-12-20 devel/liboop: Uses obsolete glib12 2018-12-20 devel/gcvs: Uses obsolete glib12 2018-12-20 print/lpr-wrapper: Uses obsolete glib12 2018-12-20 print/libppd: Uses obsolete glib12 2018-12-20 net-p2p/napshare: Uses obsolete glib12 2018-12-20 net-p2p/gnewtellium: Uses obsolete glib12 2018-12-20 editors/gnotepad+: Uses obsolete glib12 2018-12-20 editors/manedit: Uses obsolete glib12 2018-12-20 misc/gtkfind: Uses obsolete glib12 2018-12-20 games/mindguard: Uses obsolete glib12 2018-12-20 games/xbattle: Uses obsolete glib12 2018-12-20 games/xbill: Uses obsolete glib12 2018-12-20 games/corewars: Uses obsolete glib12 2018-12-20 games/dopewars: Uses obsolete glib12 2018-12-20 games/garith: Uses obsolete glib12 2018-12-20 games/wmquake: Uses obsolete glib12 2018-12-20 games/znibbles: Uses obsolete glib12 2018-12-20 games/xpuyopuyo: Uses obsolete glib12 2018-12-19 games/kajongg: Broken for more than 6 months 2018-12-20 games/netspades: Uses obsolete glib12 2018-12-20 games/gtklife: Uses obsolete glib12 2018-12-20 biology/xmolwt: Uses obsolete glib12 2018-12-20 x11-clocks/wmclockmon: Uses obsolete glib12 2018-12-20 x11-clocks/asclock-gtk: Uses obsolete glib12 2018-12-20 net-im/gale: Uses obsolete glib12 2018-12-20 audio/xmms-ahx: Uses obsolete glib12 2018-12-20 audio/xmms-curses: Uses obsolete glib12 2018-12-20 audio/scrobbler: Uses obsolete glib12 2018-12-20 audio/xmms-nsf: Uses obsolete glib12 2018-12-20 audio/xmms-nas: Uses obsolete glib12 2018-12-20 audio/xmms-gbsplay: Uses obsolete glib12 2018-12-20 audio/xmms-wavpack: Uses obsolete glib12 2018-12-20 audio/xmms-shn: Uses obsolete glib12 2018-12-20 audio/xmms-volnorm: Uses obsolete glib12 2018-12-20 audio/xmms-faad: Uses obsolete glib12 2018-12-20 audio/xmms-scrobbler: Uses obsolete glib12 2018-12-20 audio/mcplay: Uses obsolete glib12 2018-12-20 audio/gmixer: Uses obsolete glib12 2018-12-20 audio/soundtracker: Uses obsolete glib12 2018-12-20 audio/xmms-sapplug: Uses obsolete glib12 2018-12-20 audio/rio500: Uses obsolete glib12 2018-12-20 audio/xmmsctrl: Uses obsolete glib12 2018-12-20 audio/xmms-xf86audio: Uses obsolete glib12 2018-12-20 audio/xmms-mailnotify: Uses obsolete glib12 2018-12-20 audio/xmms-sexypsf: Uses obsolete glib12 2018-12-20 audio/gqmpeg: Uses obsolete glib12 2018-12-20 audio/wmalbum: Uses obsolete glib12 2018-12-20 audio/xmms-xymms: Uses obsolete glib12 2018-12-20 audio/xmms-flac: Uses obsolete glib12 2018-12-20 audio/xmms-festalon: Uses obsolete glib12 2018-12-20 audio/gkrellmms2: Uses obsolete glib12 2018-12-20 audio/xmms-ladspa: Uses obsolete glib12 2018-12-19 math/octave-forge-engine: Broken for more than 6 months 2018-12-20 math/surf: Uses obsolete glib12 2018-12-19 math/msieve: Broken for more than 6 months 2018-12-19 math/octave-forge-fl-core: Broken for more than 6 months 2018-12-19 math/octave-forge-pdb: Broken for more than 6 months 2018-12-19 math/octave-forge-audio: Broken for more than 6 months 2018-12-20 math/geg: Uses obsolete glib12 2018-12-20 math/grpn: Uses obsolete glib12 2018-12-20 x11/gdkxft: Uses obsolete glib12 2018-12-20 x11/gtk-theme-switch: Uses obsolete glib12 2018-12-19 x11/xpyb: Broken for more than 6 months 2018-12-20 x11/gtk-launch: Uses obsolete glib12 2018-12-19 x11/xpra: Broken for more than 6 months 2018-12-20 palm/pilrc: Uses obsolete glib12 2018-12-20 x11-fm/mtoolsfm: Uses obsolete glib12 2018-12-20 german/steak: Uses obsolete glib12 2018-12-20 multimedia/xmms-skins-huge: Uses obsolete glib12 2018-12-20 multimedia/openquicktime: Uses obsolete glib12 2018-12-20 multimedia/xmms-skins: Uses obsolete glib12 2018-12-20 multimedia/oqtplayer: Uses obsolete glib12 2018-12-20 multimedia/oqtencoder: Uses obsolete glib12 2018-12-20 multimedia/p5-Video-OpenQuicktime: Uses obsolete glib12 2018-12-20 multimedia/xtheater: Uses obsolete glib12 2018-12-20 multimedia/dv2jpg: Uses obsolete glib12 2018-12-20 comms/hf: Uses obsolete glib12 2018-12-20 comms/gscmxx: Uses obsolete glib12 2018-12-20 sysutils/wmcube-gdk: Uses obsolete glib12 2018-12-20 sysutils/gcombust: Uses obsolete glib12 2018-12-20 sysutils/xlogmaster: Uses obsolete glib12 2018-12-20 sysutils/mount.app: Uses obsolete glib12 2018-12-20 sysutils/bbapm: Uses obsolete glib12 Notes: svn path=/head/; revision=487992
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