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* 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
* biology/gff2ps: update 0.98d to 0.98lVinícius Zavam2018-12-192-5/+5
| | | | | | | | | | adopt port. Approved by: araujo (mentor) Differential Revision: https://reviews.freebsd.org/D18591 Notes: svn path=/head/; revision=487807
* biology/diamond: Update to 0.9.23 plus fixes after releaseJoseph Mingrone2018-12-173-10/+11
| | | | | | | | | | | | Also: - update license since upstream changed to GPLv3 - only build/package for amd64, since it is untested on other architectures and currently does not build on i386 Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23 Notes: svn path=/head/; revision=487707
* Update Qt5 to 5.12.0Tobias C. Berner2018-12-161-0/+11
| | | | | | | | | | | | http://blog.qt.io/blog/2018/12/06/qt-5-12-lts-released/ - This breaks support for libressl again. Patches are welcome. PR: 233705 Exp-run by: antoine Notes: svn path=/head/; revision=487594
* New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEYuri Victorovich2018-12-155-0/+47
| | | | Notes: svn path=/head/; revision=487491
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-1237-20/+37
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* devel/boost-*: update to 1.69.0Jan Beich2018-12-125-3/+5
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_69_0.html PR: 232525 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D17645 Notes: svn path=/head/; revision=487266
* Remove biology/njplotJoseph Mingrone2018-12-115-111/+0
| | | | | | | | The author of both NJplot and SeaView says that NJplot can be considered deprecated and replaced by SeaView. Notes: svn path=/head/; revision=487239
* biology/mummer: Add USES=compiler:c++11-langYuri Victorovich2018-12-111-1/+1
| | | | Notes: svn path=/head/; revision=487223
* biology/mummer: Update 3.23 -> 4.0.0beta2-2Yuri Victorovich2018-12-113-47/+61
| | | | | | | | | | Port changes: * Moved to github * It now installs itself * It uses yaggo during build Notes: svn path=/head/; revision=487222
* biology/mummer: Take maintainershipYuri Victorovich2018-12-111-1/+1
| | | | Notes: svn path=/head/; revision=487221
* New port: math/checkm: Quality assessment tool for the microbial genomesYuri Victorovich2018-12-074-0/+43
| | | | Notes: svn path=/head/; revision=486814
* New port: math/groopm: Metagenomic binning suiteYuri Victorovich2018-12-074-0/+35
| | | | Notes: svn path=/head/; revision=486812
* devel/gradle: Update to 5.0Yuri Victorovich2018-12-042-4/+4
| | | | | | | | | | Change biology/igv and biology/gatk to gradle4 due to build failures with gradle5. PR: 233623 Approved by: gasol.wu@gmail.com (maintainer) Notes: svn path=/head/; revision=486619
* biology/gatk: Change gradle4->gradle because it builds fine with both gradle ↵Yuri Victorovich2018-12-031-2/+2
| | | | | | | 4 and 5 Notes: svn path=/head/; revision=486561
* biology/gatk: Correct the targetYuri Victorovich2018-12-031-1/+1
| | | | Notes: svn path=/head/; revision=486503
* New port: biology/gatk: Variant discovery in high-throughput sequencing dataYuri Victorovich2018-12-036-0/+118
| | | | Notes: svn path=/head/; revision=486502
* Mark QT4 ports/functionality for removal on 2019-03-15Rene Ladan2018-12-021-0/+3
| | | | | | | | | | | | | | While here, chase some KDE4 ports and functionality, these are scheduled for removal on 2018-12-31. Change the default option/flavor to QT5 where applicable or use alternative toolkits like GTK. Submitted by: tcberner Reviewed by: adridg, jhale, rene, tcberner Approved by: portmgr (implicit, flavor hook) Differential Revision: https://reviews.freebsd.org/D17741 Notes: svn path=/head/; revision=486467
* biology/igv: Update 2.4.15 -> 2.4.16Yuri Victorovich2018-11-182-6/+6
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=485255
* biology/molden: update to 5.8.2Johannes M Dieterich2018-11-133-10/+45
| | | | | | | | | | Also add do-install-{option}-on targets and shadow ${MKDIR} commands. PR: 233060 Submitted by: yuri Notes: svn path=/head/; revision=484858
* biology/seqan-apps: fix build with GCC-based architecturesSteve Wills2018-11-091-2/+4
| | | | | | | | | PR: 232045 Submitted by: Piotr Kubaj <pkubaj@anongoth.pl> Approved by: maintainer timeout (h2+fbsdports@fsfe.org >1 month) Notes: svn path=/head/; revision=484547
* biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gccYuri Victorovich2018-11-071-1/+2
| | | | | | | | | | Add $(LDFLAGS) to makefile. While here, add USES=gl. Approved by: portmgr Notes: svn path=/head/; revision=484371
* Fix build failure with base GCC because of double typedefs.Mark Linimon2018-11-051-0/+48
| | | | | | | | | PR: 232457 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=484211
* Remove the incorrect typedefs to fix build on tier-2.Mark Linimon2018-11-052-0/+29
| | | | | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=484210
* Remove the inccorrect typedefs to fix build on tier-2.Mark Linimon2018-11-051-4/+0
| | | | | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=484209
* biology/igv: Update 2.4.10 -> 2.4.15Yuri Victorovich2018-11-043-24/+21
| | | | | | | | | | Port changes: * Change to gradle, corresponding updates in build, install, environment, etc. Reported by: portscout Notes: svn path=/head/; revision=484156
* biology/canu: Upgrade to 1.8, add experimental SLURM integrationJason W. Bacon2018-11-045-31/+102
| | | | | | | | | | | Solves build issue with gcc8. PR: 232930 Reported by: gerald Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=484077
* biology/bowtie: Patch for gcc8 and clean upJason W. Bacon2018-11-032-6/+17
| | | | | | | | | PR: 232929 Reported by: gerald Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=483954
* biology/bowtie: Revert previous commit with missing log messageJason W. Bacon2018-11-032-17/+5
| | | | Notes: svn path=/head/; revision=483953
* biology/bowtie: PatchJason W. Bacon2018-11-032-5/+17
| | | | Notes: svn path=/head/; revision=483910
* biology/py-loompy: Update 2.0.15 -> 2.0.16Yuri Victorovich2018-10-302-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=483451
* biology/iqtree: Update to version 1.6.8Joseph Mingrone2018-10-282-4/+4
| | | | | | | | Upstream release notes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8 Notes: svn path=/head/; revision=483358
* Fix build with tier-2 arches.Mark Linimon2018-10-281-1/+7
| | | | | | | | | PR: 231448 Submitted by: Piotr Kubaj Approved by: maintainer Notes: svn path=/head/; revision=483245
* biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2Yuri Victorovich2018-10-282-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=483221
* biology/p5-transdecoder: Upgrade to 5.4.0Jason W. Bacon2018-10-234-30/+44
| | | | | | | | Minor clean up to silence portlint Approved by: jrm (mentor, implicit) Notes: svn path=/head/; revision=482836
* biology/hyphy: Update to version 2.3.14.16Joseph Mingrone2018-10-203-5/+11
| | | | | | | | | | | | | | | | | | | This pulls in fixes after the 2.3.14 release. Upstream changes for version 2.3.14: https://github.com/veg/hyphy/releases/tag/2.3.14 Subsequent fixes: https://github.com/veg/hyphy/commit/1ecac31 https://github.com/veg/hyphy/commit/bec6833 https://github.com/veg/hyphy/commit/9847438 https://github.com/veg/hyphy/commit/02dcedd https://github.com/veg/hyphy/commit/8f44d3c https://github.com/veg/hyphy/commit/5297c30 https://github.com/veg/hyphy/commit/3d88d3e Notes: svn path=/head/; revision=482495
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