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* Update math/eigen3 to 3.3.7tcberner2018-12-261-0/+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
* Change cmake default behaviour to outsource.tcberner2018-12-268-8/+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
* biology/iqtree: Update to version 1.6.9jrm2018-12-232-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
* - Update to 1.73wen2018-12-222-5/+4
| | | | | | PR: 234154 Submitted by: wenheping2000@hotmail.com(myself) Approved by: maintainer
* Remove expired ports:rene2018-12-214-57/+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glib12 2018-12-20 net/bsdproxy: Uses obsolete glib12 2018-12-20 net/gini: Uses obsolete glib12 2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead 2018-12-20 net/nocatsplash: Uses obsolete glib12 2018-12-20 net/jags: Uses obsolete glib12 2018-12-19 net/scribe: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
* biology/gff2ps: update 0.98d to 0.98legypcio2018-12-202-5/+5
| | | | | | | adopt port. Approved by: araujo (mentor) Differential Revision: https://reviews.freebsd.org/D18591
* biology/diamond: Update to 0.9.23 plus fixes after releasejrm2018-12-183-10/+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
* Update Qt5 to 5.12.0tcberner2018-12-161-0/+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
* New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEyuri2018-12-155-0/+47
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* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-12-1237-20/+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
* devel/boost-*: update to 1.69.0jbeich2018-12-125-3/+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
* Remove biology/njplotjrm2018-12-115-111/+0
| | | | | The author of both NJplot and SeaView says that NJplot can be considered deprecated and replaced by SeaView.
* biology/mummer: Add USES=compiler:c++11-langyuri2018-12-111-1/+1
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* biology/mummer: Update 3.23 -> 4.0.0beta2-2yuri2018-12-113-47/+61
| | | | | | | Port changes: * Moved to github * It now installs itself * It uses yaggo during build
* biology/mummer: Take maintainershipyuri2018-12-111-1/+1
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* New port: math/checkm: Quality assessment tool for the microbial genomesyuri2018-12-074-0/+43
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* New port: math/groopm: Metagenomic binning suiteyuri2018-12-074-0/+35
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* devel/gradle: Update to 5.0yuri2018-12-052-4/+4
| | | | | | | Change biology/igv and biology/gatk to gradle4 due to build failures with gradle5. PR: 233623 Approved by: gasol.wu@gmail.com (maintainer)
* biology/gatk: Change gradle4->gradle because it builds fine with both gradle ↵yuri2018-12-041-2/+2
| | | | 4 and 5
* biology/gatk: Correct the targetyuri2018-12-031-1/+1
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* New port: biology/gatk: Variant discovery in high-throughput sequencing datayuri2018-12-036-0/+118
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* Mark QT4 ports/functionality for removal on 2019-03-15rene2018-12-021-0/+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
* biology/igv: Update 2.4.15 -> 2.4.16yuri2018-11-192-6/+6
| | | | Reported by: portscout
* biology/molden: update to 5.8.2jmd2018-11-133-10/+45
| | | | | | | Also add do-install-{option}-on targets and shadow ${MKDIR} commands. PR: 233060 Submitted by: yuri
* biology/seqan-apps: fix build with GCC-based architecturesswills2018-11-101-2/+4
| | | | | | PR: 232045 Submitted by: Piotr Kubaj <pkubaj@anongoth.pl> Approved by: maintainer timeout (h2+fbsdports@fsfe.org >1 month)
* biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gccyuri2018-11-071-1/+2
| | | | | | | Add $(LDFLAGS) to makefile. While here, add USES=gl. Approved by: portmgr
* Fix build failure with base GCC because of double typedefs.linimon2018-11-061-0/+48
| | | | | | PR: 232457 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Remove the incorrect typedefs to fix build on tier-2.linimon2018-11-062-0/+29
| | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Remove the inccorrect typedefs to fix build on tier-2.linimon2018-11-061-4/+0
| | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* biology/igv: Update 2.4.10 -> 2.4.15yuri2018-11-053-24/+21
| | | | | | | Port changes: * Change to gradle, corresponding updates in build, install, environment, etc. Reported by: portscout
* biology/canu: Upgrade to 1.8, add experimental SLURM integrationjwb2018-11-045-31/+102
| | | | | | | | Solves build issue with gcc8. PR: 232930 Reported by: gerald Approved by: jrm (mentor, implicit)
* biology/bowtie: Patch for gcc8 and clean upjwb2018-11-042-6/+17
| | | | | | PR: 232929 Reported by: gerald Approved by: jrm (mentor, implicit)
* biology/bowtie: Revert previous commit with missing log messagejwb2018-11-042-17/+5
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* biology/bowtie: Patchjwb2018-11-042-5/+17
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* biology/py-loompy: Update 2.0.15 -> 2.0.16yuri2018-10-302-4/+4
| | | | Reported by: portscout
* biology/iqtree: Update to version 1.6.8jrm2018-10-292-4/+4
| | | | | Upstream release notes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
* Fix build with tier-2 arches.linimon2018-10-281-1/+7
| | | | | | PR: 231448 Submitted by: Piotr Kubaj Approved by: maintainer
* biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2yuri2018-10-282-4/+4
| | | | Reported by: portscout
* biology/p5-transdecoder: Upgrade to 5.4.0jwb2018-10-234-30/+44
| | | | | Minor clean up to silence portlint Approved by: jrm (mentor, implicit)
* biology/hyphy: Update to version 2.3.14.16jrm2018-10-203-5/+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
* biology/py-loompy: Update 2.0.14 -> 2.0.15yuri2018-10-192-4/+4
| | | | Reported by: portscout
* New port: biology/py-gffutils: Work with GFF and GTF files in a flexible ↵yuri2018-10-194-0/+36
| | | | database framework
* New port: biology/py-pyfaidx: Efficient pythonic random access to fasta ↵yuri2018-10-194-0/+38
| | | | subsequences
* New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) ↵yuri2018-10-194-0/+32
| | | | files
* biology/ngs-sdk: Update 2.9.2 -> 2.9.3yuri2018-10-193-5/+5
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* biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2yuri2018-10-172-4/+4
| | | | Reported by: portscout
* biology/iqtree: Update to version 1.6.7.1jrm2018-10-162-4/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
* biology/py-orange3-single-cell: Update 0.8.0 -> 0.8.1yuri2018-10-142-6/+11
| | | | Reported by: portscout
* biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2yuri2018-10-142-4/+4
| | | | Reported by: portscout
* Deprecate most glib12 consumersantoine2018-10-121-0/+3
| | | | With hat: portmgr
* Update devel/tbb to version 2019.1 and bump dependent ports' revisionsmartymac2018-10-111-1/+1
| | | | Also, reintegrate HTML documentation that was removed in previous version.
* Update to 1.73sunpoet2018-10-102-6/+10
| | | | Changes: https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene
* New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkityuri2018-10-085-0/+70
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* biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06yuri2018-10-086-175/+87
| | | | | | | | Port changes: * Take maintainership * Add to LIB_DEPENDS and USExx * Remove lists of executables and manpages, use file listing instead (*) * Update WWW
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/yuri2018-10-0713-1004/+0
| | | | | | | | | | Port changes: * Take maintainership * Implement the 'benchmarks' target, and stop installing benchmarks * Add USES=gmake * Update license * Change MASTER_SITES and WWW to https * Silence some commands
* biology/py-biom-format: Update to version 2.1.7jrm2018-10-062-16/+14
| | | | Reported by: portscout
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptdes2018-10-0615-30/+30
| | | | | | | for where it resulted in a change in output from build-depends-list or run-depends-list. Approved by: portmgr (adamw)
* Update devel/tbb to version 2019 and bump dependent port's revisionsmartymac2018-10-041-0/+1
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* - Update to 1-14-10danilo2018-09-294-8/+9
| | | | - Move USES to make portlint happy
* - Unbreak by adding missing pkg-plistwen2018-09-282-2/+136
| | | | | PR: 228758 Submitted by: mzaki@niid.go.jp(maintainer)
* Allow building on powerpc64.linimon2018-09-281-1/+1
| | | | | | PR: 231759 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Update Objective-C LLVM version to 6.0.brooks2018-09-261-1/+1
| | | | | | | | | Fixes aarch64 build. Reduces depends on obsolete LLVM 4.0. PR: 230116 Submitted by: mikael.urankar@gmail.com Approved by: theraven (prior version) Sponsored by: DARPA, AFRL
* Change 4 ports from net/mpich2 to net/mpichyuri2018-09-231-3/+5
| | | | | | | mpich2 is the obsolete version 2.x, mpich is at the current version 3.x Ports: biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis
* - Update to 1.63wen2018-09-222-4/+4
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* Fix build on gcc-based archs by updating USES.linimon2018-09-221-1/+1
| | | | | | | | Tested on powerpc64 and amd64 (for no regression). While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Update to 1.5.2sunpoet2018-09-222-6/+7
| | | | Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc
* New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq datayuri2018-09-214-0/+44
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* biology/py-cutadapt: Upgrade to 1.18jwb2018-09-203-50/+9
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D17099
* biology/ngs-sdk: Update 2.9.1 -> 2.9.2yuri2018-09-203-5/+5
| | | | Reported by: portscout
* Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-basedlinimon2018-09-181-1/+1
| | | | | | | | | | archs such as powerpc64. Tested for no effect on amd64. While here, pet portlint. Approved by: portgmr (tier-2 blanket)
* More precisely specify USES=compiler to fix build on gcc-basedlinimon2018-09-183-3/+3
| | | | | | | | platforms such as powerpc64. Tested on powerpc64, amd64. Approved by: portmgr (tier-2 blanket)
* biology/py-pysam: Update 0.15.0 -> 0.15.1yuri2018-09-182-4/+4
| | | | Reported by: portscout
* Add DOCS options to ports that should have one.mat2018-09-103-0/+6
| | | | | | | | Also various fixes related to said option. PR: 230864 Submitted by: mat exp-runs by: antoine
* biology/seaview: Fix build with Clang 6tobik2018-09-083-0/+65
| | | | | | | | | | | | seaview.cxx:3352:24: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] strcat(suggested, "."PDF_OR_PS_EXT); ^ http://beefy12.nyi.freebsd.org/data/head-amd64-default/p479076_s338486/logs/errors/seaview-4.7,1.log PR: 230881 Submitted by: tobik Approved by: bofh (maintainer timeout, 2 weeks)
* Update science/hdf5 to 1.10.2sunpoet2018-09-061-1/+1
| | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt PR: 231009 Exp-run by: antoine
* Update to 1.31.0jhale2018-09-0317-181/+201
| | | | | PR: 229463 Approved by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
* biology/stacks: Enable OpenMP (oversight in previous commit)jwb2018-09-011-2/+2
| | | | | | | Upgrade to latest release will follow, after testing Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16973
* biology/iqtree: Update to version 1.6.7jrm2018-08-272-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
* biology/py-bx-python: Update 0.8.1 -> 0.8.2yuri2018-08-262-5/+5
| | | | Reported by: portscout
* biology/unanimity: Upgrade to latest release, soften dep version requirementsjwb2018-08-262-11/+10
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16902
* biology/protomol: Fix doubled USES overwriting the old valuetobik2018-08-251-3/+2
| | | | - Make sure shebangfix is actually used
* biology/protomol: Fix build with Clang 6tobik2018-08-251-0/+1
| | | | | | | | | | | | Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>')) *myStream << a; ~~~~~~~~~ ^ ~ /usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with & basic_ostream& operator<<(const void* __p); ^ ... and so on ... http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log
* biology/primer3: Fix build with Clang 6tobik2018-08-251-0/+24
| | | | | | | | | | | thal.c:426:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_f) { ~~~~ ^ ~~~~~~~ thal.c:431:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_r) { ~~~~ ^ ~~~~~~~ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/primer3-2.3.6.log
* biology/libsbml: Fix build with Clang 6tobik2018-08-251-9/+2
| | | | | | | | | | | | | In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207: /usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted {__nc = __v.__cc; return *this;} ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log
* biology/avida: Fix build with Clang 6tobik2018-08-251-0/+1
| | | | | | | | | | | | | | | | | | avida-core/source/main/cPopulation.cc:2916:20: error: no matching member function for call to 'push_back' track_founders.push_back(make_pair(organism->GetBioGroup("genotype")->GetID(), new_genome.AsString())); ~~~~~~~~~~~~~~~^~~~~~~~~ /usr/include/c++/v1/vector:688:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'const pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x); ^ /usr/include/c++/v1/vector:691:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(value_type&& __x); ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/avida-2.12.4.log libs/tcmalloc-1.4/src/sysinfo.cc:832:88: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] "%08"PRIx64"-%08"PRIx64" %c%c%c%c %08"PRIx64" %02x:%02x %-11"PRId64" %s\n", ^
* biology/lamarc: Fix build with Clang 6tobik2018-08-251-0/+2
| | | | | | | | | | | src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair' return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/utility:639:1: note: candidate function not viable: no known conversion from 'DoubleVec1d' (aka 'vector<double>') to 'std::__1::vector<double, std::__1::allocator<double> > &&' for 1st argument make_pair(_T1&& __t1, _T2&& __t2) ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/lamarc-2.1.8_1,1.log
* Mark as broken with clang6 after r473289.linimon2018-08-241-1/+9
|
* - Update to 1.72wen2018-08-242-5/+4
| | | | | | PR: 230723 Submitted by: wen@(myself) Approved by: maintainer
* Remove expired ports:rene2018-08-176-104/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-08-16 net/traceroute: Upstream gone 2018-08-15 net/e169-stats: unknown license 2018-08-15 net/l4ip: unknown license 2018-08-15 net/dhcprelay: unknown license 2018-08-15 emulators/m2000: unknown license 2018-08-15 textproc/ant-xinclude-task: unknown license 2018-08-15 textproc/bomstrip: unknown license 2018-08-15 x11-fonts/ecofont: unknown license 2018-08-15 mail/roundcube-groupvice: unknown license 2018-08-15 security/pft: unknown license 2018-08-15 devel/kickassembler: unknown license 2018-08-15 devel/gdbmods: unknown license 2018-08-15 devel/as31: unknown license 2018-08-15 databases/dbf2mysql: unknown license 2018-08-15 misc/xpns: unknown license 2018-08-15 misc/amfm: unknown license 2018-08-15 games/smashbattle: unknown license 2018-08-15 games/syobon: unknown license 2018-08-15 games/optimax: unknown license 2018-08-15 games/xgospel: unknown license 2018-08-15 biology/blat: unknown license 2018-08-15 x11-clocks/swisswatch: unknown license 2018-08-15 palm/ppmtoTbmp: unknown license 2018-08-15 dns/ghtool: unknown license 2018-08-15 x11-themes/beastie: unknown license 2018-08-15 converters/uudx: unknown license 2018-08-15 sysutils/areca-cli: unknown license
* biology/cytoscape: Fix licenseyuri2018-08-122-3/+5
| | | | Reported by: linimon
* Mark as broken on arm.linimon2018-08-121-0/+4
| | | | Approved by: portmgr (tier-2 blanket)
* devel/boost-*: update to 1.68.0jbeich2018-08-095-2/+5
| | | | | | | | | - Switch to C++14 for libboost_system to support C++14 consumers Changes: http://www.boost.org/users/history/version_1_68_0.html PR: 229569 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D16165
* biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0yuri2018-08-092-4/+4
| | | | Reported by: portscout
* biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0yuri2018-08-092-4/+4
| | | | Reported by: portscout
* Regular sorting of categories Makefiles.mat2018-08-081-1/+1
| | | | Sponsored by: Absolight
* New port: biology/py-orange3-single-cell: Orange add-on for gene expression ↵yuri2018-08-074-0/+43
| | | | of single cell data
* biology/vcftools: Update to 0.1.16, a security releasejwb2018-08-042-4/+4
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16587
* biology/bcftools: update to 1.9fernape2018-08-035-24/+41
| | | | | | | | | | | | While here: * Update LICENSE handling * Move all commands to bin/ PR: 230169 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16543
* biology/samtools: update to 1.9fernape2018-08-032-8/+7
| | | | | | | PR: 230171 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16569
* biology/htslib: update to 1.9fernape2018-08-032-6/+8
| | | | | | | PR: 230170 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16568
* biology/py-pysam: Update 0.14.1 -> 0.15.0yuri2018-07-313-8/+5
| | | | | | | | Port changes: * Remove stripping: done by the project now * Update WWW Reported by: portscout
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-07-3015-10/+15
| | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542
* biology/linux-foldingathome: reset maintainer by requesteadler2018-07-271-1/+1
| | | | | | | Jonatan lacks the time to maintain the port. Thank you for your help so far, and you're welcome back any time. Approved by: onatan@gmail.com (maintainer)
* biology/seaview: Updatye version 4.6.5=>4.7bofh2018-07-222-4/+4
| | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
* biology/molden: Unbreak by updating the MASTER_SITES URLyuri2018-07-201-2/+1
| | | | The upstream keeps changing the URL.
* Mark BROKEN: unfetchaableantoine2018-07-201-0/+1
| | | | Reported by: pkg-fallout
* biology/htslib: Update 1.6 -> 1.8yuri2018-07-174-10/+8
| | | | | | | | | | | Port changes: * Use DISTVERSION * Add USES=localbase instead of CPPFLAGS/LDFLAGS * Move USES=ssl to CURL_USES=ssl * Update WWW PR: 228908 Approved by: maintainer's timeout (cartwright@asu.edu; 35 days)
* Deprecate unmaintained ports under the NONE licenseantoine2018-07-131-0/+3
|
* biology/molden: Unbreak by updating the MASTER_SITES URLyuri2018-07-131-2/+1
|
* Mark BROKEN: unfetchableantoine2018-07-131-0/+1
| | | | | Reported by: pkg-fallout MFH: 2018Q3
* New port: biology/exonerate: Generic tool for sequence alignmentyuri2018-07-135-0/+67
| | | | | PR: 229180 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
* biology/py-orange3-bioinformatics: Update 3.1.0 -> 3.1.1yuri2018-07-132-4/+4
| | | | Reported by: portscout
* New port: biology/stringtie: Transcript assembly and quantification for RNA-seqyuri2018-07-128-0/+157
| | | | | PR: 229480 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
* biology/hmmer: update to 3.2.1swills2018-07-114-46/+23
| | | | | PR: 229693 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer)
* biology/iqtree: Update to version 1.6.6jrm2018-07-092-4/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6
* New port: biology/cytoscape: Software to visualize molecular interaction ↵yuri2018-07-034-0/+83
| | | | networks, gene expression
* Mark various ports broken on mips64 and, where appropriate, mips.linimon2018-07-021-2/+4
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Mark BROKEN: missing plistantoine2018-06-291-0/+3
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* Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mktcberner2018-06-292-4/+4
| | | | | | | | | | | | | | | From now on, ports that depend on Qt4 will have to set USES= qt:4 USE_QT= foo bar ports depending on Qt5 will use USES= qt:5 USE_QT= foo bar PR: 229225 Exp-run by: antoine Reviewed by: mat Approved by: portmgr (antoine) Differential Revision: →https://reviews.freebsd.org/D15540
* New port: biology/igv: Visualization tool for genomic datasetsyuri2018-06-266-0/+77
|
* Mark as broken on aarch64.linimon2018-06-251-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* - Update to 5.17.0wen2018-06-253-4/+5
|
* biology/phyml: update to v3.3.20180621fernape2018-06-232-5/+6
| | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D15967
* Update math/gsl to 2.5tcberner2018-06-231-0/+1
| | | | PR: 229067
* biology/ngs-sdk: Update 2.9.0 -> 2.9.1yuri2018-06-223-5/+5
| | | | Reported by: portscout
* Mark these ports as broken on aarch64.linimon2018-06-222-0/+4
| | | | Approved by: portmgr (tier-2 blanket)
* Mark as broken on aarch64, and, where appropriate, armvX.linimon2018-06-224-0/+16
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Use PY_FLAVOR for dependencies.mat2018-06-216-13/+13
| | | | | | | FLAVOR is the current port's flavor, it should not be used outside of this scope. Sponsored by: Absolight
* Mark as broken on powerpc64 pending fix for PR 199603.linimon2018-06-191-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* Adjust USES to fix builds on gcc-based architectures.linimon2018-06-191-1/+1
| | | | | | | | While here, pet portlint. Tested for no regression on amd64. Approved by: portmgr (tier-2 blanket)
* Mark ports broken on powerpc64, categories a-c.linimon2018-06-181-3/+4
| | | | | | While here, pet portlint and do some other cleanup. Approved by: portmgr (tier-2 blanket)
* biology/bedtools: Fix Makefile to respect PREFIXjwb2018-06-172-0/+22
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15851
* New port: biology/py-orange3-bioinformatics: Orange add-on providing common ↵yuri2018-06-144-0/+41
| | | | functionality for bioinformatics
* biology/py-Genesis-PyAPI: Remove stray USES=fortranyuri2018-06-131-1/+1
|
* New port: biology/py-Genesis-PyAPI: API for the Genesis platform for ↵yuri2018-06-134-0/+29
| | | | genetics information processing
* biology/artemis: Update 9 -> 17.0.1-11yuri2018-06-124-1719/+72
| | | | | | | | | | | | | | Port changes: * Take maintainership * Change to github * Change to DISTVERSION * Add LICENSE * Depends on bash * Add USES=gmake * Remove NO_BUILD: needs to build jars from java files * Update the post-extract target * Change do-install to do minimal installation * Update WWW
* New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC ↵yuri2018-06-119-0/+256
| | | | Sequence Read Archives
* Remove expired ports:rene2018-06-0751-1777/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-06-06 biology/ssaha: Broken for more than 6 months 2018-06-06 biology/crux: Broken for more than 6 months 2018-06-06 biology/ariadne: Broken for more than 6 months 2018-06-06 cad/sceptre: Broken for more than 6 months 2018-06-06 cad/cider: Broken for more than 6 months 2018-06-06 chinese/scim-array: Broken for more than 6 months 2018-06-06 chinese/xpdf: Broken for more than 6 months 2018-06-06 chinese/telnet: Broken for more than 6 months 2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring comms/java-commapi 2018-06-06 comms/soundmodem: Broken for more than 6 months 2018-06-06 comms/jsdr: Broken for more than 6 months 2018-06-06 comms/java-commapi: Broken for more than 6 months 2018-06-06 converters/pdf2djvu: Broken for more than 6 months 2018-06-06 databases/rdb: Broken for more than 6 months 2018-06-06 databases/animenfo-client: Broken for more than 6 months 2018-06-06 databases/ruby-mysql: Broken for more than 6 months 2018-06-06 databases/riak: Broken for more than 6 months 2018-06-06 databases/animenfo-client-gtk: Broken for more than 6 months 2018-06-06 databases/rdfdb: Broken for more than 6 months 2018-06-06 databases/riak2: Broken for more than 6 months 2018-06-06 devel/subversion-static: Broken for more than 6 months 2018-06-06 japanese/xgate: Broken for more than 6 months 2018-06-06 textproc/opengrm-ngram: Broken for more than 6 months 2018-06-06 textproc/ocaml-tyxml: Depends on BROKEN and expiring www/ocaml-net 2018-06-06 www/ocaml-net: Broken for more than 6 months 2018-06-06 audio/linux-genpuid: Broken for more than 6 months 2018-06-06 x11/enventor: Broken for more than 6 months 2018-06-06 audio/xmms-timidity: Broken for more than 6 months 2018-06-06 audio/kaudiocreator: Broken for more than 6 months 2018-06-06 audio/jxm: Depends on BROKEN and expiring comms/java-commapi 2018-06-06 audio/deforaos-mixer: Broken for more than 6 months 2018-06-06 audio/gkrellmss2: Broken for more than 6 months 2018-06-06 audio/ogg2mp3: Broken for more than 6 months 2018-06-06 audio/abcmidi: Broken for more than 6 months 2018-06-06 benchmarks/netpipe: Broken for more than 6 months 2018-06-06 biology/plink: Broken for more than 6 months
* Update to 2.0.0 and pass maintainership to committer.krion2018-06-068-345/+121
| | | | | PR: 228758 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
* Add new port: biology/infernalkrion2018-06-066-0/+117
| | | | | | | | | | | | Infernal is a tool for searching DNA sequence database for RNA structure and sequence similarities. The Rfam database of RNA families is based on Infernal, and we can search DNA sequences for structural homologs of Rfam families. WWW: http://eddylab.org/infernal/ PR: 228776 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
* Mark as broken on powerpc64. The entire, unhelpful, error message is:linimon2018-06-031-0/+2
| | | | | | | # gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.5.0+-src/c++/ReleaseMT/build' # gmake[1]: *** [Makefile:24: all] Error 2 Approved by: portmgr (tier-2 blanket)
* Adjust USES to fix building on gcc-based archs (in particular, powerpc64).linimon2018-06-031-1/+1
| | | | | | | | | | | | On the clang architectures, these changes have no effect: the baser compiler already includes the needed features. While here, remove now-redundant CXXFLAGS statements and pet portlint (no other content change). Tested on both powerpc64 and amd64. Approved by: portmgr (tier-2 blanket)
* Update WWWsunpoet2018-05-2813-13/+13
| | | | | | | search.cpan.org is shutting down. It will redirect to metacpan.org after June 25, 2018. With hat: perl
* biology/hyphy: Update to version 2.3.13jrm2018-05-233-5/+10
|
* biology/clustal-omega: Multiple alignment of nucleic acid and protein, ↵jwb2018-05-225-0/+64
| | | | | | | replaces clustalw Approved by: jrm Differential Revision: https://reviews.freebsd.org/D15516
* biology/clustalx: Multiple alignment of nucleic acid and protein sequences ↵jwb2018-05-225-0/+59
| | | | | | | with GUI Approved by: jrm Differential Revision: https://reviews.freebsd.org/D15505
* biology/clustalw: Fix license, take maintainershipjwb2018-05-212-5/+6
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15503
* biolog/molden: unbreak after at least two intransparent distfile updatesjmd2018-05-212-6/+4
| | | | | | Reviewed by: zeising (mentor) Approved by: zeising (mentor) Differential Revision: https://reviews.freebsd.org/D15333
* biology/fastx-toolkit: Fix build on FreeBSD 12jwb2018-05-162-2/+19
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15451
* Add upstream patch to fix the build with Qt 5.10.rakuco2018-05-162-1/+31
| | | | | | | | _tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from 'QLatin1String' to 'const QKeySequence' gbarCheckBox->setShortcut(QLatin1String("")); ^~~~~~~~~~~~~~~~~ PR: 228213
* - Update to 3.3.20180214wen2018-05-152-5/+6
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* biology/diamond: Update to version 0.9.22jrm2018-05-152-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
* biology/hyphy: Bump PORTREVISION after upstream rerolled releasejrm2018-05-153-14/+4
| | | | | | Also, remove patch that upstream incorporated in new tarball. Upstream issue: https://github.com/veg/hyphy/issues/796
* biology/py-biopython: Unbreak on python3; Add licenseyuri2018-05-141-2/+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)
* biology/iqtree: Update to version 1.6.5jrm2018-05-122-4/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5
* New port, biology/hyphy: Hypothesis testing using Phylogeniesjrm2018-05-117-0/+645
| | | | WWW: http://www.hyphy.org/
* Mark BROKEN: checksum and size mismatchantoine2018-05-071-0/+2
| | | | | Reported by: pkg-fallout MFH: 2018Q2
* Deprecate ports broken for more than 6 monthsantoine2018-05-055-0/+10
|
* biology/iqtree: Update to version 1.6.4jrm2018-05-012-4/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4
* biology/paml: Set PORTVERSION directlyjrm2018-04-261-1/+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
* biology/canu: Upgrade to 1.7 releasejwb2018-04-265-37/+51
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15201
* biology/paml: Update to version 4.9hjrm2018-04-263-27/+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).
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereamdmi32018-04-262-2/+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
* biology/unanimity: Pacific Biosciences consensus library and applicationsjwb2018-04-2411-0/+146
| | | | | Reviewed by: jrm Differential Revision: https://reviews.freebsd.org/D15172
* biology/seaview: Update version 4.6.3=>4.6.5bofh2018-04-242-6/+8
| | | | - Pet portlint
* biology/pbcopper: Core C++ library for Pacific Biosciences toolsjwb2018-04-246-0/+133
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15171
* biology/pbbam: PacBio BAM C++ library, with SWIG bindingsjwb2018-04-245-0/+182
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15154
* biology/pbseqan: Pacific Biosciences patched and stripped down SeqAnjwb2018-04-225-0/+698
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15152
* biology/diamond: Update to version 0.9.21jrm2018-04-212-5/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases
* biology/ddocent: Bash pipeline for RAD sequencingjwb2018-04-208-0/+617
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15139
* biology/freebayes: Bayesian haplotype-based polymorphism discovery and ↵jwb2018-04-2014-0/+293
| | | | | | | genotyping Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15116
* biology/bedtools: Upgrade to 2.27.1jwb2018-04-206-54/+36
| | | | | | | PR: 227272 Submitted by: jwb Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15137
* devel/boost-*: update to 1.67.0jbeich2018-04-182-1/+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
* biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF filesjwb2018-04-178-0/+511
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15109
* biology/fastahack: Utility for indexing and sequence extraction from FASTA filesjwb2018-04-166-0/+99
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15080
* biology/smithwaterman: Smith-waterman-gotoh alignment algorithmjwb2018-04-166-0/+149
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15072
* biology/tabixpp: C++ wrapper to tabix indexerjwb2018-04-155-0/+131
| | | | | | Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14977
* - Update to 1.71wen2018-04-092-5/+4
| | | | Approved by: mauricio@arareko.net(maintainer, via email)
* biology/pear-merger: Memory-efficient and accurate paired-end read mergerjwb2018-04-054-0/+37
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14959
* biology/seqtk: Tool for processing sequences in FASTA/FASTQ formatjwb2018-04-045-0/+51
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14954
* biology/trimadap: Trim adapter sequences from Illumina datajwb2018-04-046-0/+65
| | | | | | Reviewed by: mat Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14935
* biology/rainbow: Efficient clustering and assembling of short readsjwb2018-04-035-0/+50
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14924
* - Update to 1.61wen2018-04-012-6/+7
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* biology/stacks: Software pipeline for building loci from short-read sequencesjwb2018-03-317-0/+136
| | | | | | Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14885
* biology/libgtextutils: Unbreak for FreeBSD 12jwb2018-03-292-1/+12
| | | | | | Reported by: pkg-fallout Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14892
* biology/bamtools: API and toolkit for handling BAM filesjwb2018-03-287-0/+76
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14877
* biology/ncbi-blast+: Upgrade to 2.7.1jwb2018-03-286-377/+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
* biology/iqtree: Update to version 1.6.3jrm2018-03-232-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3
* biology/py-pysam: Update to 0.14.1yuri2018-03-212-5/+5
| | | | | | Also silenced STRIP_CMD. Reported by: portscout
* Mark broken on armvX and mips.linimon2018-03-181-0/+4
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* Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.linimon2018-03-181-0/+3
| | | | Approved by: portmgr (tier-2 blanket)
* biology/diamond: Update to version 0.9.19jrm2018-03-172-5/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
* biology/diamond: Update to version 0.9.18-49jrm2018-03-152-4/+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
* Return maho@'s ports to the pool after his commit bit expired.rene2018-03-111-1/+1
| | | | With hat: portmgr
* Remove now-useless, commented-out lines.linimon2018-03-111-4/+0
| | | | Approved by: portmgr (tier-2 blanket)
* Bump PORTREVISIONs of all users of math/mpc that we just updated togerald2018-03-1121-15/+21
| | | | version 1.1.0 (via revision 464079).
* biology/seqan-apps, biology/seqan: Update to 2.4.0yuri2018-03-107-1269/+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)
* biology/iqtree: Update to version 1.6.2jrm2018-03-032-5/+4
| | | | Upstream changes: http://www.iqtree.org/release/v1.6.2
* Reduce dependency on the python2 metaportantoine2018-02-191-1/+2
| | | | | PR: 225752 Submitted by: Yasuhiro KIMURA
* biology/py-pysam: Update to 0.14yuri2018-02-112-4/+4
| | | | | | | | Changelog: https://github.com/pysam-developers/pysam/releases/tag/v0.14 Reported by: portscout Approved by: tcberner (mentor, implicit)
* biology/py-bx-python: Update to 0.8.1yuri2018-02-102-8/+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
* Canonicalize PyPi WWWs:amdmi32018-02-091-1/+1
| | | | | | | - Switch to https:// - Remove trailing slashes Approved by: portmgr blanket
* biology/diamond: Update to version 0.9.17jrm2018-02-022-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
* - Update to 3.3.20180129wen2018-02-012-5/+4
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* Multiple ports:jwb2018-01-3116-29/+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
* devel/boost-*: update to 1.66.0jbeich2018-01-182-1/+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
* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSdanfe2018-01-121-2/+4
| | | | | | when it was missing) - Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN - Fix some whitespace and formatting bugs along the way
* Update Qt5 ports to 5.9.3.rakuco2018-01-071-0/+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
* biology/seaview: Update version 4.6.2=>4.6.3bofh2018-01-063-7/+8
| | | | | | - Added pkg-plist to pet portlint Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
* New USES=eigentcberner2018-01-031-5/+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
* - Update to 3.697wen2018-01-012-3/+4
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* - Update to 5.16.0wen2018-01-013-4/+9
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* biology/iqtree: Fix distinfo after upstream re-released v1.6.1jrm2017-12-302-3/+4
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* biology/iqtree: Update to version 1.6.1jrm2017-12-292-9/+8
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
* Disable the extra flag "-march=native" on arm to fix builds.linimon2017-12-271-3/+6
| | | | | Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run
* Update to 2.0.1sunpoet2017-12-273-5/+31
| | | | Changes: https://github.com/rvosa/bio-phylo/releases
* biology/canu: Replace += with = for dependsjwb2017-12-221-2/+2
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13574
* - Fix build on 11+amdmi32017-12-222-4/+11
| | | | Approved by: portmgr blanket
* [new port] biology/canu: Single molecule sequence assemblerjwb2017-12-226-0/+167
| | | | | Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574
* Try to bring some consistency to ports that have x86-specific pieces.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)
* Switch from swig 2.0 to swig 3.0bapt2017-12-211-2/+4
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* Mark more recently failing ports broken on aarch64.linimon2017-12-191-2/+3
| | | | | | While here, pet portlint and reformat some other BROKEN statements. Approved by: portmgr (tier-2 blanket)
* Back out previous commits by jbeich demand.linimon2017-12-182-10/+2
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* Bah. Remove spare line from cut-and-paste.linimon2017-12-181-1/+0
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* Attempt to fix build on non-x86 archs. Untested, but does no harmlinimon2017-12-182-2/+11
| | | | | | on x86. Approved by: portmgr (tier-2 blanket)
* biology/diamond: Update to version 0.9.14jrm2017-12-142-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
* biology/seqtools: re-try on powerpc* after r449590jbeich2017-12-121-2/+0
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* - Those ports fail to build with python3antoine2017-12-121-1/+1
| | | | - Add some explicit FLAVOR to dependencies where needed
* Mark several ports newly broken on arm.linimon2017-12-112-3/+9
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* biology/py-biom-format: Add required dependency on math/py-pandas and dojrm2017-12-101-3/+7
| | | | not install tests.
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for ↵jwb2017-12-095-0/+47
| | | | | | | adapter and quality trimming Approved by: jrm (mentor) Differential Revision: D13400
* These are also broken on aarch64 in the same way as armv6/7.linimon2017-12-091-0/+1
| | | | Approved by: portmgr (tier-2 blanket)
* Mark more ports broken that fail on both armv6 and armv7.linimon2017-12-091-0/+3
| | | | Approved by: portmgr (tier-2 blanket)
* Revert previous fat-fingered commit. These are the error messages fromlinimon2017-12-081-2/+2
| | | | | | | benchmarks/libmicro. Pointy hat to: self Approved by: portmgr (tier-2 blanket)
* Update errror message on armvX.linimon2017-12-081-2/+2
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* biology/fasttree: update to version 2.1.10jwb2017-12-054-19/+45
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D8187
* biology/py-macs2: Restrict to python 2.7.jwb2017-12-051-2/+2
| | | | | | | Use ${PYNUMPY} per mat suggestion. Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13350
* Add a USES=python:env, that will not add a dependency on Python.mat2017-12-042-4/+2
| | | | | | | It has the same effect than setting PYTHON_NO_DEPENDS, but in a more compact way. Sponsored by: Absolight
* Fix configure options for gnustep-maketheraven2017-12-031-1/+1
| | | | | | | We were not setting the flag to select the GNUstep ABI, so were defaulting to using the GCC-compatible version, which was likely to trigger a lot of subtle bugs. This was noticed when C++ exceptions thrown through Objective-C stack frames caused segfaults.
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation ↵jwb2017-12-034-0/+41
| | | | | | | (ChIP) sequences Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13322
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ↵jwb2017-12-035-0/+91
| | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13328
* Fix packaging with python3antoine2017-12-012-14/+14
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* [unbreak] biology/bwa: Remove old patch filesjwb2017-12-013-37/+0
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13314
* [new port] biology/fastqc: Quality control tool for high throughput sequence ↵jwb2017-12-015-0/+260
| | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13304
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentjwb2017-12-011-1/+0
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13303
* Convert Python ports to FLAVORS.mat2017-11-309-17/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464
* For ports that are marked BROKEN on armv6, and also fail to build onlinimon2017-11-305-0/+5
| | | | | | | | | | armv7, mark them so. This is part two of a multipart commit to bring armv7 ports to parity with armv6. Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run
* biology/bowtie2: Upgrade to 2.3.3.1jwb2017-11-305-50/+19
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13300
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2017-11-305-0/+74
| | | | | | ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294
* biology/bwa: Upgrade to 0.7.17jwb2017-11-282-5/+10
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13283
generated by cgit (git 2.34.1) at 2025-03-09 22:07:52 +0800