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Author SHA1 Message Date
Jason W. Bacon
6a0e6d81f2 biology/ncbi-blast+: Upgrade to 2.8.1 
Remove hacks that are no longer needed
New patch for endian.h location

Approved by:    jrm (mentor, implicit)
 2019-01-01 19:55:44 +00:00
Joseph Mingrone
3b7c3a4880 biology/diamond: Update to version 0.9.24 
Port changes: Tune for package building based on the author's
recommendation.

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24
 2018-12-31 19:00:00 +00:00
Joseph Mingrone
8e9f700daa biology/iqtree: switch to outsource cmake build 2018-12-27 18:34:44 +00:00
Tobias C. Berner
8a4ab05d84 Update math/eigen3 to 3.3.7 
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
 2018-12-26 09:06:34 +00:00
Tobias C. Berner
707c6bf295 Change cmake default behaviour to outsource. 
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
 2018-12-25 20:25:39 +00:00
Joseph Mingrone
04ee035998 biology/iqtree: Update to version 1.6.9 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
 2018-12-23 13:21:11 +00:00
Wen Heping
1534498735 - Update to 1.73 
PR:		234154
Submitted by:	wenheping2000@hotmail.com(myself)
Approved by:	maintainer
 2018-12-22 04:54:51 +00:00
Rene Ladan
e5aaf05932 Remove expired ports: 
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2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead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
 2018-12-21 13:19:02 +00:00
Vinícius Zavam
488a827e97 biology/gff2ps: update 0.98d to 0.98l 
adopt port.

Approved by:	araujo (mentor)
Differential Revision:	https://reviews.freebsd.org/D18591
 2018-12-19 17:34:29 +00:00
Joseph Mingrone
c9ff93b67d biology/diamond: Update to 0.9.23 plus fixes after release 
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
 2018-12-17 19:12:38 +00:00
Tobias C. Berner
ea792330aa Update Qt5 to 5.12.0 
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
 2018-12-16 14:49:16 +00:00
Yuri Victorovich
a8badfa6b1 New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE 2018-12-15 08:58:05 +00:00
Gerald Pfeifer
a9f015d155 Bump PORTREVISION for ports depending on the canonical version of GCC 
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
 2018-12-12 01:35:33 +00:00
Jan Beich
7c879267dc devel/boost-*: update to 1.69.0 
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
 2018-12-12 00:15:49 +00:00
Joseph Mingrone
a65cd96f01 Remove biology/njplot 
The author of both NJplot and SeaView says that NJplot can be considered
deprecated and replaced by SeaView.
 2018-12-11 15:04:12 +00:00
Yuri Victorovich
df1cfe66a6 biology/mummer: Add USES=compiler:c++11-lang 2018-12-11 07:48:12 +00:00
Yuri Victorovich
da87b8a1d5 biology/mummer: Update 3.23 -> 4.0.0beta2-2 
Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build
 2018-12-11 07:43:45 +00:00
Yuri Victorovich
5054438501 biology/mummer: Take maintainership 2018-12-11 07:23:54 +00:00
Yuri Victorovich
ad4ef5b010 New port: math/checkm: Quality assessment tool for the microbial genomes 2018-12-07 00:26:04 +00:00
Yuri Victorovich
d7dad4c249 New port: math/groopm: Metagenomic binning suite 2018-12-07 00:10:05 +00:00
Yuri Victorovich
1d5163c9b6 devel/gradle: Update to 5.0 
Change biology/igv and biology/gatk to gradle4 due to build failures with gradle5.

PR:		233623
Approved by:	gasol.wu@gmail.com (maintainer)
 2018-12-04 17:53:46 +00:00
Yuri Victorovich
679c56a0d9 biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4 and 5 2018-12-03 23:04:23 +00:00
Yuri Victorovich
933c3e178c biology/gatk: Correct the target 2018-12-03 08:52:03 +00:00
Yuri Victorovich
0298e2c8ef New port: biology/gatk: Variant discovery in high-throughput sequencing data 2018-12-03 08:40:53 +00:00
Rene Ladan
99d6d12a38 Mark QT4 ports/functionality for removal on 2019-03-15 
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
 2018-12-02 15:41:47 +00:00
Yuri Victorovich
8700889032 biology/igv: Update 2.4.15 -> 2.4.16 
Reported by:	portscout
 2018-11-18 20:02:40 +00:00
Johannes M Dieterich
7feb3fa279 biology/molden: update to 5.8.2 
Also add do-install-{option}-on targets and shadow ${MKDIR} commands.

PR:		233060
Submitted by:	yuri
 2018-11-13 07:03:15 +00:00
Steve Wills
9bd4256613 biology/seqan-apps: fix build with GCC-based architectures 
PR:		232045
Submitted by:	Piotr Kubaj <pkubaj@anongoth.pl>
Approved by:	maintainer timeout (h2+fbsdports@fsfe.org >1 month)
 2018-11-09 21:37:01 +00:00
Yuri Victorovich
0ddfd47db4 biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gcc 
Add $(LDFLAGS) to makefile.
While here, add USES=gl.

Approved by:	portmgr
 2018-11-07 00:03:34 +00:00
Mark Linimon
cd80a41fb1 Fix build failure with base GCC because of double typedefs. 
PR:		232457
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
 2018-11-05 19:47:42 +00:00
Mark Linimon
84d32eb935 Remove the incorrect typedefs to fix build on tier-2. 
PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
 2018-11-05 19:45:23 +00:00
Mark Linimon
a49b9e822c Remove the inccorrect typedefs to fix build on tier-2. 
PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
 2018-11-05 19:42:37 +00:00
Yuri Victorovich
1caf88f57e biology/igv: Update 2.4.10 -> 2.4.15 
Port changes:
* Change to gradle, corresponding updates in build, install, environment, etc.

Reported by:	portscout
 2018-11-04 22:55:24 +00:00
Jason W. Bacon
9726120ffe biology/canu: Upgrade to 1.8, add experimental SLURM integration 
Solves build issue with gcc8.

PR:             232930
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
 2018-11-04 14:29:02 +00:00
Jason W. Bacon
aa9337b9b9 biology/bowtie: Patch for gcc8 and clean up 
PR:             232929
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
 2018-11-03 23:24:29 +00:00
Jason W. Bacon
8503d5208f biology/bowtie: Revert previous commit with missing log message 2018-11-03 23:16:49 +00:00
Jason W. Bacon
1ca57db43e biology/bowtie: Patch 2018-11-03 21:10:06 +00:00
Yuri Victorovich
32a9a75433 biology/py-loompy: Update 2.0.15 -> 2.0.16 
Reported by:	portscout
 2018-10-30 05:57:43 +00:00
Joseph Mingrone
97a4339219 biology/iqtree: Update to version 1.6.8 
Upstream release notes:
https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
 2018-10-28 22:00:18 +00:00
Mark Linimon
ff4e0e08dd Fix build with tier-2 arches. 
PR:		231448
Submitted by:	Piotr Kubaj
Approved by:	maintainer
 2018-10-28 08:58:00 +00:00
Yuri Victorovich
404d2aa54d biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2 
Reported by:	portscout
 2018-10-28 04:34:14 +00:00
Jason W. Bacon
d201617835 biology/p5-transdecoder: Upgrade to 5.4.0 
Minor clean up to silence portlint
Approved by:    jrm (mentor, implicit)
 2018-10-23 12:51:20 +00:00
Joseph Mingrone
6c672c455f biology/hyphy: Update to version 2.3.14.16 
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
 2018-10-20 12:21:15 +00:00
Yuri Victorovich
8dccd74585 biology/py-loompy: Update 2.0.14 -> 2.0.15 
Reported by:	portscout
 2018-10-19 05:01:45 +00:00
Yuri Victorovich
4daaa701d3 New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00
Yuri Victorovich
ac2652a877 New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subsequences 2018-10-19 02:05:37 +00:00
Yuri Victorovich
ee084d897a New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) files 2018-10-19 02:03:40 +00:00
Yuri Victorovich
9f41dfce85 biology/ngs-sdk: Update 2.9.2 -> 2.9.3 2018-10-18 21:38:21 +00:00
Yuri Victorovich
689ccfa7ff biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2 
Reported by:	portscout
 2018-10-17 07:31:34 +00:00
Joseph Mingrone
53a7170018 biology/iqtree: Update to version 1.6.7.1 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
 2018-10-16 13:49:54 +00:00