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2723 commits

Author SHA1 Message Date
Antoine Brodin
5ae8688c07 Deprecate some ports using deprecated version of python 
With hat:	portmgr
 2020-03-08 17:01:46 +00:00
Yuri Victorovich
fc1bc32320 biology/ngs-sdk: Update 2.10.2 -> 2.10.4 
Reported by:	portscout
 2020-03-07 19:58:39 +00:00
Jason W. Bacon
4906705775 biology/jellyfish: Patch for clang 10 
Add cast to silence implicit conversion error

PR:             ports/244645
Submitted by:   dim
 2020-03-07 19:25:54 +00:00
Rene Ladan
7fc8f970bb Return theraven's ports to the pool after safekeeping his commit bit. 2020-03-05 20:49:05 +00:00
Yuri Victorovich
21b5af6ba3 biology/gatk: Update 4.1.4.1 -> 4.1.5.0 
Reported by:	repology
 2020-03-04 08:47:55 +00:00
Joseph Mingrone
aef8ee9db0 biology/hyphy: Update to version 2.5.5 
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5
 2020-03-02 01:31:56 +00:00
Jason W. Bacon
c37fa58a73 biology/bowtie2: Upgrade to 2.4.1 
Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
 2020-03-01 16:01:12 +00:00
Joseph Mingrone
5d6414200c biology/mrbayes: Update to version 3.2.7 
PR:		243237
Submitted by:	mzaki@e-mail.ne.jp (maintainer, with modifications)
 2020-02-29 23:24:39 +00:00
Antoine Brodin
41a5348a3b Deprecate a few ports 
With hat:	portmgr
 2020-02-23 15:25:53 +00:00
Piotr Kubaj
b16dee0b1d biology/stringtie: fix build on GCC architectures 
Use C++11 compiler:
cc1plus: error: unrecognized command line option "-std=c++0x"
 2020-02-23 10:52:44 +00:00
Joseph Mingrone
6bb8f81a44 biology/hyphy: Update to version 2.5.4 
Upstream changes: https://github.com/veg/hyphy/releases
 2020-02-21 12:22:17 +00:00
Jason W. Bacon
9a9f11b704 biology/vsearch: Upgrade to 2.14.2 
Numerous small bug fixes and enhancements

Reported by:    portscout
 2020-02-19 22:34:36 +00:00
Yuri Victorovich
0d3f38dc37 biology/stringtie: Update 1.3.4d -> 2.1.1 
PR:		243718
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp> (maintainer)
 2020-02-16 20:54:52 +00:00
Jason W. Bacon
0a20a7661d biology/kallisto: Upgrade to 0.46.2 
Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout
 2020-02-15 23:09:19 +00:00
Yuri Victorovich
faad29a703 biology/py-bx-python: Update 0.8.6 -> 0.8.8 
Reported by:	portscout
 2020-02-15 20:08:30 +00:00
Jason W. Bacon
05713ec073 biology/py-macs2: Bump revision for previous run dep addition 2020-02-09 14:23:43 +00:00
Jason W. Bacon
a64364d4e4 biology/py-macs2: Add missing numpy run depend 2020-02-09 14:21:28 +00:00
Yuri Victorovich
8b908b1f84 biology/gatk: Change from gradle5 to gradle6 2020-02-09 05:57:04 +00:00
Sunpoet Po-Chuan Hsieh
32be5bcc79 Clean up Makefile 2020-02-08 19:01:40 +00:00
Muhammad Moinur Rahman
b0aa2a1214 biology/seaview: Update version 4.7=>5.0 
Relnotes:http://doua.prabi.fr/software/seaview
 2020-02-05 18:35:42 +00:00
Joseph Mingrone
586a7eaabb biology/diamond: Update to version 0.9.30 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
 2020-02-03 15:55:05 +00:00
Steve Wills
fb44dca45d Fix math/openblas and bump dependent ports 
* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix
 2020-01-30 14:17:44 +00:00
Fernando Apesteguía
b1a429edf6 biology/hmmer: update to 3.3 
PR:	243244
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
 2020-01-29 05:55:12 +00:00
Fernando Apesteguía
03b31d4416 biology/infernal: update to 1.1.3 
PR:     243247
Submitted by:   mzaki@e-mail.ne.jp (maintainer)
 2020-01-27 17:57:14 +00:00
Rene Ladan
aa27691193 Remove expired ports: 
2020-01-27 accessibility/py-papi: Unmaintained, uses EOLed python27
2020-01-27 archivers/py-czipfile: Unmaintained, uses EOLed python27
2020-01-27 audio/boodler: Unmaintained, uses EOLed python27
2020-01-27 audio/dir2ogg: Unmaintained, uses EOLed python27
2020-01-27 audio/jokosher: Unmaintained, uses EOLed python27
2020-01-27 audio/mpdbrowser: Unmaintained, uses EOLed python27
2020-01-27 audio/nekobee: Unmaintained, uses EOLed python27
2020-01-27 audio/patchage: Unmaintained, uses EOLed python27
2020-01-27 audio/py-ao: Unmaintained, uses EOLed python27
2020-01-27 audio/py-id3: Unmaintained, uses EOLed python27
2020-01-27 audio/py-shout: Unmaintained, uses EOLed python27
2020-01-27 audio/py-speex: Unmaintained, uses EOLed python27
2020-01-27 audio/pytone: Unmaintained, uses EOLed python27
2020-01-27 audio/solfege: Unmaintained, uses EOLed python27
2020-01-27 audio/trommler: Unmaintained, uses EOLed python27
2020-01-27 benchmarks/pybench: Unmaintained, uses EOLed python27
2020-01-27 biology/pycogent: Unmaintained, uses EOLed python27
2020-01-27 biology/unanimity: Unmaintained, uses EOLed python27
2020-01-27 cad/pythoncad: Unmaintained, uses EOLed python27
2020-01-27 chinese/bg5pdf: Unmaintained, uses EOLed python27
2020-01-27 comms/py-libimobiledevice: Unmaintained, uses EOLed python27
2020-01-27 converters/py-bcode: Unmaintained, uses EOLed python27
2020-01-27 converters/py-iconv: Unmaintained, uses EOLed python27
2020-01-27 converters/py-zfec: Unmaintained, uses EOLed python27
2020-01-27 databases/gadfly: Unmaintained, uses EOLed python27
2020-01-27 databases/metakit: Unmaintained, uses EOLed python27
2020-01-27 databases/openark-kit: Unmaintained, uses EOLed python27
2020-01-27 databases/py-MySQLdb55: Unmaintained, uses EOLed python27
2020-01-27 databases/py-MySQLdb56: Unmaintained, uses EOLed python27
2020-01-27 databases/py-forgetsql: Unmaintained, uses EOLed python27
2020-01-27 databases/py-oops: Unmaintained, uses EOLed python27
2020-01-27 databases/py-rrdtool_lgpl: Unmaintained, uses EOLed python27
2020-01-27 deskutils/conkyemail: No longer maintained by upstream
2020-01-27 deskutils/cycle: Unmaintained, uses EOLed python27
2020-01-27 deskutils/everygui: Unmaintained, uses EOLed python27
2020-01-27 deskutils/ganyremote: Unmaintained, uses EOLed python27
2020-01-27 deskutils/pypanel: Unmaintained, uses EOLed python27
2020-01-27 deskutils/taskcoach: Unmaintained, uses EOLed python27
2020-01-27 deskutils/tel: Unmaintained, uses EOLed python27
2020-01-27 deskutils/tnote: Unmaintained, uses EOLed python27
2020-01-27 deskutils/vnc2flv: Unmaintained, uses EOLed python27
2020-01-27 deskutils/wammu: Unmaintained, uses EOLed python27
2020-01-27 devel/bbfreeze: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-builder: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-colo: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-externals: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-git: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-gtk: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-loom: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-pipeline: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-rewrite: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-scmproj: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-stats: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-svn: Unmaintained, uses EOLed python27
2020-01-27 devel/bzr-upload: Unmaintained, uses EOLed python27
2020-01-27 devel/ditrack: Unmaintained, uses EOLed python27
2020-01-27 devel/drpython: Unmaintained, uses EOLed python27
2020-01-27 devel/epydoc: Unmaintained, uses EOLed python27
2020-01-27 devel/fb303: Unmaintained, uses EOLed python27
2020-01-27 devel/fnorb: Unmaintained, uses EOLed python27
2020-01-27 devel/gazpacho: Unmaintained, uses EOLed python27
2020-01-27 devel/libmpsse: Unmaintained, uses EOLed python27
2020-01-27 devel/open-usp-tukubai: Unmaintained, uses EOLed python27
2020-01-27 devel/phpbt: Unmaintained, uses EOLed python27
2020-01-27 devel/py-anonfunc: Unmaintained, uses EOLed python27
2020-01-27 devel/py-bison: Unmaintained, uses EOLed python27
2020-01-27 devel/py-fortran: Unmaintained, uses EOLed python27
2020-01-27 devel/py-grouch: Unmaintained, uses EOLed python27
2020-01-27 devel/py-mwlib.rl: Unmaintained, uses EOLed python27
2020-01-27 devel/py-nagioscheck: Unmaintained, uses EOLed python27
2020-01-27 devel/py-ncurses: Unmaintained, uses EOLed python27
2020-01-27 devel/py-ocempgui: Unmaintained, uses EOLed python27
2020-01-27 devel/py-palm: Unmaintained, uses EOLed python27
2020-01-27 devel/py-pyechonest: Unmaintained, uses EOLed python27
2020-01-27 devel/py-resourcepackage: Unmaintained, uses EOLed python27
2020-01-27 devel/py-rlcompleter2: Unmaintained, uses EOLed python27
2020-01-27 devel/py-spark: Unmaintained, uses EOLed python27
2020-01-27 devel/py-xoltar-toolkit: Unmaintained, uses EOLed python27
2020-01-27 devel/py-zkpython: Unmaintained, uses EOLed python27
2020-01-27 devel/pychecker: Unmaintained, uses EOLed python27
2020-01-27 devel/pymacs: Unmaintained, uses EOLed python27
2020-01-27 devel/trac-bitten: Unmaintained, uses EOLed python27
2020-01-27 devel/wxGlade: Unmaintained, uses EOLed python27
2020-01-27 emulators/catapult: Unmaintained, uses EOLed python27
2020-01-27 emulators/dynagui: Unmaintained, uses EOLed python27
2020-01-27 finance/mybudget: Unmaintained, uses EOLed python27
2020-01-27 finance/sabernetdcs-client: Unmaintained, uses EOLed python27
2020-01-27 games/4stattack: Unmaintained, uses EOLed python27
2020-01-27 games/barbie_seahorse_adventures: Unmaintained, uses EOLed python27
2020-01-27 games/battletanks: Unmaintained, uses EOLed python27
2020-01-27 games/bombz: Unmaintained, uses EOLed python27
2020-01-27 games/bouncy: Unmaintained, uses EOLed python27
2020-01-27 games/bubbros: Unmaintained, uses EOLed python27
2020-01-27 games/childsplay: Unmaintained, uses EOLed python27
2020-01-27 games/crossfire-server: Unmaintained, uses EOLed python27
2020-01-27 games/duckmaze: Unmaintained, uses EOLed python27
2020-01-27 games/farblazer: Unmaintained, uses EOLed python27
2020-01-27 games/gbottler: Unmaintained, uses EOLed python27
2020-01-27 games/glchess: Unmaintained, uses EOLed python27
2020-01-27 games/gretools: Unmaintained, uses EOLed python27
2020-01-27 games/kye: Unmaintained, uses EOLed python27
2020-01-27 games/liquidwar: Unmaintained, uses EOLed python27
2020-01-27 games/mopesnake: Unmaintained, uses EOLed python27
2020-01-27 games/nelly: Unmaintained, uses EOLed python27
2020-01-27 games/oneisenough: Unmaintained, uses EOLed python27
2020-01-27 games/ptkei: Unmaintained, uses EOLed python27
2020-01-27 games/py-poker-eval: Unmaintained, uses EOLed python27
2020-01-27 games/pycadia: Unmaintained, uses EOLed python27
2020-01-27 games/pydance: Unmaintained, uses EOLed python27
2020-01-27 games/pysycache: Unmaintained, uses EOLed python27
2020-01-27 games/pythonchess: Unmaintained, uses EOLed python27
2020-01-27 games/pytowerdefense: Unmaintained, uses EOLed python27
2020-01-27 games/rtb: Unmaintained, uses EOLed python27
2020-01-27 games/schiff: Unmaintained, uses EOLed python27
2020-01-27 games/schwarzweiss: Unmaintained, uses EOLed python27
2020-01-27 games/secrettower: Unmaintained, uses EOLed python27
2020-01-27 games/slune: Unmaintained, uses EOLed python27
2020-01-27 games/super_mario_bros_python: Unmaintained, uses EOLed python27
2020-01-27 games/tuxfighter: Unmaintained, uses EOLed python27
2020-01-27 games/twitch: Unmaintained, uses EOLed python27
2020-01-27 games/vegastrike: Unmaintained, uses EOLed python27
2020-01-27 games/zephulor: Unmaintained, uses EOLed python27
2020-01-27 graphics/boxer: Unmaintained, uses EOLed python27
2020-01-27 graphics/electrix: Unmaintained, uses EOLed python27
2020-01-27 graphics/exact-image: Unmaintained, uses EOLed python27
2020-01-27 graphics/gnofract4d: Unmaintained, uses EOLed python27
2020-01-27 graphics/gsculpt: Unmaintained, uses EOLed python27
2020-01-27 graphics/imgtops: Unmaintained, uses EOLed python27
2020-01-27 graphics/imgv: Unmaintained, uses EOLed python27
2020-01-27 graphics/lcms-python: Unmaintained, uses EOLed python27
2020-01-27 graphics/mirage: Unmaintained, uses EOLed python27
2020-01-27 graphics/partio: Unmaintained, uses EOLed python27
2020-01-27 graphics/py-exif: Unmaintained, uses EOLed python27
2020-01-27 graphics/py-gd: Unmaintained, uses EOLed python27
2020-01-27 graphics/py-paint: Unmaintained, uses EOLed python27
2020-01-27 graphics/pygts: Unmaintained, uses EOLed python27
2020-01-27 graphics/pysvg: Unmaintained, uses EOLed python27
2020-01-27 irc/py-supybot-plugins: Unmaintained, uses EOLed python27
2020-01-27 japanese/kana-no-quiz: Unmaintained, uses EOLed python27
2020-01-27 lang/py-prolog: Unmaintained, uses EOLed python27
2020-01-27 lang/sdcc: Unmaintained, uses EOLed python27
2020-01-27 mail/archivemail: Unmaintained, uses EOLed python27
2020-01-27 mail/mailfmt: Unmaintained, uses EOLed python27
2020-01-27 mail/py-libgmail: Unmaintained, uses EOLed python27
2020-01-27 mail/py-ppolicy: Unmaintained, uses EOLed python27
2020-01-27 mail/rss2email2: Unmaintained, uses EOLed python27
2020-01-27 mail/svnmailer: Unmaintained, uses EOLed python27
2020-01-27 math/biggles: Unmaintained, uses EOLed python27
2020-01-27 math/py-gato: Unmaintained, uses EOLed python27
2020-01-27 math/py-gnuplot: Unmaintained, uses EOLed python27
2020-01-27 math/py-mathdom: Unmaintained, uses EOLed python27
2020-01-27 math/py-probstat: Unmaintained, uses EOLed python27
2020-01-27 math/py-rpy: Unmaintained, uses EOLed python27
2020-01-27 misc/gnome-osd: Unmaintained, uses EOLed python27
2020-01-27 misc/gonvert: Unmaintained, uses EOLed python27
2020-01-27 misc/metalink-editor: Unmaintained, uses EOLed python27
2020-01-27 misc/py-YABT: Unmaintained, uses EOLed python27
2020-01-27 misc/xdg-menu: Unmaintained, uses EOLed python27
2020-01-27 multimedia/devede: Unmaintained, uses EOLed python27
2020-01-27 multimedia/gdvrecv: Unmaintained, uses EOLed python27
2020-01-27 multimedia/mmpython: Unmaintained, uses EOLed python27
2020-01-27 multimedia/pymp: Unmaintained, uses EOLed python27
2020-01-27 net/gtknetcat: Unmaintained, uses EOLed python27
2020-01-27 net/ntlmaps: Unmaintained, uses EOLed python27
2020-01-27 net/polyorb: Unmaintained, uses EOLed python27
2020-01-27 net/py-zsi: Unmaintained, uses EOLed python27
2020-01-27 net/pythondirector: Unmaintained, uses EOLed python27
2020-01-27 net/sippy_b2bua: Unmaintained, uses EOLed python27
2020-01-27 net-im/py-jabber: Unmaintained, uses EOLed python27
2020-01-27 net-im/py-jabberbot: Unmaintained, uses EOLed python27
2020-01-27 net-im/py-libturpial: Unmaintained, uses EOLed python27
2020-01-27 net-im/py-xmpppy-irc: Unmaintained, uses EOLed python27
2020-01-27 net-mgmt/pdagent-integrations: Unmaintained, uses EOLed python27
2020-01-27 net-p2p/tribler: Unmaintained, uses EOLed python27
2020-01-27 news/papercut: Unmaintained, uses EOLed python27
2020-01-27 print/pkipplib: Unmaintained, uses EOLed python27
2020-01-27 print/pkpgcounter: Unmaintained, uses EOLed python27
2020-01-27 print/ttfquery: Unmaintained, uses EOLed python27
2020-01-27 science/gwyddion: Unmaintained, uses EOLed python27
2020-01-27 science/psychopy: Unmaintained, uses EOLed python27
2020-01-27 science/py-hcluster: Unmaintained, uses EOLed python27
2020-01-27 science/py-pyteomics.biolccc: Unmaintained, uses EOLed python27
2020-01-27 science/pycdf: Unmaintained, uses EOLed python27
2020-01-27 security/blindelephant: Unmaintained, uses EOLed python27
2020-01-27 security/cfv: Unmaintained, uses EOLed python27
2020-01-27 security/fsh: Unmaintained, uses EOLed python27
2020-01-27 security/gcipher: Unmaintained, uses EOLed python27
 2020-01-27 15:34:18 +00:00
Yuri Victorovich
797bbee24e biology/py-pysam: Update 0.15.3 -> 0.15.4 
Reported by:	portscout
 2020-01-23 02:53:09 +00:00
Steve Wills
033b9daecd math/openblas: Update to 0.3.7 
While here, improve formatting and fix build of dependant ports.

PR:		231371
Submitted by:	yuri (initial version), pkubaj (ppc fixes)
Approved by:	Eijiro Shibusawa <phd_kimberlite@yahoo.co.jp> (maintainer)
 2020-01-21 22:03:19 +00:00
Yuri Victorovich
078536789a biology/gatk: Update 4.1.3.0 -> 4.1.4.1 2020-01-20 02:12:37 +00:00
Dmitry Marakasov
20968a8ab8 - Update WWW 2020-01-19 09:30:22 +00:00
Yuri Victorovich
b5c3fe0cf2 biology/abyss: Broken on i386 
Reported by:	fallout
 2020-01-18 19:46:26 +00:00
Fernando Apesteguía
534e960d68 biology/muscle: unbreak in -CURRENT 
Don't compile problematic (and unnecessary) file.

PR:	243206
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
 2020-01-17 16:49:03 +00:00
Yuri Victorovich
78cc67f0aa biology/ngs-sdk: Update 2.10.1 -> 2.10.2 
Reported by:	portscout
 2020-01-17 07:05:29 +00:00
Jason W. Bacon
93f42ee115 biology/gemma: Unbreak build 
Conflict between cblas.h and gsl_cblas.h
 2020-01-14 22:35:36 +00:00
Yuri Victorovich
fe6826dccc devel/jsoncpp: Update 1.8.1 -> 1.9.2 
PR:		229677
Differential Revision:	D22905
 2020-01-13 21:38:35 +00:00
Fernando Apesteguía
5fd9586f06 biology/muscle: update to 3.8.1551 
* Bug fix for long sequences.
 * Unbreak '/dev/tty' problem during a build
 * Update maintainer's mail address

PR:	243206
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
 2020-01-13 17:42:22 +00:00
Fernando Apesteguía
350f03198a biology/tRNAscan-SE: update to 2.0.5 
This commit also changes maintainer's email.

PR:	243248
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
 2020-01-13 17:36:57 +00:00
Yuri Victorovich
b9c91f23ea biology/abyss: Update 2.1.5 -> 2.2.3 
Reported by:	portscout
 2020-01-13 04:06:14 +00:00
Yuri Victorovich
3c6a38b801 biology/ngs-sdk: Update 2.10.0 -> 2.10.1 
Reported by:	portscout
 2020-01-12 02:43:06 +00:00
Jason W. Bacon
1fc347bbfb biology/py-macs2: Upgrade to 2.2.6 
Bug fixes and performance improvements
Now require python 3.6+

Reported by:    portscout
 2020-01-11 14:20:00 +00:00
Sunpoet Po-Chuan Hsieh
470ff96c7f Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +00:00
Sunpoet Po-Chuan Hsieh
79141a5bb7 Update to 1.7.5 
Changes:	https://metacpan.org/changes/distribution/Bio-Variation
 2020-01-08 18:36:35 +00:00
Sunpoet Po-Chuan Hsieh
251e56f6da Update *_DEPENDS 
- Bump PORTREVISION for dependency change

The circular dependency among p5-Bio-Cluster, p5-Bio-DB-NCBIHelper, p5-Bio-Variation and this port has been resolved in p5-Bio-Variation 1.7.5 update.
 2020-01-08 18:36:30 +00:00
Yuri Victorovich
92ee9cc235 biology/viennarna: Update 2.4.13 -> 2.4.14 
Reported by:	repology
 2020-01-06 04:17:48 +00:00
Yuri Victorovich
3d89953811 biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0 
Reported by:	repology
 2020-01-05 10:33:08 +00:00
Antoine Brodin
dc9af20b3c Mark a few ports broken (unfetchable) 2020-01-05 10:26:04 +00:00
Yuri Victorovich
c34891001f biology/py-gffutils: Update 0.9 -> 0.10 
Reported by:	portscout
 2019-12-31 05:16:09 +00:00
Ganael LAPLANCHE
23cb661f63 Update devel/tbb to 2020.0 and bump dependent ports' revisions [1] 
Also, while here, re-generate patches using the makepatch target

[1] Changelog: https://github.com/intel/tbb/blob/v2020.0/CHANGES
 2019-12-26 16:25:22 +00:00
Jason W. Bacon
de445f717c biology/ncbi-blast+: Upgrade to 2.10.0 
Numerous minor bug fixes, enhancements and dependency upgrades
Minor port clean-up
1 patch from previous version upstreamed

Reported by:    portscout
 2019-12-26 16:21:17 +00:00
Antoine Brodin
de61a87208 Deprecate a few ports 
With hat:	portmgr
 2019-12-26 07:54:28 +00:00
Jason W. Bacon
f49c0f9022 biology/bedtools: Upgrade to 2.29.2 
Fixed a bug that mistakenly removed a BAM/CRAM header line

Reported by:    portscout
 2019-12-19 01:04:11 +00:00
Jan Beich
701aa3bcf8 devel/boost-*: update to 1.72.0 
Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
 2019-12-11 17:53:48 +00:00
Jason W. Bacon
d34aa59b6f biology/bedtools: Upgrade to 2.29.1 
Several important bug fixes.

Reported by:    portscout
 2019-12-11 15:13:20 +00:00
Sunpoet Po-Chuan Hsieh
1ef994ae37 Update to 1.007007 (1.7.7) 
Changes:	https://metacpan.org/changes/distribution/BioPerl
 2019-12-08 16:57:23 +00:00
Sunpoet Po-Chuan Hsieh
3a7c9b7900 Update *_DEPENDS 
- Bump PORTREVISION for dependency change
 2019-12-08 16:57:18 +00:00
Sunpoet Po-Chuan Hsieh
6356c6acbc Install Bio::SeqIO::entrezgene 
- Bump PORTREVISION for package change
- Take maintainership

Bio::SeqIO::entrezgene has been removed from BioPerl since 1.7.3.
 2019-12-08 16:57:13 +00:00
Sunpoet Po-Chuan Hsieh
1f75530f6c Add p5-Bio-Variation 1.7.4 
Bio::Variation::* provides BioPerl variation-related functionality.

WWW: https://metacpan.org/release/Bio-Variation
 2019-12-08 16:49:31 +00:00
Sunpoet Po-Chuan Hsieh
2b9ee80386 Add p5-Bio-DB-NCBIHelper 1.7.6 
Bio::DB::NCBIHelper provides a single place to setup some common methods for
querying NCBI web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the common
HTML stripping done in postprocess_data().

WWW: https://metacpan.org/release/Bio-DB-NCBIHelper
 2019-12-08 16:49:25 +00:00
Sunpoet Po-Chuan Hsieh
876817898e Add p5-Bio-DB-EMBL 1.7.4 
Bio::DB::EMBL allows the dynamic retrieval of sequence objects Bio::Seq from the
EMBL database using the dbfetch script at EBI.

In order to make changes transparent we have host type (currently only ebi) and
location (defaults to ebi) separated out. This allows later additions of more
servers in different geographical locations.

The functionality of this module is inherited from Bio::DB::DBFetch which
implements Bio::DB::WebDBSeqI.

WWW: https://metacpan.org/release/Bio-DB-EMBL
 2019-12-08 16:49:19 +00:00
Piotr Kubaj
b60ee034a6 biology/phyml: disable -march=native 
Ports shouldn't build for the host CPU, it also breaks compilation on non-x86.

Approved by:    mentors (implicit approval)
 2019-12-06 13:04:41 +00:00
Jason W. Bacon
c4b007e3b2 biology/unanimity: Remove erroneous BROKEN 
Unsure why this was marked unfetchable.  Fetch works fine and the port is
still useful, though it cannot be upgraded to newer releases, which are
closed-source.
 2019-11-28 05:46:04 +00:00
Jung-uk Kim
5a52a08234 Clean up after java/openjdk6 and java/openjdk6-jre removal 
java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and
java/openjdk6 and java/openjdk6-jre were removed from the ports tree
(r512663).  Now this patch completely removes remaining stuff from the
ports tree.

PR:			241953 (exp-run)
Reviewed by:		glewis
Approved by:		portmgr (antoine)
Differential Revision:	https://reviews.freebsd.org/D22342
 2019-11-26 21:46:12 +00:00
Jason W. Bacon
795a4fecb2 biology/py-multiqc: Upgrade to 1.8 
Major enhancements including 6 new modules and improvements to existing modules
Numerous minor fixes and enhancements

Reported by:    portscout
 2019-11-26 16:25:08 +00:00
Jason W. Bacon
698e8c8201 biology/p5-TrimGalore: Upgrade to 0.6.5 
Minor bugfixes and enhancements

Reported by:    portscout
 2019-11-26 16:20:12 +00:00
Jason W. Bacon
b85fc34eb7 biology/unanimity and dependencies: Flag as no longer open source 
PacBio now provides unanimity only as a binary package through bioconda.
See https://github.com/PacificBiosciences/ccs.
 2019-11-24 15:53:00 +00:00
Jason W. Bacon
b6b56692de biology/py-cutadapt: Upgrade to 2.7 
Numerous minor fixes and enhancements.
Upstreamed setup.py patches for dependency versions.

Reported by:    portscout
 2019-11-23 14:45:53 +00:00
Jason W. Bacon
f6d1d1963f biology/py-dnaio: Upgrade to 0.4.1 
Needed for py-cutadapt 2.7
 2019-11-23 14:40:00 +00:00
Yuri Victorovich
10cb022e32 biology/py-bx-python: Update 0.8.4 -> 0.8.6 
Reported by:	portscout
 2019-11-23 05:53:50 +00:00
Joseph Mingrone
110a0bfa20 biology/paml: Update to version 4.9j 
- Remove BROKEN=. Version 4.9i became unfetchable when the author pulled
  the tarball to prevent users from downloading a version with new, serious
  bugs.

Upstream changes described by the author:

  - mcmctree: Initial values have ages that are too old, exceeding max
    bounds.  In theory bounds in mcmctree are always soft so that the node
    ages will move to the area of posterior mode when burnin is long enough.
    In practice the poor starting values are problematic and requires long
    burn-in.  I have rewritten the code for generating initial values to
    respect the min and max bounds specified in the fossil calibrations.

  - codeml: A bug introduced in 4.9i caused the clade labels ($) to be
    ignored.  This affects the branch, branch-site and clade models.  If
    your tree has branch labels (#) only and no clade models, everything
    will be fine.  If you have used the clade label ($) in the tree with or
    without the branch label (#), either the program will abort or the
    results will be incorrect.  The clade label ($) is supposed to label
    all branches in the clade as well as the branch itself, but all clade
    labels in the tree are ignored in 4.9i.  Earlier versions are correct.
 2019-11-22 15:32:40 +00:00
Joseph Mingrone
8eb84e2015 biology/diamond: Update to v0.9.29 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
 2019-11-20 17:14:29 +00:00
Tobias Kortkamp
456263afc3 Create devel/gradle5 in preparation of devel/gradle update 
Many consumers fail to build with newer Gradle versions.

PR:		239875, 239900, 239901, 239902
 2019-11-20 09:51:43 +00:00
Jason W. Bacon
c8eb3c6e6c biology/haplohseq: Switch to distfile with example data 
Add script to run on example input
Minor fix to report inadequate VCF input
 2019-11-17 15:00:13 +00:00
Jason W. Bacon
e4868fdb92 biology/canu: Upgrade to 1.9 
Numerous bug fixes and enhancements

Reported by:    portscout
 2019-11-08 14:03:15 +00:00
Dmitry Marakasov
d696ac2f3b - Limit python version (does not build with 3.7+) 
Approved by:	portmgr blanket
 2019-11-08 12:12:42 +00:00
Tobias Kortkamp
6a379e2d3a a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Niclas Zeising
ef5d45aaa6 Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
Joseph Mingrone
47738adc67 biology/diamond: Update to version 0.9.28 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
 2019-11-07 14:12:07 +00:00
Antoine Brodin
cc8ad7de9b Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
Jason W. Bacon
6098bf59b8 biology/kallisto: Upgrade to 0.46.1 
Minor bug fixes and enhancements

Reported by:    portscout
 2019-11-06 00:18:14 +00:00
Niclas Zeising
f01bbf652d Add USES=xorg USES=gl, ports categories b 
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
 2019-11-04 21:08:20 +00:00
Joseph Mingrone
cf2251f192 biology/diamond: Update to version 0.9.27 (plus one fix) 
Since compiling from source no longer performs a native build, remove
-mtune=generic from CLFAGS when package building.

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.27
 2019-11-03 01:34:11 +00:00
Tobias C. Berner
4e896a50f8 math/gsl: update to 2.6 
- math/p5-Math-GSL does not seem to have any upstream activity to make it work with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
 2019-10-25 23:41:34 +00:00
Piotr Kubaj
6cf4d2cdda biology/avida: unbreak on powerpc64 
Builds fine with GCC 9.

Approved by:	mentors (implicit approval)
 2019-10-23 16:25:10 +00:00
Rene Ladan
13d4527a34 Remove expired ports: 
2019-10-16 archivers/freetar: Unfetchable, unmaintained
2019-10-16 archivers/hffzip: Unfetchable, unmaintained
2019-10-16 archivers/hpack.non-usa.only: Unfetchable, unmaintained
2019-10-16 archivers/untar: Unfetchable, unmaintained
2019-10-16 astro/gpsdrive: Unfetchable, unmaintained
2019-10-16 astro/planets: Unfetchable, unmaintained
2019-10-16 audio/ascd: Unfetchable, unmaintained
2019-10-16 audio/audiotag: Unfetchable, unmaintained
2019-10-16 audio/gmidimonitor: Unfetchable, unmaintained
2019-10-16 audio/gmpc-lyricwiki: Unfetchable, unmaintained
2019-10-16 audio/jack_mixer: Unfetchable, unmaintained
2019-10-16 audio/jmusic: Unfetchable, unmaintained
2019-10-16 audio/maplay: Unfetchable, unmaintained
2019-10-16 audio/mbox: Unfetchable, unmaintained
2019-10-16 audio/nuvolaplayer: Unfetchable, unmaintained
2019-10-16 audio/vagalume: Unfetchable, unmaintained
2019-10-16 audio/wmsmixer: Unfetchable, unmaintained
2019-10-16 audio/xmms2-scrobbler: Unfetchable, unmaintained
2019-10-16 benchmarks/filebench: Unfetchable, unmaintained
2019-10-16 biology/chemeq: Unfetchable, unmaintained
2019-10-16 biology/linux-foldingathome: Unfetchable, unmaintained
2019-10-16 cad/dxf2fig: Unfetchable, unmaintained
2019-10-16 cad/gerbv: Unfetchable, unmaintained
2019-10-16 cad/ghdl: Unfetchable, unmaintained
2019-10-16 comms/gsmlib: Unfetchable, unmaintained
2019-10-16 comms/nokryptia: Unfetchable, unmaintained
2019-10-16 databases/mrtg-mysql-load: Unfetchable, unmaintained
2019-10-16 databases/postgres-xl: Unfetchable, unmaintained
2019-10-16 databases/wmjsql: Unfetchable, unmaintained
2019-10-16 deskutils/dlume: Unfetchable, unmaintained
2019-10-16 deskutils/gkrellm-reminder2: Unfetchable, unmaintained
2019-10-16 deskutils/ljit: Unfetchable, unmaintained
2019-10-16 deskutils/mdh: Unfetchable, unmaintained
2019-10-16 devel/atlassian-plugin-sdk: Unfetchable, unmaintained
2019-10-15 devel/bingo: Abandoned upstream
2019-10-16 devel/dprog: Unfetchable, unmaintained
2019-10-16 devel/eblob: Unfetchable, unmaintained
2019-10-16 devel/elftoaout: Unfetchable, unmaintained
2019-10-16 devel/fga: Unfetchable, unmaintained
2019-10-16 devel/fib: Unfetchable, unmaintained
2019-10-16 devel/flickrnet: Unfetchable, unmaintained
2019-10-16 devel/fujaba: Unfetchable, unmaintained
2019-10-16 devel/funnelweb: Unfetchable, unmaintained
2019-10-16 devel/genproto: Unfetchable, unmaintained
2019-10-16 devel/gitphp: Unfetchable, unmaintained
2019-10-16 devel/gnatcoll: Unfetchable, unmaintained
2019-10-16 devel/kimwitu: Unfetchable, unmaintained
2019-10-16 devel/libghthash: Unfetchable, unmaintained
2019-10-16 devel/lua-alien: Unfetchable, unmaintained
2019-10-16 devel/monotone-viz: Unfetchable, unmaintained
2019-10-16 devel/noweb: Unfetchable, unmaintained
2019-10-16 devel/p65: Unfetchable, unmaintained
2019-10-16 devel/py-fileutils: Unfetchable, unmaintained
2019-10-16 devel/py-mercurialserver: Unfetchable, unmaintained
2019-10-16 devel/py-pqueue: Unfetchable, unmaintained
2019-10-16 devel/pypersrc: Unfetchable, unmaintained
2019-10-16 devel/root-doc: Unfetchable, unmaintained
2019-10-16 devel/sfio: Unfetchable, unmaintained
2019-10-16 devel/styx: Unfetchable, unmaintained
2019-10-16 devel/tclmore: Unfetchable, unmaintained
2019-10-16 devel/umem: Unfetchable, unmaintained
2019-10-16 dns/ez-ipupdate: Unfetchable, unmaintained
2019-10-16 editors/zoinks: Unfetchable, unmaintained
2019-10-16 emulators/aftp: Unfetchable, unmaintained
2019-10-16 emulators/ia64sim: Unfetchable, unmaintained
2019-10-16 emulators/loemu: Unfetchable, unmaintained
2019-10-16 emulators/pipelight: Unfetchable, unmaintained
2019-10-16 finance/ledgersmb: Unfetchable, unmaintained
2019-10-16 ftp/atftp: Unfetchable, unmaintained
2019-10-16 ftp/cftp: Unfetchable, unmaintained
2019-10-16 games/arkanoidsb: Unfetchable, unmaintained
2019-10-16 games/balazar: Unfetchable, unmaintained
2019-10-16 games/blockade: Unfetchable, unmaintained
2019-10-16 games/cleanq3: Unfetchable, unmaintained
2019-10-16 games/conquest: Unfetchable, unmaintained
2019-10-16 games/crafty-tablebase-no-pawn: Unfetchable, unmaintained
2019-10-16 games/epiar: Unfetchable, unmaintained
2019-10-16 games/exmars: Unfetchable, unmaintained
2019-10-16 games/fteqw: Unfetchable, unmaintained
2019-10-16 games/gnake: Unfetchable, unmaintained
2019-10-16 games/gru: Unfetchable, unmaintained
2019-10-16 games/gtkpool: Unfetchable, unmaintained
2019-10-16 games/imaze: Unfetchable, unmaintained
2019-10-16 games/inform: Unfetchable, unmaintained
2019-10-16 games/iourbanterror: Unfetchable, unmaintained
2019-10-16 games/iourbanterror-server: Unfetchable, unmaintained
2019-10-16 games/jools: Unfetchable, unmaintained
2019-10-16 games/legends: Unfetchable, unmaintained
2019-10-16 games/linux-enemyterritory-etpro: Unfetchable, unmaintained
2019-10-16 games/linux-worldofgoo-demo: Unfetchable, unmaintained
2019-10-16 games/noegnud-data: Unfetchable, unmaintained
2019-10-16 games/poker-engine: Unfetchable, unmaintained
2019-10-16 games/ptools: Unfetchable, unmaintained
2019-10-16 games/pyawale: Unfetchable, unmaintained
2019-10-16 games/pysycache-lang: Unfetchable, unmaintained
2019-10-16 games/qmars: Unfetchable, unmaintained
2019-10-16 games/quake-reaper: Unfetchable, unmaintained
2019-10-16 games/quake3-ra3: Unfetchable, unmaintained
2019-10-16 games/sdlCC: Unfetchable, unmaintained
2019-10-16 games/speyes: Unfetchable, unmaintained
2019-10-16 games/vodovod: Unfetchable, unmaintained
2019-10-16 games/wmeyes: Unfetchable, unmaintained
2019-10-16 games/wmshuffle: Unfetchable, unmaintained
2019-10-16 games/xabacus: Unfetchable, unmaintained
2019-10-16 games/xpacman: Unfetchable, unmaintained
2019-10-16 games/xscorch: Unfetchable, unmaintained
2019-10-16 graphics/aeskulap: Unfetchable, unmaintained
2019-10-16 graphics/agave: Unfetchable, unmaintained
2019-10-16 graphics/cbview: Unfetchable, unmaintained
2019-10-16 graphics/copperspice: Unfetchable, unmaintained
2019-10-16 graphics/cthumb: Unfetchable, unmaintained
2019-10-16 graphics/fujiplay: Unfetchable, unmaintained
2019-10-16 graphics/gimp-ez-perspective-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-focusblur-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-jagged-border-script: Unfetchable, unmaintained
2019-10-16 graphics/gimp-manual-html: Unfetchable, unmaintained
2019-10-16 graphics/gimp-save-for-web: Unfetchable, unmaintained
2019-10-16 graphics/gimp-wavelet-denoise-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-wavelet-sharpen-plugin: Unfetchable, unmaintained
2019-10-16 graphics/giram: Unfetchable, unmaintained
2019-10-16 graphics/inventor: Unfetchable, unmaintained, Depends on expiring graphics/libGLw
2019-10-16 graphics/jpg2pdf: Unfetchable, unmaintained
2019-10-16 graphics/jpgraph2: Unfetchable, unmaintained
2019-10-16 graphics/makehuman: Unfetchable, unmaintained
2019-10-16 graphics/pstoepsi: Unfetchable, unmaintained
2019-10-16 graphics/xmandel: Unfetchable, unmaintained
2019-10-16 irc/minbif: Unfetchable, unmaintained
2019-10-16 japanese/VTPSfont: Unfetchable, unmaintained
2019-10-16 japanese/asterisk-sounds: Unfetchable, unmaintained
2019-10-16 japanese/cannadic: Unfetchable, unmaintained
2019-10-16 japanese/edict-utf-8: Unfetchable, unmaintained
2019-10-16 japanese/kpcal: Unfetchable, unmaintained
2019-10-16 japanese/multiskkserv: Unfetchable, unmaintained
2019-10-16 japanese/skkfep: Unfetchable, unmaintained
2019-10-16 java/eclipse-log4e: Unfetchable, unmaintained
2019-10-16 java/eclipse-lomboz: Unfetchable, unmaintained
2019-10-16 java/java-checkstyle: Unfetchable, unmaintained
2019-10-16 korean/baekmukfonts-ttf: Unfetchable, unmaintained
2019-10-16 korean/gtkcomm: Unfetchable, unmaintained
2019-10-16 lang/arena: Unfetchable, unmaintained
2019-10-16 lang/diveintopython: Unfetchable, unmaintained
2019-10-16 lang/modula3: Unfetchable, unmaintained
2019-10-16 lang/p2c: Unfetchable, unmaintained
2019-10-16 lang/quack: Unfetchable, unmaintained
2019-10-16 lang/stldoc: Unfetchable, unmaintained
2019-10-16 mail/altermime: Unfetchable, unmaintained
2019-10-16 mail/autosig: Unfetchable, unmaintained
2019-10-16 mail/gkrellmmailwatch2: Unfetchable, unmaintained
2019-10-16 mail/mboxcheck-applet: Unfetchable, unmaintained
2019-10-16 mail/nmzmail: Unfetchable, unmaintained
2019-10-16 mail/poppy: Unfetchable, unmaintained
2019-10-16 mail/prom-wl: Unfetchable, unmaintained
2019-10-16 mail/py-apolicy: Unfetchable, unmaintained
2019-10-16 mail/spamdb-curses: Unfetchable, unmaintained
2019-10-16 mail/xlbiff: Unfetchable, unmaintained
2019-10-16 math/algotutor: Unfetchable, unmaintained
2019-10-16 math/nyh-hoc: Unfetchable, unmaintained
2019-10-16 math/superlu_mt: Unfetchable, unmaintained
2019-10-16 math/testu01: Unfetchable, unmaintained
2019-10-16 misc/astrolog: Unfetchable, unmaintained
2019-10-16 misc/chord2html: Unfetchable, unmaintained
2019-10-16 misc/crosspad: Unfetchable, unmaintained
2019-10-16 misc/detachtty: Unfetchable, unmaintained
2019-10-16 misc/dphys-config: Unfetchable, unmaintained
2019-10-16 misc/dvorakng: Unfetchable, unmaintained
2019-10-16 misc/gctpc: Unfetchable, unmaintained
2019-10-16 misc/gkrellm-helium: Unfetchable, unmaintained
2019-10-16 misc/gkrellweather2: Unfetchable, unmaintained
2019-10-16 misc/linm: Unfetchable, unmaintained
2019-10-16 misc/mc-light: Unfetchable, unmaintained
2019-10-16 misc/newer: Unfetchable, unmaintained
2019-10-16 misc/telbook: Unfetchable, unmaintained
2019-10-16 misc/valspeak: Unfetchable, unmaintained
2019-10-16 misc/xd: Unfetchable, unmaintained
2019-10-16 multimedia/audiopreview: Unfetchable, unmaintained
2019-10-16 multimedia/dvts: Unfetchable, unmaintained
2019-10-16 multimedia/gcfilms: Unfetchable, unmaintained
2019-10-16 multimedia/kissdx: Unfetchable, unmaintained
2019-10-16 multimedia/playd: Unfetchable, unmaintained
2019-10-16 multimedia/subtitleeditor: Unfetchable, unmaintained
2019-10-16 multimedia/umr: Unfetchable, unmaintained
2019-10-16 net/bluemix-cli: Unfetchable, unmaintained
2019-10-16 net/boclient: Unfetchable, unmaintained
2019-10-16 net/csync2: Unfetchable, unmaintained
2019-10-16 net/dictd-database: Unfetchable, unmaintained
2019-10-16 net/gtic: Unfetchable, unmaintained
2019-10-16 net/hidentd: Unfetchable, unmaintained
2019-10-16 net/ldap2dns: Unfetchable, unmaintained
2019-10-16 net/libmxp: Unfetchable, unmaintained
2019-10-16 net/librouteros: Unfetchable, unmaintained
2019-10-16 net/nettest: Unfetchable, unmaintained
2019-10-16 net/py-netstring: Unfetchable, unmaintained
2019-10-16 net/radiusd-cistron: Unfetchable, unmaintained
2019-10-16 net/rtptools: Unfetchable, unmaintained
2019-10-16 net/smbldap-tools: Unfetchable, unmaintained
2019-10-16 net/tcptrace: Unfetchable, unmaintained
2019-10-16 net/wackford-squeers: Unfetchable, unmaintained
2019-10-16 net/wmnet2: Unfetchable, unmaintained
2019-10-16 net-im/pidgin-birthday-reminder: Unfetchable, unmaintained
2019-10-16 net-im/pidgin-pidgimpd: Unfetchable, unmaintained
2019-10-16 net-im/poezio: Unfetchable, unmaintained
2019-10-16 net-mgmt/bsnmp-jails: Unfetchable, unmaintained
2019-10-16 net-mgmt/iog: Unfetchable, unmaintained
2019-10-16 net-mgmt/lanmap: Unfetchable, unmaintained
2019-10-16 net-mgmt/nagios-spamd-plugin: Unfetchable, unmaintained
2019-10-16 net-mgmt/nefu: Unfetchable, unmaintained
2019-10-16 net-mgmt/pixilate: Unfetchable, unmaintained
2019-10-16 net-mgmt/slate: Unfetchable, unmaintained
2019-10-16 net-mgmt/weplab: Unfetchable, unmaintained
2019-10-16 net-p2p/bnbt: Unfetchable, unmaintained
2019-10-16 net-p2p/btpd: Unfetchable, unmaintained
2019-10-16 net-p2p/gkremldk: Unfetchable, unmaintained
2019-10-16 news/newscache: Unfetchable, unmaintained
2019-10-16 news/nntpbtr: Unfetchable, unmaintained
2019-10-16 news/slrnconf: Unfetchable, unmaintained
2019-10-16 news/xpn: Unfetchable, unmaintained
2019-10-16 polish/ekg: Unfetchable, unmaintained
2019-10-16 polish/ekg2: Unfetchable, unmaintained
2019-10-16 ports-mgmt/fastest_sites: Unfetchable, unmaintained
2019-10-16 ports-mgmt/pkg-plist: Unfetchable, unmaintained
2019-10-16 ports-mgmt/symports: Unfetchable, unmaintained
2019-10-16 print/poster: Unfetchable, unmaintained
2019-10-16 russian/d1489: Unfetchable, unmaintained
2019-10-16 science/metaf2xml: Unfetchable, unmaintained
2019-10-16 security/authforce: Unfetchable, unmaintained
2019-10-16 security/avcheck: Unfetchable, unmaintained
2019-10-16 security/digest: Unfetchable, unmaintained
2019-10-16 security/fpm2: Unfetchable, unmaintained
2019-10-16 security/fwipe: Unfetchable, unmaintained
2019-10-16 security/gnome-password-generator: Unfetchable, unmaintained
2019-10-16 security/httprint: Unfetchable, unmaintained
2019-10-16 security/ike-scan: Unfetchable, unmaintained
2019-10-16 security/ipfwcount: Unfetchable, unmaintained
2019-10-16 security/libsparkcrypto: Unfetchable, unmaintained
2019-10-16 security/md4coll: Unfetchable, unmaintained
2019-10-16 security/md5coll: Unfetchable, unmaintained
2019-10-16 security/osiris: Unfetchable, unmaintained
2019-10-16 security/ranpwd: Unfetchable, unmaintained
2019-10-16 security/rdigest: Unfetchable, unmaintained
2019-10-16 security/smap: Unfetchable, unmaintained
2019-10-16 security/sshblock: Unfetchable, unmaintained
2019-10-16 shells/bashc: Unfetchable, unmaintained
2019-10-16 shells/flash: Unfetchable, unmaintained
2019-10-16 sysutils/cotty: Unfetchable, unmaintained
2019-10-16 sysutils/dt: Unfetchable, unmaintained
2019-10-16 sysutils/gkrellfire: Unfetchable, unmaintained
2019-10-16 sysutils/log_analysis: Unfetchable, unmaintained
2019-10-16 sysutils/mksunbootcd: Unfetchable, unmaintained
2019-10-16 sysutils/rfstool: Unfetchable, unmaintained
2019-10-16 sysutils/skill: Unfetchable, unmaintained
2019-10-16 sysutils/sloth: Unfetchable, unmaintained
2019-10-16 sysutils/snowlog: Unfetchable, unmaintained
2019-10-16 sysutils/wmfire: Unfetchable, unmaintained
2019-10-16 sysutils/xbattbar: Unfetchable, unmaintained
2019-10-16 textproc/bedic-data: Unfetchable, unmaintained
2019-10-16 textproc/clit: Unfetchable, unmaintained
2019-10-16 textproc/docbook-tdg: Unfetchable, unmaintained
2019-10-16 textproc/emacs-wiki: Depends on expiring ports
2019-10-16 textproc/htmlize.el: Unfetchable, unmaintained
2019-10-16 textproc/libflate: Unfetchable, unmaintained
2019-10-16 textproc/mguesser: Unfetchable, unmaintained
2019-10-16 textproc/opensched: Unfetchable, unmaintained
2019-10-16 textproc/opentoken: Unfetchable, unmaintained
2019-10-16 textproc/rot: Unfetchable, unmaintained
2019-10-16 textproc/rtfx: Unfetchable, unmaintained
2019-10-16 textproc/supercat: Unfetchable, unmaintained
2019-10-16 textproc/xml_ez_out: Unfetchable, unmaintained
2019-10-16 textproc/xmldiff: Unfetchable, unmaintained
2019-10-16 textproc/xqilla: Unfetchable, unmaintained
2019-10-16 www/WebMagick: Unfetchable, unmaintained
2019-10-16 www/bins: Unfetchable, unmaintained
2019-10-16 www/blogsum: Unfetchable, unmaintained
2019-10-16 www/boa: Unfetchable, unmaintained
2019-10-16 www/cgihtml: Unfetchable, unmaintained
2019-10-16 www/cgiparse: Unfetchable, unmaintained
2019-10-16 www/flot: Unfetchable, unmaintained
2019-10-16 www/ftasv: Unfetchable, unmaintained
2019-10-16 www/hastymail2-devel: Unfetchable, unmaintained
2019-10-16 www/htmlpp: Unfetchable, unmaintained
2019-10-16 www/http-analyze: Unfetchable, unmaintained
2019-10-16 www/junkbuster: Unfetchable, unmaintained
2019-10-16 www/links-hacked: Unfetchable, unmaintained
2019-10-16 www/llgal: Unfetchable, unmaintained
2019-10-16 www/mgstat: Unfetchable, unmaintained
2019-10-16 www/php-screw: Unfetchable, unmaintained
2019-10-16 www/phproxy: Unfetchable, unmaintained
2019-10-16 www/py-prewikka: Unfetchable, unmaintained
2019-10-16 www/redmine-backlogs: Unfetchable, unmaintained
2019-10-16 www/swfdec-plugin: Unfetchable, unmaintained
2019-10-16 www/swish-e: Unfetchable, unmaintained
2019-10-16 x11/blast: Unfetchable, unmaintained
2019-10-16 x11/dynamag: Unfetchable, unmaintained
2019-10-16 x11/xcurs: Unfetchable, unmaintained
2019-10-16 x11/xscreensaver-gnome: Unfetchable, unmaintained
2019-10-16 x11/xscreensaver-gnome-hacks: Unfetchable, unmaintained
2019-10-16 x11-clocks/cairo-clock: Unfetchable, unmaintained
2019-10-16 x11-clocks/pclock: Unfetchable, unmaintained
2019-10-16 x11-clocks/stopwatch: Unfetchable, unmaintained
2019-10-16 x11-clocks/wmfuzzy: Unfetchable, unmaintained
2019-10-16 x11-fm/emelfm2: Unfetchable, unmaintained
2019-10-16 x11-fm/ezfm: Unfetchable, unmaintained
2019-10-16 x11-fm/ultracopier: Unfetchable, unmaintained
2019-10-16 x11-fm/xplore: Unfetchable, unmaintained
2019-10-16 x11-fonts/indic-ttf: Unfetchable, unmaintained
2019-10-16 x11-fonts/pingwi: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-ecliz: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-grounation-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-neutral-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-polar-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-envy-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-equinox-engine: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-qnxtheme: Unfetchable, unmaintained
2019-10-16 x11-themes/plank-theme-moka: Unfetchable, unmaintained
2019-10-15 x11-toolkits/swt-devel: Obsolete. Superseded by x11-toolkits/swt
2019-10-16 x11-wm/genmenu: Unfetchable, unmaintained
2019-10-16 x11-wm/musca: Unfetchable, unmaintained
2019-10-16 x11-wm/weewm: Unfetchable, unmaintained
2019-10-16 x11-wm/windowlab: Unfetchable, unmaintained
2019-10-16 x11-wm/wmfs: Unfetchable, unmaintained
 2019-10-16 15:29:32 +00:00
Yuri Victorovich
2182a49d0e biology/prodigal: Eliminate a very old version from the portscout discovery process 2019-10-12 15:40:21 +00:00
Yuri Victorovich
179ca4e700 biology/prodigal: Update 2.6.3-2 -> 2.6.3-7 2019-10-12 15:36:47 +00:00
Jason W. Bacon
c904df3468 biology/star: Upgrade to 2.7.2d 
Fix chimeric output bug.

Numerous other minor fixes and enhancements since 2.7.0.

Reported by:    portscout
 2019-10-06 22:18:31 +00:00
Jason W. Bacon
899d6cc0cd biology/fastahack: Upgrade to 1.0.0 
Very few changes, upstream just finally got around to cutting a release.

Reported by:    portscout
 2019-10-06 21:34:32 +00:00
Yuri Victorovich
d844b03004 biology/mothur: Update 1.42.3 -> 1.43.0 
Reported by:	portscout
 2019-10-05 17:04:42 +00:00
Niclas Zeising
dcb57b7643 biologi/ncbi-toolkit: Remove dependency on libXp 
Remove the dependency on libXp from ncbi-toolkit, since libXp is deprecated
and it isn't needed.
Remove deprecation from ncbi-toolkit.
 2019-09-28 10:52:57 +00:00
Niclas Zeising
45ce25247b Deprecate x11/libXp, it is deprecated upstream 
Deprecate x11/libXp, since it is about to be deprecated upstream.  Do *not*
yet set a removal date for x11/libXp, this will be decided later, once most
dependencies are fixed.
Deprecate all ports depending on x11/libXp.
* astro/xephem
* audio/xmcd
* audio/xmmix
* biology/ncbi-toolkit
* deskutils/xmdiary
* ftp/llnlxdir
* ftp/llnlxftp
* graphics/SciPlot
* misc/xtar
* multimedia/mpeg2play
* science/afni
* textproc/mgdiff

Sprinkle USES=xorg as needed.

Discussed with:	bapt
 2019-09-27 16:18:58 +00:00
Jason W. Bacon
a0498a53b5 biology/tophat: Fast splice junction mapper for RNA-Seq reads 
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

Note:

TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.
 2019-09-27 00:49:48 +00:00
Ganael LAPLANCHE
03166a4b36 Update devel/tbb to 2019.8 and bump dependent ports' revisions 
Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
 2019-09-25 10:03:49 +00:00
Jason W. Bacon
490aa151f9 biology/py-multiqc: Aggregate bioinformatics analysis reports 
MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.
 2019-09-23 16:09:30 +00:00
Jan Beich
b03c67869c devel/openmp: update to 9.0.0 
- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/
 2019-09-21 18:59:57 +00:00
Jason W. Bacon
2eee6a30e8 biology/p5-TrimGalore: Upgrade to 0.6.4 
Improved adapter autodetection, minor bug fixes.
 2019-09-21 02:51:26 +00:00
Jason W. Bacon
8a83d3eb39 biology/fastqc: Upgrade to 0.11.8 
Minor bug fixes and edge case handling.

Minor Makefile clean up.
 2019-09-21 02:44:54 +00:00
Joseph Mingrone
1aeb4149fc biology/diamond: Update to version 0.9.26 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
 2019-09-18 18:45:09 +00:00
Tobias Kortkamp
c8b9433fc5 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
Jason W. Bacon
6ee3cbecfe biology/haplohseq: Identify regions of allelic imbalance 
Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample.  Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
 2019-09-16 01:07:31 +00:00
Antoine Brodin
637b3d75f3 Deprecate a few ports 2019-09-15 17:28:08 +00:00