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500,208 Commits 46 Branches 101 Tags 3.4 GiB
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2665 Commits

Author SHA1 Message Date
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