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2734 commits

Author SHA1 Message Date
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470ff96c7f Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +00:00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
Jan Beich
e5688543b0 Drop C++11 workaround for GCC < 6 after r449590 
lang/gcc5 will expire in ~1 month. If someone still uses lang/gcc48
they should backport C++11 fix instead. QA on GCC architecuters is
currently limited to powerpc64 which uses GCC_DEFAULT.

PR:		193528
 2019-09-14 22:01:13 +00:00
Jason W. Bacon
848c6ffeb5 biology/trimmomatic: Upgrade to 0.39 
Add convenience script to run without knowing the location of the Java jar
 2019-09-14 14:45:49 +00:00
Jason W. Bacon
6e04e12944 biology/bedtools: Upgrade to 2.29.0 
Add test target to run test scripts in dist

Reported by:    portscout
 2019-09-13 13:21:59 +00:00
Jason W. Bacon
95b394ac5a biology/py-cutadapt: Upgrade to 2.5 
Add pigz run depend for parallel gzip/gunzip
 2019-09-13 13:17:26 +00:00
Fernando Apesteguía
fc8669c808 biology/phyml: update to 3.3.20190909 
While here, add license.

Reported by:	portscout
 2019-09-10 21:04:16 +00:00
Sunpoet Po-Chuan Hsieh
20b6ec5afb Update to 1.007006 (1.7.6) 
- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions

Changes:	https://metacpan.org/changes/distribution/BioPerl
 2019-09-07 22:44:02 +00:00
Cy Schubert
4b8362f61d Fix after gets(3) retirement using gets_s(3). 
Bump PORTREVISION as this is a security issue too.

PR:		222796
MFH:		2019Q3
 2019-09-02 05:00:43 +00:00
Li-Wen Hsu
5bf9108d86 Add a patch to remove use of gets(3) 
PR:		238685
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	emaste
Sponsored by:	The FreeBSD Foundation
 2019-09-01 16:40:06 +00:00
Yuri Victorovich
e6c3d1ddd9 biology/py-pysam: Update 0.15.2 -> 0.15.3 
Reported by:	portscout
 2019-08-31 15:49:18 +00:00
Yuri Victorovich
c90779610e biology/ngs-sdk: Update 2.9.6 -> 2.10.0 
Reported by:	portscout
 2019-08-31 15:09:47 +00:00
Joseph Mingrone
e4f4ed9cec biology/iqtree: Update to version 1.6.12 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12
 2019-08-27 01:19:11 +00:00
Kurt Jaeger
bc7e4c2f4a biology/gperiodic: fix NLS and other rough edges 
PR:		239642
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	bapt
 2019-08-23 15:26:55 +00:00
Jan Beich
befa71e0f3 devel/boost-*: update to 1.71.0 
Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
 2019-08-19 15:35:27 +00:00
Yuri Victorovich
ba3c2338e8 biology/checkm: Update 1.0.17 -> 1.0.18 
Reported by:	portscout
 2019-08-19 08:25:29 +00:00
Mathieu Arnold
a6c40a689b Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Jason W. Bacon
cdd2c0e9b9 biology/bolt-lmm: Upgrade to 2.3.4 
Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
 2019-08-13 15:30:21 +00:00
Yuri Victorovich
d9c09cd680 biology/checkm: Update 1.0.16 -> 1.0.17 
Reported by:	portscout
 2019-08-11 19:16:49 +00:00
Kurt Jaeger
ad26c38bf6 biology/gperiodic: upgrade 2.0.10 -> 3.0.3 
- new mastersite

PR:		239642
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Relnotes:	https://sourceforge.net/p/gperiodic/code/HEAD/tree/branches/3.0.3/ChangeLog
 2019-08-11 17:29:10 +00:00
Sunpoet Po-Chuan Hsieh
b470f47c18 Update to 1.007005 (1.7.5) 
- Fix DISTNAME
- Bump PORTREVISION for package change

Changes:	https://metacpan.org/changes/distribution/BioPerl
 2019-08-11 16:49:24 +00:00
Sunpoet Po-Chuan Hsieh
303b9c7e48 Update WWW 2019-08-11 11:28:16 +00:00
Yuri Victorovich
d5c0a71815 biology/checkm: Update 1.0.13 -> 1.0.16 
Reported by:	portscout
 2019-08-09 07:22:48 +00:00
Piotr Kubaj
488e433066 biology/hhsuite: fix build on powerpc64 
This port can't use Altivec. Instead, it's possible to use GCC's translation layer from SSE. Adjust build flags to do it.

PR:		239645
Approved by:	yuri (maintainer), tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D21160
 2019-08-05 14:23:23 +00:00
Jason W. Bacon
f81b82f68d PR: 239613 
Submitted by:   pkubaj
 2019-08-04 23:48:22 +00:00
Joseph Mingrone
4d67ec8def biology/diamond: Update to version 0.9.25 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
 2019-08-04 23:35:15 +00:00
Antoine Brodin
28ca9c0b13 Mark BROKEN: unfetchable 2019-08-04 08:31:22 +00:00
Gerald Pfeifer
ea8c8ec7da Bump PORTREVISION for ports depending on the canonical version of GCC 
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
 2019-07-26 20:46:53 +00:00
Yuri Victorovich
fe375c5637 biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43 
Now it builds with gradle-5.

Improvements im Makefile to simplify the port update process, in line with some other gradle-based ports.

Reported by:	repology
 2019-07-26 18:03:08 +00:00
Dmitry Marakasov
8c79ef8a40 - Update WWW 
Approved by:	portmgr blanket
 2019-07-25 09:02:20 +00:00
Tobias Kortkamp
87b5f55bdb Prepare for devel/gradle4 and java/openjfx8-devel updates 
openjfx8-devel now requires at least Gradle 4.8.  biology/gatk
however does not build with Gradle 4.10.3.  Preserve Gradle 4.6 for
now.

PR:		239392
 2019-07-23 05:28:46 +00:00
Piotr Kubaj
86062e221e biology/treekin: fix build on GCC architectures 
Needs C++11 compiler:
configure: error: *** A compiler with support for C++11 language features is required.

Approved by:	mentors (implicit approval)
 2019-07-19 08:49:33 +00:00
Jason W. Bacon
df8230f473 ncbi-blast+: Unbreak build with gcc8 following gcc9 patch 
GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none).  All const variables default to shared even with default(none)
present.  8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.

Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.

Reported by:    jrm
 2019-07-12 23:58:22 +00:00
Yuri Victorovich
18bfb7c9c1 New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
Jason W. Bacon
4d261c2cce ncbi-blast+: Fix build with gcc9 
GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default.  New patch sent upstream.

PR:             238471
Reported by:    gerald
 2019-07-11 13:53:30 +00:00
Sunpoet Po-Chuan Hsieh
d99d942bb0 Update security/nettle to 3.5.1 
- Bump PORTREVISION of dependent ports for shlib change
- Fix build of devel/pijul [1]

Changes:	https://git.lysator.liu.se/nettle/nettle/blob/master/NEWS
PR:		238991
Exp-run by:	antoine
Thanks to:	tobik [1]
 2019-07-09 17:13:07 +00:00
Dmitry Marakasov
8687848456 - Update WWW 
Approved by:	portmgr blanket
 2019-07-08 09:32:08 +00:00
Yuri Victorovich
57ca301450 biology/mothur: Update 1.42.2 -> 1.42.3 
Reported by:	portscout
 2019-06-28 04:02:22 +00:00
Mark Linimon
08f171f732 Mark this port as not buildable on powerpc64: 
*** File 'Makefile.config.FreeBSD.powerpc' is missing. Please run ./configure

The configuration script may have other problems as well.  This needs
to be addressed by upstream (if there is interest).

Approved by:	portmgr (tier-2 blanket)
 2019-06-25 12:17:04 +00:00
Joseph Mingrone
85a64655aa biology/iqtree: Update to version 1.6.11 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11
 2019-06-24 21:47:34 +00:00
Yuri Victorovich
428a2eddb1 biology/viennarna: Make it less/not prone to failures due to hardcoded C++ library name 
configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might fail on gcc systems, depending on which C++ library is used.

This change adds USES=autoreconf which makes it to regenerate configure and Makefile.in and hopefully have the proper C++ library in these files.

GNU libtool links with the C compiler, not with the C++ compiler, in this project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and it uses the C compiler to link and fails due to wrong C++ libraries added there.
 2019-06-24 19:30:15 +00:00
Yuri Victorovich
f848ca2897 New port: biology/viennarna: Alignment tools for the structural analysis of RNA 2019-06-24 09:29:05 +00:00
Sunpoet Po-Chuan Hsieh
47c6c8bc57 Use USES=pathfix 
- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership
 2019-06-22 21:48:14 +00:00
Piotr Kubaj
ba101b3372 biology/abyss: fix build on big-endian architectures 
Use new GCC from ports on GCC architectures.

Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures.

Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ).

PR:		238737
Approved by:	yuri (maintainer), mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D20717
 2019-06-21 11:43:09 +00:00
Mark Linimon
6ec44c3ad2 Enable workaround for building on powerpc64. 
Autoconf reports that HAVE_ASM_BSR is true (1).  However, it's a false
positive.

I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure.  Patches welcome.

A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.

Approved by:	portmgr (tier-2 blanket)
 2019-06-21 11:15:08 +00:00
Yuri Victorovich
bc633cff70 biology/mothur: Update 1.42.1-3 -> 1.42.2 2019-06-19 23:54:44 +00:00
Yuri Victorovich
f04a95e391 biology/py-bx-python: Update 0.8.2 -> 0.8.4 
Reported by:	pirtscout
 2019-06-19 08:08:31 +00:00
Yuri Victorovich
656bb703a3 New port: biology/treekin: Efficient computation of RNA folding dynamics 2019-06-15 20:37:06 +00:00
Jason W. Bacon
e66bb2a167 biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl 2019-06-14 00:37:59 +00:00
Jason W. Bacon
071d3229c9 biology/ncbi-blast+: Upgrade to 2.9.0 
Fixes build issue with gcc9

PR:             238471
Reported by:    gerald
 2019-06-12 23:53:32 +00:00
Jason W. Bacon
8786bbbbce biology/kallisto: Upgrade to 0.46.0 
Reported by:    portscout
 2019-06-12 15:24:55 +00:00
Steve Wills
f0b00e7fb7 biology/tRNAscan-SE: Update to 2.0.3 
PR:		238253
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>
 2019-06-08 01:31:18 +00:00
Yuri Victorovich
be0311dc43 biology/igv: Update 2.5.2 -> 2.5.3 
Reported by:	portscout
 2019-06-01 20:49:20 +00:00
Piotr Kubaj
4ee9ce4ad7 biology/tRNAscan-SE: fix build with GCC-based architecturs 
Add MAKE_JOBS_UNSAFE=yes to fix build.

Remove USES=compiler:c11, it's not necessary.

PR:		237848
Approved by:	mzaki@niid.go.jp (maintainer), linimon (mentor)
Differential Revision:	https://reviews.freebsd.org/D20439
 2019-05-30 07:39:06 +00:00
Yuri Victorovich
af04051df9 biology/cufflinks: Fix build on i386 by removing the hard-coded -m64 
Reported by:	fallout
 2019-05-29 07:02:28 +00:00
Jason W. Bacon
e6e8db340a biology/bolt-lmm: Mixed model association testing and variance component analysis 
The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
 2019-05-26 03:36:49 +00:00
Yuri Victorovich
806c31f29d New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their abundance, etc 2019-05-25 22:28:12 +00:00
Yuri Victorovich
16421979c0 biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist or isn't detected. 
It forces it to default to SSE2 on amd64/i386 and relaxes the SIMD requirement on all other platforms.

Reported by:	fallout
 2019-05-22 02:50:56 +00:00
Jason W. Bacon
a0cddd98e1 biology/fastp: Remove redundant USE_GCC 2019-05-20 23:41:08 +00:00
Yuri Victorovich
119875252d biology/mothur: Add USES=compiler:c++11-lang 2019-05-20 21:20:56 +00:00
Yuri Victorovich
9114406e04 New port: biology/mothur: Software for bioinformatics of the microbial ecology community 2019-05-20 17:59:17 +00:00
Wen Heping
33386b503a - Update to 3.3.20190321 2019-05-20 09:17:29 +00:00
Wen Heping
6779cec238 - Update to 5.18.0 2019-05-20 09:12:41 +00:00
Yuri Victorovich
31d6c9230d New port: biology/hhsuite: Remote protein homology detection suite 2019-05-19 06:52:38 +00:00
Jason W. Bacon
7e01a08d9b biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC 
Reported by:    danfe, Gerald Pfeifer
 2019-05-18 22:41:15 +00:00
Jason W. Bacon
3ee18ac50b biology/gemma: Genome-wide Efficient Mixed Model Association 
GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
 2019-05-17 14:45:19 +00:00
Jason W. Bacon
3cdd6aac74 biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64 
PR:             237868
Submitted by:   pkubaj
 2019-05-13 16:23:35 +00:00
Jason W. Bacon
75055f8a7f biology/vsearch: Update to 2.13.4 
FreeBSD patches incorporated into new upstream release

Reported by:    portscout
 2019-05-11 13:42:33 +00:00
Yuri Victorovich
8d1988e52d biology/igv: Update 2.5.0 -> 2.5.2 
Reported by:	portscout
 2019-05-11 05:59:29 +00:00
Jason W. Bacon
839e242bac biology/trimadap: Mark only for amd64 and i386 
Contains hard-coded SSE instructions
 2019-05-11 00:18:24 +00:00
Jason W. Bacon
1fa06bb9b8 biology/stacks: Remove obsolete pkg-message regarding web interface 
PHP code no longer included in dist as of v2.4
 2019-05-10 21:15:42 +00:00
Jason W. Bacon
047a903a15 biology/stacks: Upgrade to 2.4 
Improve check to avoid outdated GCC on 2nd tier platforms

Reported by:    portscout
 2019-05-10 21:04:43 +00:00
Jason W. Bacon
037bd13c9c biology/vsearch: Remove powerpc64 support 
Requires little endian mode and FreeBSD currently does not support it
 2019-05-09 22:12:26 +00:00
Jason W. Bacon
0be0763624 biology/vsearch: Versatile open-source tool for metagenomics 
VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.

The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).
 2019-05-09 21:28:49 +00:00
Jan Beich
3b1a1bcee4 devel/openmp: phase out 
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767
 2019-05-08 16:05:53 +00:00
Piotr Kubaj
544262f7ef biology/tRNAscan-SE: fix build with GCC-based architectures 
Add USES=compiler:c11 to fix build.

Approved by:	mentors (implicit approval)
 2019-05-07 19:45:17 +00:00
Jason W. Bacon
21a82c027a biology/minimap2: Upgrade to 2.17 
Reported by:    portscout
 2019-05-05 14:56:07 +00:00
Jason W. Bacon
861a0890f8 biology/ddocent: Upgrade to 2.7.8 
Reported by:    portscout
 2019-05-04 15:09:10 +00:00
Jason W. Bacon
2c99faaf3f biology/fastp: Respect WITH_DEBUG - do not strip binary 2019-05-04 02:07:07 +00:00
Mark Linimon
922dee671e These ports now build on aarch64. 
Where necessary, pet portlint.

Approved by:	portmgr
Obtained from:	aarch64 TRYBROKEN run
 2019-05-03 21:06:51 +00:00
Jason W. Bacon
19a9ba64fc biology/fastp: Ultra-fast all-in-one FASTQ preprocessor 
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
 2019-05-03 14:41:57 +00:00
Jason W. Bacon
70dde62191 biology/star: Force newer GCC on platforms with GCC 4.2 base 
PR:             237700
Submitted by:   pkubaj
 2019-05-02 00:39:51 +00:00
Jason W. Bacon
a158326e6e biology/py-cutadapt: Upgrade to 2.3 
Numerous bugfixes and enhancements since 2.1
 2019-04-27 01:26:17 +00:00
Antoine Brodin
e013b5dc59 Clean up plist 2019-04-25 13:25:50 +00:00
Jason W. Bacon
196e812dbd biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences 
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.
 2019-04-24 18:03:49 +00:00
Jason W. Bacon
3c65c04264 biology/bowtie2: Clarify CPU-specificity 2019-04-24 17:41:27 +00:00
Jason W. Bacon
c8844419a0 biology/star: Modify PKGBASE to avoid conflict with archivers/star 2019-04-23 15:03:29 +00:00
Sunpoet Po-Chuan Hsieh
c5a54c8c3a Fix typo 
- Bump PORTREVISION for dependency change

Notified by:	mat
 2019-04-23 14:11:50 +00:00
Sunpoet Po-Chuan Hsieh
71717e8e5c Sort PLIST 2019-04-22 20:42:08 +00:00
Gerald Pfeifer
879e75a659 Related to revision 499061 bump ports with USES=fortran to have them 
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl
 2019-04-22 13:16:33 +00:00
Jason W. Bacon
d3e770598b biology/star: Spliced Transcripts Alignment to a Reference 
STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.
 2019-04-21 20:30:55 +00:00