Commit graph

264 commits

Author SHA1 Message Date
Jason W. Bacon
c81fc00817 biology/bioawk: BWK awk modified for biological data
Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
2020-06-05 02:45:33 +00:00
Jason W. Bacon
a156fdcf52 biology/subread: Read alignment, quantification and mutation discovery
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.
2020-06-05 01:55:49 +00:00
Jason W. Bacon
c468c4c36e bioloty/vt: Discovers short variants from Next Generation Sequencing data 2020-06-04 18:28:13 +00:00
Yuri Victorovich
14a9e6c989 New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments 2020-05-16 03:11:05 +00:00
Yuri Victorovich
b1b7f59bd1 New port: biology/py-scikit-bio: Data structures, algorithms, educational resources for bioinformatics 2020-05-16 02:25:35 +00:00
Yuri Victorovich
634ce3b531 New port: biology/py-pandas-charm: Library for getting character matrices into and out of pandas 2020-05-16 00:14:16 +00:00
Yuri Victorovich
02a5c651ae New port: biology/py-ete3: Framework for the analysis and visualization of trees 2020-05-16 00:13:09 +00:00
Yuri Victorovich
04c132a637 New port: biology/scrm: Coalescent simulator for biological sequences 2020-05-15 04:58:27 +00:00
Alexey Dokuchaev
52ea511a14 - Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
2020-05-10 15:42:32 +00:00
Rene Ladan
0786acb315 Remove expired ports:
Adjusted for ports rescued since r534032

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2020-05-05 textproc/pcrs: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_RSS: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_XML: Broken for more than 6 months
2020-05-05 textproc/permute: Broken for more than 6 months
2020-05-05 textproc/pocketreader: Broken for more than 6 months
2020-05-05 textproc/py-sgrep: Broken for more than 6 months
2020-05-05 textproc/rss2html: Broken for more than 6 months
2020-05-05 textproc/ruby-xmlparser: Broken for more than 6 months
2020-05-05 textproc/sv-hyphen: Broken for more than 6 months
2020-05-05 textproc/tclExpat: Broken for more than 6 months
2020-05-05 textproc/tex2im: Broken for more than 6 months
2020-05-05 textproc/topic: Broken for more than 6 months
2020-05-05 textproc/uz-hunspell: Broken for more than 6 months
2020-05-05 textproc/xmlprpr: Broken for more than 6 months
2020-05-05 www/ach: Broken for more than 6 months
2020-05-05 www/apache-forrest: Broken for more than 6 months
2020-05-05 www/apercu: Broken for more than 6 months
2020-05-05 www/cblog: Broken for more than 6 months
2020-05-05 www/drood: Broken for more than 6 months
2020-05-05 www/drraw: Broken for more than 6 months
2020-05-05 www/flood: Broken for more than 6 months
2020-05-05 www/grafana2: Broken for more than 6 months
2020-05-05 www/imgsizer: Broken for more than 6 months
2020-05-05 www/jdresolve: Broken for more than 6 months
2020-05-05 www/linkcheck: Broken for more than 6 months
2020-05-05 www/madsonic-standalone: Broken for more than 6 months
2020-05-05 www/mod_auth_external2: Broken for more than 6 months
2020-05-05 www/mod_chroot: Broken for more than 6 months
2020-05-05 www/mod_cvs2: Broken for more than 6 months
2020-05-05 www/mod_domaintree: Broken for more than 6 months
2020-05-05 www/mod_encoding: Broken for more than 6 months
2020-05-05 www/mod_flickr: Broken for more than 6 months
2020-05-05 www/mod_gzip2: Broken for more than 6 months
2020-05-05 www/mod_layout22: Broken for more than 6 months
2020-05-05 www/mod_proctitle: Broken for more than 6 months
2020-05-05 www/mod_tsa: Broken for more than 6 months
2020-05-05 www/mod_vhs: Broken for more than 6 months
2020-05-05 www/p5-AnyEvent-Mojo: Broken for more than 6 months
2020-05-05 www/p5-Apache-Gallery: Broken for more than 6 months
2020-05-05 www/p5-WWW-Google-Video: Broken for more than 6 months
2020-05-05 www/p5-WWW-Shorten-KUSO: Broken for more than 6 months
2020-05-05 www/p5-WWW-Shorten-isgd: Broken for more than 6 months
2020-05-05 www/photo_gallery: Broken for more than 6 months
2020-05-05 www/pwebstats: Broken for more than 6 months
2020-05-05 www/py-django-profiles: Broken for more than 6 months
2020-05-05 www/red5: Broken for more than 6 months
2020-05-05 www/redmine-sidebar_hide: Broken for more than 6 months
2020-05-05 www/rssowl: Broken for more than 6 months
2020-05-05 www/skytemplate: Broken for more than 6 months
2020-05-05 www/surfraw: Broken for more than 6 months
2020-05-05 www/sws: Broken for more than 6 months
2020-05-05 www/tickr: Broken for more than 6 months
2020-05-05 www/tinytinyhttpd: Broken for more than 6 months
2020-05-05 www/udmsearch: Broken for more than 6 months
2020-05-05 www/vee: Broken for more than 6 months
2020-05-05 www/webreport: Broken for more than 6 months
2020-05-05 www/webstats: Broken for more than 6 months
2020-05-05 www/www6to4: Broken for more than 6 months
2020-05-05 x11/deskpaint: Broken for more than 6 months
2020-05-05 x11/dmenu2: Broken for more than 6 months
2020-05-05 x11/gcb: Broken for more than 6 months
2020-05-05 x11/gpctool: Broken for more than 6 months
2020-05-05 x11/ipager: Broken for more than 6 months
2020-05-05 x11/keylaunch: Broken for more than 6 months
2020-05-05 x11/props: 64-bit unsupported
2020-05-05 x11/roxbg: Broken for more than 6 months
2020-05-05 x11/sisctrl: Broken for more than 6 months
2020-05-05 x11/wdm: Broken for more than 6 months
2020-05-05 x11/xaniroc: Broken for more than 6 months
2020-05-05 x11/xmove: Broken for more than 6 months
2020-05-05 x11/xnodecor: Broken for more than 6 months
2020-05-05 x11/xvattr: Broken for more than 6 months
2020-05-05 x11-clocks/tktz: Broken for more than 6 months
2020-05-05 x11-clocks/xtimer: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-dropline-neu: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-dropline-nou: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-gion: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-jini: Broken for more than 6 months
2020-05-05 x11-themes/gtk-aurora-engine: Broken for more than 6 months
2020-05-05 x11-themes/gtk-blueprint-engine: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrina-fancy-clearlooks: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrina-lightblue: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrine-themes: Broken for more than 6 months
2020-05-05 x11-themes/murrine-configurator: Broken for more than 6 months
2020-05-05 x11-themes/nimbus: Broken for more than 6 months
2020-05-05 x11-themes/openbox-themes: Broken for more than 6 months
2020-05-05 x11-themes/rezlooks: Broken for more than 6 months
2020-05-05 x11-themes/ubuntulooks: Broken for more than 6 months
2020-05-05 x11-toolkits/slingshot: 64-bit unsupported
2020-05-05 x11-toolkits/xview-clients: 64-bit unsupported
2020-05-05 x11-wm/fluxconf: Broken for more than 6 months
2020-05-05 x11-wm/ion: Broken for more than 6 months
2020-05-05 x11-wm/matwm2: Broken for more than 6 months
2020-05-05 x11-wm/nickleby: Broken for more than 6 months
2020-05-05 x11-wm/olvwm: 64-bit unsupported
2020-05-05 x11-wm/ratmenu: Broken for more than 6 months
2020-05-05 15:38:11 +00:00
Jason W. Bacon
3001cc8b83 biology/plink: Whole genome association analysis toolset
Reversed removal, commit r471892 2018/06/07
Upgraded to 1.90 beta 6.17

PR:             ports/243733
Submitted by:   mzaki@e-mail.ne.jp
2020-05-04 23:01:57 +00:00
Jason W. Bacon
64673b1e81 biology/gcta: Genome-wide Complex Trait Analysis
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate
the proportion of phenotypic variance explained by genome- or chromosome-wide
SNPs for complex traits (the GREML method), and has subsequently extended for
many other analyses to better understand the genetic architecture of complex
traits.
2020-04-15 15:22:04 +00:00
Mateusz Piotrowski
28f362fae3 Resurrect biology/linux-foldingathome
Special thanks to netchild for inspiring bringing back this piece software
to ports!

Reviewed by:	netchild, pi, salvadore
Differential Revision:	https://reviews.freebsd.org/D24127
2020-03-21 23:03:05 +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
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
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
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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
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2019-10-16 mail/py-apolicy: Unfetchable, unmaintained
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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
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
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
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
Yuri Victorovich
18bfb7c9c1 New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +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
Yuri Victorovich
656bb703a3 New port: biology/treekin: Efficient computation of RNA folding dynamics 2019-06-15 20:37:06 +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
9114406e04 New port: biology/mothur: Software for bioinformatics of the microbial ecology community 2019-05-20 17:59:17 +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
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
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
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
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
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
Yuri Victorovich
74ca3eaba7 New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub 2019-04-12 17:01:10 +00:00
Jason W. Bacon
1775de91c8 biology/py-dnaio: Read and write FASTQ and FASTA
Factored out of py-cutadapt

Reviewed by:    jrm
2019-03-24 19:40:26 +00:00
Tobias C. Berner
369eb054b0 Qt4 deprecation: Remove Qt4 and its consumes.
2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015
2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015
2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015
2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015
2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015
2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015
2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015
2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015
2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015
2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015
2019-03-15 audio/mumble: Qt4 has been EOL since december 2015
2019-03-15 audio/murmur: Qt4 has been EOL since december 2015
2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015
2019-03-15 audio/qmpdclient: Qt4 has been EOL since december 2015
2019-03-15 audio/skype-call-recorder: Qt4 has been EOL since december 2015
2019-03-15 audio/virtual_oss_ctl: Qt4 has been EOL since december 2015
2019-03-15 biology/clustalx: Qt4 has been EOL since december 2015
2019-03-15 cad/klayout: Qt4 has been EOL since december 2015
2019-03-15 cad/layouteditor: Qt4 has been EOL since december 2015
2019-03-15 cad/leocad: Qt4 has been EOL since december 2015
2019-03-15 cad/meshlab: Qt4 has been EOL since december 2015
2019-03-15 cad/qfsm: Qt4 has been EOL since december 2015
2019-03-15 cad/qucs: Qt4 has been EOL since december 2015
2019-03-15 chinese/gcin-qt4: Qt4 has been EOL since december 2015
2019-03-15 chinese/qt4-codecs-cn: Qt4 has been EOL since december 2015
2019-03-15 chinese/qt4-codecs-tw: Qt4 has been EOL since december 2015
2019-03-15 chinese/qterm: Qt4 has been EOL since december 2015
2019-03-15 comms/dabstick-radio: Qt4 has been EOL since december 2015
2019-03-15 comms/hamfax: Qt4 has been EOL since december 2015
2019-03-15 comms/linpsk: Qt4 has been EOL since december 2015
2019-03-15 databases/py-qt4-sql: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-ibase-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-mysql-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-odbc-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-pgsql-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sql: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sqlite-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sqlite3-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/sqliteman: Qt4 has been EOL since december 2015
2019-03-15 databases/tora: Qt4 has been EOL since december 2015
2019-03-15 deskutils/cdcat: Qt4 has been EOL since december 2015
2019-03-15 deskutils/fbreader: Qt4 has been EOL since december 2015
2019-03-15 deskutils/launchy: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qorganizer: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qrfcview: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qtm: Qt4 has been EOL since december 2015
2019-03-15 deskutils/tuxcards: Qt4 has been EOL since december 2015
2019-03-15 deskutils/vym: Qt4 has been EOL since december 2015
2019-03-15 devel/apiextractor: Qt4 has been EOL since december 2015
2019-03-15 devel/automoc4: Qt4 has been EOL since december 2015
2019-03-15 devel/edb: Qt4 has been EOL since december 2015
2019-03-15 devel/generatorrunner: Qt4 has been EOL since december 2015
2019-03-15 devel/grantlee: Qt4 has been EOL since december 2015
2019-03-15 devel/gwenhywfar-qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/kaptain: Qt4 has been EOL since december 2015
2019-03-15 devel/ninja-ide: Qt4 has been EOL since december 2015
2019-03-12 devel/physfs-devel: is the same as devel/physfs, serving no purpose
2019-03-15 devel/piklab: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-assistant: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-core: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-dbus: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-dbussupport: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-declarative: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-designer: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-help: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-qscintilla2: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-script: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-scripttools: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-test: Qt4 has been EOL since december 2015
2019-03-15 devel/pyside: Qt4 has been EOL since december 2015
2019-03-15 devel/pyside-tools: Qt4 has been EOL since december 2015
2019-03-15 devel/qbzr: Qt4 has been EOL since december 2015
2019-03-15 devel/qct: Qt4 has been EOL since december 2015
2019-03-15 devel/qdevelop: Qt4 has been EOL since december 2015
2019-03-15 devel/qprog: Qt4 has been EOL since december 2015
2019-03-15 devel/qross: Qt4 has been EOL since december 2015
2019-03-15 devel/qscintilla2: Qt4 has been EOL since december 2015
2019-03-15 devel/qscintilla2-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-assistant: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-assistant-adp: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-corelib: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-dbus: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-designer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-help-tools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-libqtassistantclient: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-linguist: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-linguisttools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-makeqpf: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-moc: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-porting: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qdbusviewer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qdoc3: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qmake: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qmlviewer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qt3support: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qtsolutions-singleapplication: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qtsolutions-soap: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qvfb: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-rcc: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-script: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-scripttools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-testlib: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-uic: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-uic3: Qt4 has been EOL since december 2015
2019-03-15 devel/qtscriptgenerator: Qt4 has been EOL since december 2015
2019-03-15 devel/shiboken: Qt4 has been EOL since december 2015
2019-03-15 devel/subcommander2: Qt4 has been EOL since december 2015
2019-03-15 devel/universalindentgui: Qt4 has been EOL since december 2015
2019-03-15 editors/leo: Qt4 has been EOL since december 2015
2019-03-15 editors/lfhex: Qt4 has been EOL since december 2015
2019-03-15 editors/plume-creator-devel: Qt4 has been EOL since december 2015
2019-03-15 editors/textroom: Qt4 has been EOL since december 2015
2019-03-15 editors/yzis: Qt4 has been EOL since december 2015
2019-03-15 emulators/dboxfe: Qt4 has been EOL since december 2015
2019-03-15 emulators/q4wine: Qt4 has been EOL since december 2015
2019-03-15 emulators/qtemu: Qt4 has been EOL since december 2015
2019-03-15 emulators/swine: Qt4 has been EOL since december 2015
2019-03-15 finance/alkimia-qt4: Qt4 has been EOL since december 2015
2019-03-15 finance/bitcoin-armory: Qt4 has been EOL since december 2015
2019-03-15 finance/qhacc: Qt4 has been EOL since december 2015
2019-03-15 ftp/scythia: Qt4 has been EOL since december 2015
2019-03-15 games/bubble-chains: Qt4 has been EOL since december 2015
2019-03-15 games/capicity: Qt4 has been EOL since december 2015
2019-03-15 games/capitalism: Qt4 has been EOL since december 2015
2019-03-15 games/flukz: Qt4 has been EOL since december 2015
2019-03-15 games/goldencheetah: Qt4 has been EOL since december 2015
2019-03-15 games/jag: Qt4 has been EOL since december 2015
2019-03-15 games/kardsgt: Qt4 has been EOL since december 2015
2019-03-15 games/kcheckers: Qt4 has been EOL since december 2015
2019-03-15 games/openpref: Qt4 has been EOL since december 2015
2019-03-15 games/pokerth: Qt4 has been EOL since december 2015
2019-03-15 games/qgo: Qt4 has been EOL since december 2015
2019-03-15 games/qtads: Qt4 has been EOL since december 2015
2019-03-15 games/quackle: Qt4 has been EOL since december 2015
2019-03-15 games/spellathon: Qt4 has been EOL since december 2015
2019-03-15 games/sudoku-sensei: Qt4 has been EOL since december 2015
2019-03-15 games/tbe: Qt4 has been EOL since december 2015
2019-03-15 games/xptools: Qt4 has been EOL since december 2015
2019-03-15 german/tipp10: Qt4 has been EOL since december 2015
2019-03-15 graphics/appleseed: Qt4 has been EOL since december 2015
2019-03-15 graphics/aqsis: Qt4 has been EOL since december 2015
2019-03-15 graphics/autoq3d: Qt4 has been EOL since december 2015
2019-03-15 graphics/burplex: Qt4 has been EOL since december 2015
2019-03-15 graphics/darknock: Qt4 has been EOL since december 2015
2019-03-15 graphics/djview4-qt4: Qt4 has been EOL since december 2015
2019-03-15 graphics/easypaint: Qt4 has been EOL since december 2015
2019-03-15 graphics/eos-movrec: Qt4 has been EOL since december 2015
2019-03-15 graphics/gle-graphics: Qt4 has been EOL since december 2015
2019-03-15 graphics/lprof-devel: Qt4 has been EOL since december 2015
2019-03-15 graphics/luminance: Qt4 has been EOL since december 2015
2019-03-15 graphics/luxrender: Qt4 has been EOL since december 2015
2019-03-15 graphics/luxrender14: Qt4 has been EOL since december 2015
2019-03-15 graphics/meshviewer: Qt4 has been EOL since december 2015
2019-03-15 graphics/natron: Qt4 has been EOL since december 2015
2019-03-15 graphics/oyranos: Qt4 has been EOL since december 2015
2019-03-15 graphics/pencil: Qt4 has been EOL since december 2015
2019-03-15 graphics/prison: Qt4 has been EOL since december 2015
2019-03-15 graphics/py-qt4-svg: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-iconengines: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-imageformats: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-opengl: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-pixeltool: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-svg: Qt4 has been EOL since december 2015
2019-03-15 graphics/qxv: Qt4 has been EOL since december 2015, qxv is unmaintained
2019-03-15 graphics/scantailor: Qt4 has been EOL since december 2015
2019-03-15 graphics/seexpr: Qt4 has been EOL since december 2015
2019-03-15 graphics/smillaenlarger: Qt4 has been EOL since december 2015
2019-03-15 graphics/structuresynth: Qt4 has been EOL since december 2015
2019-03-15 graphics/yagf: Qt4 has been EOL since december 2015
2019-03-15 japanese/qt4-codecs-jp: Qt4 has been EOL since december 2015
2019-03-15 korean/qt4-codecs-kr: Qt4 has been EOL since december 2015
2019-03-15 mail/qgmailnotifier: Qt4 has been EOL since december 2015
2019-03-15 math/qtiplot: Qt4 has been EOL since december 2015
2019-03-15 math/qtoctave: Qt4 has been EOL since december 2015
2019-03-15 math/qwtplot3d-qt4: Qt4 has been EOL since december 2015
2019-03-15 misc/py-qt4-demo: Qt4 has been EOL since december 2015
2019-03-15 misc/py-qt4-doc: Qt4 has been EOL since december 2015
2019-03-15 misc/qmetro: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-doc: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-l10n: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-qtconfig: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-qtdemo: Qt4 has been EOL since december 2015
2019-03-15 misc/saaghar: Qt4 has been EOL since december 2015
2019-03-15 multimedia/2mandvd: Qt4 has been EOL since december 2015
2019-03-15 multimedia/abby: Qt4 has been EOL since december 2015
2019-03-15 multimedia/avidemux-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/gstreamer-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/mediadownloader: Qt4 has been EOL since december 2015
2019-03-15 multimedia/mlt-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/phonon-xine: Qt4 has been EOL since december 2015
2019-03-15 multimedia/py-qt4-multimedia: Qt4 has been EOL since december 2015
2019-03-15 multimedia/py-qt4-phonon: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qmmp: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qmmp-plugin-pack: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qt4-mobility: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qt4-multimedia: Qt4 has been EOL since december 2015
2019-03-15 multimedia/umplayer: Qt4 has been EOL since december 2015
2019-03-15 net/avahi-qt4: Qt4 has been EOL since december 2015
2019-03-15 net/cagibi: Qt4 has been EOL since december 2015
2019-03-15 net/hupnp: Qt4 has been EOL since december 2015
2019-03-15 net/ostinato: Qt4 has been EOL since december 2015
2019-03-15 net/py-qt4-network: Qt4 has been EOL since december 2015
2019-03-15 net/qjsonrpc: Qt4 has been EOL since december 2015
2019-03-15 net/qoauth: Qt4 has been EOL since december 2015
2019-03-15 net/qt4-network: Qt4 has been EOL since december 2015
2019-03-15 net/qtweetlib: Qt4 has been EOL since december 2015
2019-03-15 net-im/libjreen: Qt4 has been EOL since december 2015
2019-03-15 net-im/psimedia: Qt4 has been EOL since december 2015
2019-03-15 net-im/ramblercontacts: Qt4 has been EOL since december 2015
2019-03-15 net-im/telepathy-logger-qt4: Qt4 has been EOL since december 2015
2019-03-15 net-im/turpial: Qt4 has been EOL since december 2015
2019-03-15 net-im/vacuum-im: Qt4 has been EOL since december 2015
2019-03-15 net-mgmt/nagiosagent: Qt4 has been EOL since december 2015
2019-03-15 net-mgmt/qkismet: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/bitmessage: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/eiskaltdcpp-qt: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/valknut: Qt4 has been EOL since december 2015
2019-03-15 polish/qfaktury: Qt4 has been EOL since december 2015
2019-03-15 print/kpdftool: Qt4 has been EOL since december 2015
2019-03-15 print/scribus: Qt4 has been EOL since december 2015
2019-03-15 science/MOOSE-neural-simulator: Qt4 has been EOL since december 2015
2019-03-15 science/avogadro: Qt4 has been EOL since december 2015
2019-03-15 science/openstructure: Qt4 has been EOL since december 2015
2019-03-15 science/py-veusz: Qt4 has been EOL since december 2015
2019-03-15 science/qtresistors: Qt4 has been EOL since december 2015
2019-03-15 security/keepassx2: Qt4 has been EOL since december 2015
2019-03-15 security/kqoauth: Qt4 has been EOL since december 2015
2019-03-15 security/tpmmanager: Qt4 has been EOL since december 2015
2019-03-15 sysutils/android-file-transfer-qt4: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bacula9-bat: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos-traymonitor: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos16-bat: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos16-traymonitor: Qt4 has been EOL since december 2015
2019-03-15 sysutils/policykit-qt: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qpxtool: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qsynergy: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qzeitgeist: Qt4 has been EOL since december 2015
2019-03-15 sysutils/searchmonkey: Qt4 has been EOL since december 2015
2019-03-15 sysutils/unetbootin: Qt4 has been EOL since december 2015
2019-03-15 textproc/beediff: Qt4 has been EOL since december 2015
2019-03-15 textproc/dixit: Qt4 has been EOL since december 2015
2019-03-15 textproc/goldendict: Qt4 has been EOL since december 2015
2019-03-15 textproc/ibus-qt: Qt4 has been EOL since december 2015
2019-03-15 textproc/py-qt4-xml: Qt4 has been EOL since december 2015
2019-03-15 textproc/py-qt4-xmlpatterns: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-clucene: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xml: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xmlpatterns: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xmlpatterns-tool: Qt4 has been EOL since december 2015
2019-03-15 textproc/scim-bridge-qt4: Qt4 has been EOL since december 2015
2019-03-15 textproc/uim-qt4: Qt4 has been EOL since december 2015
2019-03-15 textproc/xxdiff: Qt4 has been EOL since december 2015
2019-03-15 www/aria2fe: Qt4 has been EOL since december 2015
2019-03-15 www/cutycapt: Qt4 has been EOL since december 2015
2019-03-15 www/py-qt4-webkit: Qt4 has been EOL since december 2015
2019-03-15 www/qt4-webkit: Qt4 has been EOL since december 2015
2019-03-15 www/qupzilla-qt4: Qt4 has been EOL since december 2015
2019-03-15 x11/leechcraft: Qt4 has been EOL since december 2015
2019-03-15 x11/py-qt4-opengl: Qt4 has been EOL since december 2015
2019-03-15 x11/qimageblitz: Qt4 has been EOL since december 2015
2019-03-15 x11/qt4-graphicssystems-opengl: Qt4 has been EOL since december 2015
2019-03-15 x11/qt4-inputmethods: Qt4 has been EOL since december 2015
2019-03-15 x11/qxkb: Qt4 has been EOL since december 2015
2019-03-15 x11-fonts/fontmatrix: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-float: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-phase: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-quantumstyle: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qtcurve-qt4: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/attica: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/py-qt4-gui: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4-declarative: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4-gui: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4pas: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qwt5: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qwt5-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/soqt: Qt4 has been EOL since december 2015
2019-03-15 x11-wm/qlwm: Qt4 has been EOL since december 2015

Approved by:	portmgr (implicit)
2019-03-16 21:55:51 +00:00
Yuri Victorovich
e2f6302b8e New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler 2019-02-25 07:56:45 +00:00
Sunpoet Po-Chuan Hsieh
dcf929510c Add p5-Bio-Cluster 1.7.3
Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe
the basic structure for a cluster of BioPerl objects.

WWW: https://metacpan.org/release/Bio-Cluster
2019-02-20 20:46:37 +00:00
Yuri Victorovich
095098d6c8 New port: biology/figtree: Graphical viewer of phylogenetic trees 2019-02-03 21:14:38 +00:00
Yuri Victorovich
733be80eb6 New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees 2019-02-03 20:13:26 +00:00
Yuri Victorovich
540f58a8fb New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities 2019-02-03 18:49:23 +00:00
Yuri Victorovich
a1bcae4a2a New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes 2019-02-03 18:08:14 +00:00
Yuri Victorovich
80435b015b New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description format) 2019-01-29 07:56:30 +00:00
Mathieu Arnold
08c11c4978 Sort categories Makefiles. 2019-01-22 16:26:49 +00:00
Jason W. Bacon
0d9c05781a New port: biology/hisat2: Program for mapping next-generation sequencing reads
Approved by:    jrm (mentor, implicit)
2019-01-11 16:02:05 +00:00
Rene Ladan
e5aaf05932 Remove expired ports:
2018-12-19 net/py-libstorj: Broken for more than 6 months
2018-12-20 net/xferstats: Uses obsolete glib12
2018-12-20 net/wmlj: Uses obsolete glib12
2018-12-20 net/ipsorc: Uses obsolete glib12
2018-12-20 net/bsdproxy: Uses obsolete glib12
2018-12-20 net/gini: Uses obsolete glib12
2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead
2018-12-20 net/nocatsplash: Uses obsolete glib12
2018-12-20 net/jags: Uses obsolete glib12
2018-12-19 net/scribe: Broken for more than 6 months
2018-12-20 net/libnetdude: Uses obsolete glib12
2018-12-20 net/nepim: Uses obsolete glib12
2018-12-20 emulators/generator: Uses obsolete glib12
2018-12-19 emulators/py-nova: Broken for more than 6 months
2018-12-20 emulators/generator-cbiere: Uses obsolete glib12
2018-12-20 x11-toolkits/p5-Gtk-Perl: Uses obsolete glib12
2018-12-20 deskutils/ithought: Uses obsolete glib12
2018-12-20 deskutils/gaddr: Uses obsolete glib12
2018-12-20 x11-fonts/gfe: Uses obsolete glib12
2018-12-20 graphics/graphopt: Uses obsolete glib12
2018-12-19 graphics/fotoxx: Broken for more than 6 months
2018-12-20 graphics/gcolor: Uses obsolete glib12
2018-12-20 graphics/danpei: Uses obsolete glib12
2018-12-20 graphics/chbg: Uses obsolete glib12
2018-12-20 mail/pop3lite: Uses obsolete glib12
2018-12-20 mail/gbuffy: Uses obsolete glib12
2018-12-20 security/gtk-knocker: Uses obsolete glib12
2018-12-20 security/gpasman: Uses obsolete glib12
2018-12-20 security/crank: Uses obsolete glib12
2018-12-20 security/stegdetect: Uses obsolete glib12
2018-12-20 devel/liboop: Uses obsolete glib12
2018-12-20 devel/gcvs: Uses obsolete glib12
2018-12-20 print/lpr-wrapper: Uses obsolete glib12
2018-12-20 print/libppd: Uses obsolete glib12
2018-12-20 net-p2p/napshare: Uses obsolete glib12
2018-12-20 net-p2p/gnewtellium: Uses obsolete glib12
2018-12-20 editors/gnotepad+: Uses obsolete glib12
2018-12-20 editors/manedit: Uses obsolete glib12
2018-12-20 misc/gtkfind: Uses obsolete glib12
2018-12-20 games/mindguard: Uses obsolete glib12
2018-12-20 games/xbattle: Uses obsolete glib12
2018-12-20 games/xbill: Uses obsolete glib12
2018-12-20 games/corewars: Uses obsolete glib12
2018-12-20 games/dopewars: Uses obsolete glib12
2018-12-20 games/garith: Uses obsolete glib12
2018-12-20 games/wmquake: Uses obsolete glib12
2018-12-20 games/znibbles: Uses obsolete glib12
2018-12-20 games/xpuyopuyo: Uses obsolete glib12
2018-12-19 games/kajongg: Broken for more than 6 months
2018-12-20 games/netspades: Uses obsolete glib12
2018-12-20 games/gtklife: Uses obsolete glib12
2018-12-20 biology/xmolwt: Uses obsolete glib12
2018-12-20 x11-clocks/wmclockmon: Uses obsolete glib12
2018-12-20 x11-clocks/asclock-gtk: Uses obsolete glib12
2018-12-20 net-im/gale: Uses obsolete glib12
2018-12-20 audio/xmms-ahx: Uses obsolete glib12
2018-12-20 audio/xmms-curses: Uses obsolete glib12
2018-12-20 audio/scrobbler: Uses obsolete glib12
2018-12-20 audio/xmms-nsf: Uses obsolete glib12
2018-12-20 audio/xmms-nas: Uses obsolete glib12
2018-12-20 audio/xmms-gbsplay: Uses obsolete glib12
2018-12-20 audio/xmms-wavpack: Uses obsolete glib12
2018-12-20 audio/xmms-shn: Uses obsolete glib12
2018-12-20 audio/xmms-volnorm: Uses obsolete glib12
2018-12-20 audio/xmms-faad: Uses obsolete glib12
2018-12-20 audio/xmms-scrobbler: Uses obsolete glib12
2018-12-20 audio/mcplay: Uses obsolete glib12
2018-12-20 audio/gmixer: Uses obsolete glib12
2018-12-20 audio/soundtracker: Uses obsolete glib12
2018-12-20 audio/xmms-sapplug: Uses obsolete glib12
2018-12-20 audio/rio500: Uses obsolete glib12
2018-12-20 audio/xmmsctrl: Uses obsolete glib12
2018-12-20 audio/xmms-xf86audio: Uses obsolete glib12
2018-12-20 audio/xmms-mailnotify: Uses obsolete glib12
2018-12-20 audio/xmms-sexypsf: Uses obsolete glib12
2018-12-20 audio/gqmpeg: Uses obsolete glib12
2018-12-20 audio/wmalbum: Uses obsolete glib12
2018-12-20 audio/xmms-xymms: Uses obsolete glib12
2018-12-20 audio/xmms-flac: Uses obsolete glib12
2018-12-20 audio/xmms-festalon: Uses obsolete glib12
2018-12-20 audio/gkrellmms2: Uses obsolete glib12
2018-12-20 audio/xmms-ladspa: Uses obsolete glib12
2018-12-19 math/octave-forge-engine: Broken for more than 6 months
2018-12-20 math/surf: Uses obsolete glib12
2018-12-19 math/msieve: Broken for more than 6 months
2018-12-19 math/octave-forge-fl-core: Broken for more than 6 months
2018-12-19 math/octave-forge-pdb: Broken for more than 6 months
2018-12-19 math/octave-forge-audio: Broken for more than 6 months
2018-12-20 math/geg: Uses obsolete glib12
2018-12-20 math/grpn: Uses obsolete glib12
2018-12-20 x11/gdkxft: Uses obsolete glib12
2018-12-20 x11/gtk-theme-switch: Uses obsolete glib12
2018-12-19 x11/xpyb: Broken for more than 6 months
2018-12-20 x11/gtk-launch: Uses obsolete glib12
2018-12-19 x11/xpra: Broken for more than 6 months
2018-12-20 palm/pilrc: Uses obsolete glib12
2018-12-20 x11-fm/mtoolsfm: Uses obsolete glib12
2018-12-20 german/steak: Uses obsolete glib12
2018-12-20 multimedia/xmms-skins-huge: Uses obsolete glib12
2018-12-20 multimedia/openquicktime: Uses obsolete glib12
2018-12-20 multimedia/xmms-skins: Uses obsolete glib12
2018-12-20 multimedia/oqtplayer: Uses obsolete glib12
2018-12-20 multimedia/oqtencoder: Uses obsolete glib12
2018-12-20 multimedia/p5-Video-OpenQuicktime: Uses obsolete glib12
2018-12-20 multimedia/xtheater: Uses obsolete glib12
2018-12-20 multimedia/dv2jpg: Uses obsolete glib12
2018-12-20 comms/hf: Uses obsolete glib12
2018-12-20 comms/gscmxx: Uses obsolete glib12
2018-12-20 sysutils/wmcube-gdk: Uses obsolete glib12
2018-12-20 sysutils/gcombust: Uses obsolete glib12
2018-12-20 sysutils/xlogmaster: Uses obsolete glib12
2018-12-20 sysutils/mount.app: Uses obsolete glib12
2018-12-20 sysutils/bbapm: Uses obsolete glib12
2018-12-21 13:19:02 +00:00
Yuri Victorovich
a8badfa6b1 New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE 2018-12-15 08:58:05 +00:00
Joseph Mingrone
a65cd96f01 Remove biology/njplot
The author of both NJplot and SeaView says that NJplot can be considered
deprecated and replaced by SeaView.
2018-12-11 15:04:12 +00:00
Yuri Victorovich
ad4ef5b010 New port: math/checkm: Quality assessment tool for the microbial genomes 2018-12-07 00:26:04 +00:00
Yuri Victorovich
d7dad4c249 New port: math/groopm: Metagenomic binning suite 2018-12-07 00:10:05 +00:00