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* Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.Mathieu Arnold2016-03-081-2/+2
| | | | | | | | | | | | | | | Fix distinfo for the offending ports. lang/yorick's tag was moved, and the added patch was no longer needed. PR: 207644 Submitted by: mat Exp-run by by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D4268 Notes: svn path=/head/; revision=410613
* New port: biology/bowtie.Raphael Kubo da Costa2016-03-056-0/+194
| | | | | | | | | | | | | | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com> Notes: svn path=/head/; revision=410180
* New port: biology/vcftools.Raphael Kubo da Costa2016-02-265-0/+59
| | | | | | | | | | | | | A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. WWW: https://github.com/vcftools/vcftools PR: 206926 Submitted by: Jason Bacon <bacon4000@gmail.com> Notes: svn path=/head/; revision=409624
* - Update to 3.2.0Wen Heping2016-02-263-34/+62
| | | | | | | | | | - Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=409605
* - Update to 1.14.7Danilo Egea Gondolfo2016-02-202-3/+3
| | | | Notes: svn path=/head/; revision=409251
* - Update to 1.34Wen Heping2016-02-122-3/+3
| | | | Notes: svn path=/head/; revision=408731
* biology/seqtools: 4.39.3 -> 4.40.0Kurt Jaeger2016-02-062-3/+3
| | | | | | | | | | - Blixem can now accept a 'command' tag in a gff line for a region feature. The given command should return gff and will be run by blixem on the given region. - Blixem now supports fetching sequence data over https. Notes: svn path=/head/; revision=408287
* biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGSJohn Marino2016-02-011-0/+2
| | | | | | | | | Also link with libncurses, not libtermcap approved by: infrastructure blanket Notes: svn path=/head/; revision=407778
* biology/samtools: document ncurses requirement (USES+=ncurses)John Marino2016-02-011-1/+1
| | | | | | | approved by: infrastructure blanket Notes: svn path=/head/; revision=407776
* biology/molden: updated distfile, take maintainerKurt Jaeger2016-01-202-4/+4
| | | | | | | | | - upstream distfile is moving target with same version number Submitted by: antoine Notes: svn path=/head/; revision=406795
* Mark BROKEN: checksum and size mismatchAntoine Brodin2016-01-201-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=406791
* The bedtools utilities are a suite of tools for performing a wide range ofWen Heping2016-01-196-0/+135
| | | | | | | | | | | | | | | | | | | | genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. WWW: http://bedtools.readthedocs.org/ PR: 204536 Submitted by: scottcheloha@gmail.com Notes: svn path=/head/; revision=406676
* biology/molden: 5.0.7 -> 5.4Kurt Jaeger2016-01-185-192/+799
| | | | | | | | | | | | | | | | | Changes: - Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally. - Pdb files can now be clipped. - Fixes missing residues. Introduces an alternative way of generating rotamers, without using z-matrices. This potentially a faster algorithm. - Supports Movie making through avconv/ffmpeg. - calculates the Electron Localization Function (ELF). - Updated code of ambfor/ambmd to speed up optimisations/MD of proteins solvated in water (Jan, 2014). PR: 204341 Notes: svn path=/head/; revision=406605
* mark ports that don't work with Ruby 2.3Steve Wills2016-01-171-0/+1
| | | | | | | PR: 205774 Notes: svn path=/head/; revision=406285
* Convert LICENSE= "GPLxx # or later" to "GPLxx+"Dmitry Marakasov2016-01-124-4/+4
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=405891
* Add Public Domain support to ports license framework. You can now useDmitry Marakasov2016-01-121-3/+1
| | | | | | | | | | | | | | | | LICENSE= PD Note that although Public Domain is not technically a license, it's handled in the same way as licenses here, which is a common practice (Arch, Gentoo, Fedora, Debian, even FOSSology do the same). Convert all ports which redefine Public Domain LICENSE to LICENSE=PD. Approved by: portmgr (bapt) Differential Revision: D4149 Notes: svn path=/head/; revision=405874
* Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRSPawel Pekala2016-01-091-2/+0
| | | | Notes: svn path=/head/; revision=405652
* biology/crux is not jobs safeJohn Marino2015-12-301-0/+2
| | | | | | | | This cython-based port has failed on me a couple of times in a bulk build. I'm not sure what the actual problem is but the issue is itermittent. Notes: svn path=/head/; revision=404876
* biology/htslib: Replace FreeBSD-specific fix with a generic oneJohn Marino2015-12-291-5/+4
| | | | | | | | | | This port will not build if ENOTRECOVERABLE is not defined, period. It's not necessary to check OPSYS and version, just apply the fallback definition if it's not defined. This unbreaks DragonFly after last commit. Notes: svn path=/head/; revision=404749
* Cleanup GH_* and variables order.Mathieu Arnold2015-12-293-3/+1
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=404743
* biology/consed: undeprecate, it presumably builds fine but it is restricted.Rene Ladan2015-12-261-5/+1
| | | | | | | Add a note to ports/LEGAL Notes: svn path=/head/; revision=404510
* - Update to 7.266Wen Heping2015-12-255-42/+133
| | | | | | | | PR: 205558 Submitted by: cartwright@asu.edu(maintainer) Notes: svn path=/head/; revision=404405
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3Jason Unovitch2015-12-2527-173/+930
| | | | | | | | | | | | | | | | - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer) Notes: svn path=/head/; revision=404398
* mark some of the ports that don't build on powerpc64 for meSteve Wills2015-12-134-0/+7
| | | | Notes: svn path=/head/; revision=403676
* - Update maintainer mail addressMartin Wilke2015-12-1112-23/+22
| | | | | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493 Notes: svn path=/head/; revision=403506
* - Update to 1.32Wen Heping2015-12-113-6/+8
| | | | | | | | - Add LICENSE - Pet portlint Notes: svn path=/head/; revision=403479
* biology/seqtools: 4.39.2 -> 4.39.3Kurt Jaeger2015-12-052-3/+3
| | | | | | | | | | - Blixem Further improve the display of features in the detail view when they have transparent fill, making sure that they have a visible border. Notes: svn path=/head/; revision=403064
* biology/seqtools: 4.39.1 -> 4.39.2Kurt Jaeger2015-12-012-3/+3
| | | | | | | | | - Blixem: Improve the display of features in the detail view when they have transparent fill. Notes: svn path=/head/; revision=402787
* - Mark BROKEN: checksum mismatch:Dmitry Marakasov2015-11-291-0/+2
| | | | | | | fetch: http://www.platonsoft.nl/spek/xraysoft/unix/platon.tar.gz: size mismatch: expected 12080181, actual 12080357 Notes: svn path=/head/; revision=402567
* Remove expired ports:Rene Ladan2015-11-2815-933/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2015-11-26 audio/pecl-id3: Broken for more than 6 months 2015-11-26 dns/geta: Broken for more than 6 months 2015-11-26 finance/openerp-web: Broken for more than 6 months 2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream 2015-11-26 chinese/kon2: Depends on expiring chinese/cce 2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi 2015-11-26 archivers/wzip: Broken for more than 6 months 2015-11-26 databases/sybtcl: Broken for more than 6 months 2015-11-26 biology/povchem: Broken for more than 6 months 2015-11-26 audio/btc: Broken for more than 6 months 2015-11-26 astro/wmglobe: Broken for more than 6 months 2015-11-26 graphics/pyro: Broken for more than 6 months 2015-11-26 graphics/jpeg2ps: Broken for more than 6 months 2015-11-26 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Broken for more than 6 months 2015-11-26 editors/e93: Broken for more than 6 months 2015-11-26 audio/tepsonic: Broken for more than 6 months 2015-11-26 astro/ephem: Broken for more than 6 months 2015-11-26 chinese/cce: Broken for more than 6 months 2015-11-26 graphics/qcread: Broken for more than 6 months 2015-11-26 databases/py-sqlkit: Broken for more than 6 months 2015-11-26 databases/usogres: Broken for more than 6 months 2015-11-26 cad/libgeda: Broken for more than 6 months 2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months 2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months 2015-11-26 deskutils/mrundlg: Broken for more than 6 months 2015-11-26 databases/erlang-mysql: Broken for more than 6 months 2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months 2015-11-26 deskutils/akamaru: Broken for more than 6 months 2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months 2015-11-26 astro/dgpsip: Broken for more than 6 months 2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months 2015-11-26 audio/cymbaline: Broken for more than 6 months 2015-11-26 french/dico: Broken for more than 6 months 2015-11-26 comms/qpage: Broken for more than 6 months 2015-11-26 audio/sonice: Broken for more than 6 months 2015-11-26 cad/geda-symbols: Broken for more than 6 months 2015-11-26 databases/java-mybatis: Broken for more than 6 months 2015-11-26 databases/openbase-jdbc: Broken for more than 6 months 2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25 2015-11-28 www/R-cran-Rpad: Unmaintained upstream Notes: svn path=/head/; revision=402562
* biology/platon: fix fetchingRuslan Makhmatkhanov2015-11-193-6/+4
| | | | | | | | | | | | | Add working mirror. Also update file size in distinfo - checksum is not changed and I dunno why. But with old file size it warns that expected size was different. PR: 204491 Submitted by: Walter Schwarzenfeld <w.litter@aon.at> Notes: svn path=/head/; revision=401960
* - Switch to options helpersDmitry Marakasov2015-11-191-1/+1
| | | | Notes: svn path=/head/; revision=401907
* biology/seqtools: Fix distinfo, WWWKurt Jaeger2015-11-182-3/+3
| | | | | | | | | - Side effect of the seqtools automated build system Submitted by: pkg-fallout Notes: svn path=/head/; revision=401862
* biology/seqtools: 4.39.0 -> 4.39.1Kurt Jaeger2015-11-132-3/+3
| | | | | | | | - Fix a bug in Belvu where the display was being initialised in command-line-only modes. Notes: svn path=/head/; revision=401527
* - Update to 1.14.6Danilo Egea Gondolfo2015-11-093-4/+4
| | | | Notes: svn path=/head/; revision=401113
* Mark a few ports BROKEN: unfetchableAntoine Brodin2015-11-091-0/+2
| | | | Notes: svn path=/head/; revision=401096
* biology/seqtools: 4.36 -> 4.39.0Kurt Jaeger2015-11-082-3/+3
| | | | | | | | | | | | | | | | | - Blixem o There is now an optional setting to highlight "maybe-canonical" splice sites in Blixem. This can be used to help identify problems where the strand is incorrect in the input data - it highlights splice sites in a different colour if they would be canonical were they on the other strand. o Fixed a bug with colinearity lines when an alignment's cigar string contains introns. o There are now separate feedback boxes for the selected sequence name coordinates. Hover over each box to see a tooltip describing its contents. Notes: svn path=/head/; revision=401065
* - Update to 1.14.5Danilo Egea Gondolfo2015-11-063-4/+4
| | | | Notes: svn path=/head/; revision=400926
* Fix ports that confused the meaning of WRKDIR and WRKSRC.Mathieu Arnold2015-11-051-5/+5
| | | | | | | | | | | PR: 204056 Submitted by: mat Reviewed by: bapt Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D2735 Notes: svn path=/head/; revision=400848
* biology/seaview: Broken, Does not fetch (checksum mismatch)John Marino2015-11-021-0/+2
| | | | Notes: svn path=/head/; revision=400638
* - Update to 2015.09.21Guido Falsi2015-10-275-25/+60
| | | | | | | | | | | | | | | - Add License - Add SIMD option disabled by default to avoid creating official packags with CPU specific optimizations - Add pkg-message explaining how to get an optimized binary - Assign maintainership to submitter PR: 203334 Submitted by: jwbacon at tds.net Approved by: Maintainer timeout Notes: svn path=/head/; revision=400336
* Deprecate ports broken for more than 6 monthsAntoine Brodin2015-10-254-0/+8
| | | | Notes: svn path=/head/; revision=400160
* biology/seaview: Update version 4.5.4.7=>4.5.4.8Muhammad Moinur Rahman2015-10-202-3/+3
| | | | Notes: svn path=/head/; revision=399820
* - Update to 36.3.8Danilo Egea Gondolfo2015-10-162-4/+4
| | | | | | | | | | - Pass maintainership to submitter PR: 203817 Submitted by: Wendell Borges <wendell@bsd.com.br> Notes: svn path=/head/; revision=399468
* - Add LICENSE_FILEDmitry Marakasov2015-10-141-1/+2
| | | | | | | - Switch to options helpers Notes: svn path=/head/; revision=399316
* - Pet portlintDmitry Marakasov2015-10-141-4/+5
| | | | | | | | - Add LICENSE - Drop unneeded WX_UNICODE Notes: svn path=/head/; revision=399306
* - Fix typoSunpoet Po-Chuan Hsieh2015-10-101-1/+1
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=399072
* - Update to 1.14.4Danilo Egea Gondolfo2015-10-073-4/+4
| | | | Notes: svn path=/head/; revision=398730
* - Update to 1.14.3Danilo Egea Gondolfo2015-10-013-4/+4
| | | | Notes: svn path=/head/; revision=398397
* biology/seaview: Update version 4.5.4.6=>4.5.4.7Muhammad Moinur Rahman2015-10-012-4/+3
| | | | Notes: svn path=/head/; revision=398266
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