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* Fix PKGNAMEPREFIX of biology/ncbi-blast+, so that the resulting package isMichael Gmelin2014-12-311-1/+2
| | | | | | | | | named like the port. Approved by: mentors (implicit) Notes: svn path=/head/; revision=375866
* Rename biology/ncbi-blast to biology/ncbi-blast+Michael Gmelin2014-12-305-2/+2
| | | | | | | Approved by: mentors (implicit) Notes: svn path=/head/; revision=375848
* - Update to 5.11.0Wen Heping2014-12-303-5/+28
| | | | | | | | PR: 196377 Submitted by: koue@chaosophia.net Notes: svn path=/head/; revision=375831
* Convert to USES=autoreconfBaptiste Daroussin2014-12-281-2/+2
| | | | Notes: svn path=/head/; revision=375747
* Bump portrevision after png updateBaptiste Daroussin2014-12-253-1/+3
| | | | Notes: svn path=/head/; revision=375598
* Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgradeAntoine Brodin2014-12-253-4/+4
| | | | Notes: svn path=/head/; revision=375594
* Change my non-FreeBSD MAINTAINER mail to bofh@Muhammad Moinur Rahman2014-12-241-1/+1
| | | | | | | Approved by: bapt Notes: svn path=/head/; revision=375378
* Cleanup plistBaptiste Daroussin2014-12-207-8/+0
| | | | Notes: svn path=/head/; revision=375014
* - Upadate biology/mopac to version 1.15Pawel Pekala2014-12-166-41/+17
| | | | | | | | | | | | - Bump affected ports - Switch ports to new mastersite, add LICENSE - Reformat ports pkg descriptions PR: 194493 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=374828
* Samtools implements various utilities for post-processing alignments in thePawel Pekala2014-12-158-0/+169
| | | | | | | | | | | | | SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=374767
* HTSlib is an implementation of a unified C library for accessing common filePawel Pekala2014-12-146-0/+131
| | | | | | | | | | | | | formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. WWW: http://www.htslib.org/ PR: 195591 Submitted by: Reed A. Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=374729
* biology/seqtools: 4.30 -> 4.31Kurt Jaeger2014-12-132-3/+3
| | | | | | | Some changes to sqlite dependencies Notes: svn path=/head/; revision=374668
* - Update to 2.39Wen Heping2014-12-072-4/+3
| | | | | | | Changes: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.39/Changes Notes: svn path=/head/; revision=374175
* - Update to 0.58Wen Heping2014-12-073-8/+9
| | | | Notes: svn path=/head/; revision=374171
* - Update to 3.6.5Wen Heping2014-12-063-6/+19
| | | | | | | - Reset maintainer to ports@ Notes: svn path=/head/; revision=374114
* Update to version 1.15.0.Alexey Dokuchaev2014-12-033-16/+34
| | | | Notes: svn path=/head/; revision=373799
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-2623-125/+125
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Before, we had: site_perl : lib/perl5/site_perl/5.18 site_perl/perl_arch : lib/perl5/site_perl/5.18/mach perl_man3 : lib/perl5/5.18/man/man3 Now we have: site_perl : lib/perl5/site_perl site_arch : lib/perl5/site_perl/mach/5.18 perl_man3 : lib/perl5/site_perl/man/man3 Modules without any .so will be installed at the same place regardless of the Perl version, minimizing the upgrade when the major Perl version is changed. It uses a version dependent directory for modules with compiled bits. As PERL_ARCH is no longer needed in plists, it has been removed from PLIST_SUB. The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now always removed, as is perllocal.pod. The old site_perl and site_perl/arch directories have been kept in the default Perl @INC for all Perl ports, and will be phased out as these old Perl versions expire. PR: 194969 Differential Revision: https://reviews.freebsd.org/D1019 Exp-run by: antoine Reviewed by: perl@ Approved by: portmgr Notes: svn path=/head/; revision=373448
* biology/seqtools: 4.29 -> 4.30Kurt Jaeger2014-11-042-4/+3
| | | | | | | | | - Blixem o Fix potential crash with internal processing o Fix two bugs in data input Notes: svn path=/head/; revision=372142
* - Update to version 3.696Pawel Pekala2014-11-023-30/+18
| | | | | | | | | | | - Add LICENSE, no EXAMPLES included in distfile now - Rework pkg-descr, remove author info - it's available on homepage PR: 194163 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=372070
* Cleanup plistBaptiste Daroussin2014-10-2036-644/+0
| | | | Notes: svn path=/head/; revision=371237
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-196-16/+10
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371171
* - Fix various distinfo errorsAlex Kozlov2014-10-161-1/+0
| | | | | | | | | | | | - Remove unused USE_* knobs - Fix typos in USE_* knobs - Remove empty lines after .include <bsd.port.mk> Approved by: portmgr (bapt) Differential Revision: https://reviews.freebsd.org/D911 Notes: svn path=/head/; revision=370983
* biology/seqtools: 4.28 -> 4.29Kurt Jaeger2014-10-153-4/+3
| | | | | | | | | | | | | | - Blixem o Added the facility to run Dotter on an ad-hoc sequence (RT:408836). o Added the facility to run Dotter against a transcript. - Dotter Minimise the greyramp tool to a simple contrast slider. Use Ctrl-G to toggle between this and the full greyramp tool. - Belvu Fix a bug with tree bootstrapping in Belvu. Notes: svn path=/head/; revision=370943
* Update to version 1.14.2.Alexey Dokuchaev2014-10-133-4/+13
| | | | Notes: svn path=/head/; revision=370764
* - Update to 0.10Wen Heping2014-10-125-58/+32
| | | | | | | | PR: 194309 Submitted by: jwbacon@tds.net(maintainer) Notes: svn path=/head/; revision=370680
* Fix pkg-plistRene Ladan2014-10-081-0/+3
| | | | | | | Submitted by: bapt Notes: svn path=/head/; revision=370429
* biology/boinc-simap: clean up pkg-plistRene Ladan2014-10-081-7/+5
| | | | | | | Requested by: bapt Notes: svn path=/head/; revision=370428
* Add new port biology/ncbi-blastJohn Marino2014-10-065-0/+3961
| | | | | | | | | | | | | | | PR: 190854 Submitted by: Jason Bacon The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Notes: svn path=/head/; revision=370220
* - Update to 2.6.0Sunpoet Po-Chuan Hsieh2014-10-041-1/+1
| | | | | | | | | | | | | | | | - Update MASTER_SITES - Add my LOCAL to MASTER_SITES - Use USE_CSTD - Use MAKE_CMD - Reformat pkg-descr - Update WWW - Take maintainership - Bump PORTREVISION for devel/protobuf shlib change Changes: https://code.google.com/p/protobuf/source/browse/trunk/CHANGES.txt Notes: svn path=/head/; revision=369969
* - any version for RUN_DEPENDSDirk Meyer2014-09-211-2/+2
| | | | Notes: svn path=/head/; revision=368754
* - update RUN_DEPENDS for rubygems-dbiDirk Meyer2014-09-211-2/+2
| | | | Notes: svn path=/head/; revision=368736
* biology/boinc-simap: Deprecate, project shutting down on 2015-01-01Rene Ladan2014-09-191-0/+3
| | | | | | | Obtained from: http://boincsimap.org/boincsimap/forum_thread.php?id=88 Notes: svn path=/head/; revision=368606
* devel/glib12 x11-toolkits/gtk12:Tijl Coosemans2014-09-131-1/+1
| | | | | | | | | | - Convert to USES=libtool and bump dependent ports - Add INSTALL_TARGET=install-strip - Remove patches that renamed include directories and libraries so they didn't conflict with early development versions of glib/gtk 2.0 Notes: svn path=/head/; revision=368108
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-1018-13/+18
| | | | | | | | | | | | | to GCC 4.8.3. Part II, Bump PORTREVISIONs. PR: 192025 Tested by: antoine (-exp runs) Approved by: portmgr (implicit) Notes: svn path=/head/; revision=367888
* Fix MASTER_SITESAntoine Brodin2014-09-051-1/+1
| | | | | | | Submitted by: tijl@ Notes: svn path=/head/; revision=367328
* Second run at cleaning out non staged ports without pending PRBaptiste Daroussin2014-09-025-69/+0
| | | | Notes: svn path=/head/; revision=366995
* Remove non staged ports without pending PR from b*Baptiste Daroussin2014-09-0115-1973/+0
| | | | Notes: svn path=/head/; revision=366862
* - Update Unipro UGENE and documentation to version 1.14.0Alexey Dokuchaev2014-09-017-226/+71
| | | | | | | | | | - Remove patches integrated upstream (it's nice to have direct contact) - Sort USES and pkg-plist, cleanup Makefile a bit while here Approved by: maintainer (implicit) Notes: svn path=/head/; revision=366842
* biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanupsRene Ladan2014-08-264-46/+63
| | | | | | | | PR: 193026 Submitted by: Ports Fury Notes: svn path=/head/; revision=366266
* - StagifyDmitry Marakasov2014-08-258-3/+124
| | | | | | | - Fix build Notes: svn path=/head/; revision=366104
* update ports:Kurt Jaeger2014-08-2331-1187/+735
| | | | | | | | | | | | | | | biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=365765
* Fix build. Hopefully it doesn't break the app.Adam Weinberger2014-08-221-0/+11
| | | | Notes: svn path=/head/; revision=365607
* Fix build on -current by un-clobbering LDFLAGS. Also, don'tAdam Weinberger2014-08-152-4/+13
| | | | | | | mute installation commands. Notes: svn path=/head/; revision=364996
* - Update to 5.10.2Wen Heping2014-08-104-270/+232
| | | | | | | | PR: 192198 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=364504
* Convert the Python framework bits to USES=python.Marcus von Appen2014-08-091-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Please use USES=python instead of USE_PYTHON. USE_PYTHON=yes becomes USES=python USE_PYTHON=2.7+ becomes USES=python:2.7+ USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build ... A new PYTHON_FEATURES variable was added, which enables certain features for a port and replaces some knobs at the same time; PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX Some knobs have been deprecated and are to be removed in the near future: PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement Some knobs have been removed completely: PYTHON_MASTER_SITE_SUBDIR PYTHON_DISTNAME PYTHON_WRKSRC Several variables specific to the Python framework are no longer passed to the build environment to avoid polluting dependency builds. PYTHON_VERSION is not passed to .MAKEFLAGS anymore PYTHON_DEFAULT_VERSION, PYTHON_DEFAULT_PORTVERSION and PYTHONBASE are not passed to the make environment anymore The conversion required a couple of ports to be updated to fit the changes and new requirements. Those included "bsd.python.mk" directly or contained checks in places, for which the USES framework would fail to provide correct values. Python modules directly using the upstream Python package (such as py-tkinter or py-sqlite3) were updated to avoid using the now unnecessary and remmoved knobs from "bsd.python.mk". Phabric: D399 exp-run: 167368 192357 PR: 167368 192357 Reviewed by: antoine, wg Exp-run award: antoine With hat: python@ Approved by: portmgr Notes: svn path=/head/; revision=364450
* - Switch to USES=libtool, drop .la filesDmitry Marakasov2014-08-062-4/+4
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=364198
* USES=execinfoBaptiste Daroussin2014-08-042-6/+2
| | | | Notes: svn path=/head/; revision=364067
* biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagifyKurt Jaeger2014-08-045-217/+296
| | | | Notes: svn path=/head/; revision=363975
* biology/p5-bioperl: fix pkg-descr sidenote linkKurt Jaeger2014-08-041-1/+1
| | | | Notes: svn path=/head/; revision=363961
* Add a DOCS option.Adam Weinberger2014-08-032-5/+7
| | | | Notes: svn path=/head/; revision=363943
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