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* misc/otter & biology/ariadne: Not jobs safeJohn Marino2015-01-211-0/+2
| | | | | | | | | The otter port tries to build libotter.a before an object is completely built (share.o in my case) and ariadne tries to start building in a directory before it is created (under multiple jobs). Notes: svn path=/head/; revision=377623
* biology/py-biopython:Max Brazhnikov2015-01-191-3/+5
| | | | | | | | | - Convert to options framework Approved by: portmgr blanket Notes: svn path=/head/; revision=377466
* Designatate 4 ports as unsafe for parallel buildingJohn Marino2015-01-191-0/+1
| | | | | | | | | All had similar errors that it couldn't find something during the build, yet built on a subsequent pass with no adjustments. Most I've seen before on previous bulk runs. Notes: svn path=/head/; revision=377443
* - Pass maintainership to submitterWen Heping2015-01-191-1/+1
| | | | | | | | PR: 196859 Submitted by: Joseph Mingrone<jrm@ftfl.ca> Notes: svn path=/head/; revision=377397
* - Simplify MakefileSunpoet Po-Chuan Hsieh2015-01-182-135/+130
| | | | | | | | | - Use tab instead of space - Sort PLIST - Pass maintainership to perl@ Notes: svn path=/head/; revision=377369
* - Update to 1.13.8Danilo Egea Gondolfo2015-01-143-4/+4
| | | | Notes: svn path=/head/; revision=377013
* Mark BROKEN: UnfetchableAntoine Brodin2015-01-101-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=376682
* Update to version 1.15.1.Alexey Dokuchaev2015-01-063-10/+10
| | | | Notes: svn path=/head/; revision=376383
* biology/tinker: 6.2.6 -> 7.0.1Kurt Jaeger2015-01-046-65/+94
| | | | | | | | PR: 196376 Submitted by: Nikola Kolev <koue@chaosophia.net> Notes: svn path=/head/; revision=376238
* - Convert USE_PYTHON -> USES leftovers missed in the previous commitsMarcus von Appen2015-01-041-1/+1
| | | | | | | | Spotted by: antoine With hat: python Notes: svn path=/head/; revision=376179
* Update to upstream version 36Thomas Zander2015-01-012-7/+6
| | | | | | | | PR: 196339 Submitted by: koue@chaosophia.net Notes: svn path=/head/; revision=376018
* Remove expired ports:Rene Ladan2015-01-017-166/+0
| | | | | | | | | | 2015-01-01 biology/boinc-simap: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88 2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will be removed. There is no real need for foot-shooting. 2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead 2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa package instead Notes: svn path=/head/; revision=375913
* 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
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