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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSAlexey Dokuchaev2018-01-111-2/+4
| | | | | | | | | when it was missing) - Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN - Fix some whitespace and formatting bugs along the way Notes: svn path=/head/; revision=458761
* 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
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-261-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-191-1/+1
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371171
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...Adam Weinberger2014-07-291-2/+1
| | | | | | | Approved by: portmgr (not really, but touches unstaged ports) Notes: svn path=/head/; revision=363374
* Fix shebang line in Perl and Python scripts.Raphael Kubo da Costa2014-06-201-13/+6
| | | | | | | | PR: 191146 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358567
* Update to 1.2.10.Raphael Kubo da Costa2014-06-173-35/+23
| | | | | | | | PR: 191129 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358183
* - add stage supportOlli Hauer2014-06-011-12/+6
| | | | Notes: svn path=/head/; revision=356099
* - Convert USE_GMAKE to USESMartin Wilke2014-03-131-2/+1
| | | | Notes: svn path=/head/; revision=348042
* Remove trailing whitespaces from category biologyEmanuel Haupt2014-02-211-1/+1
| | | | Notes: svn path=/head/; revision=345397
* According to the Porter's Handbook (5.12.2.3.) default options must be added toEmanuel Haupt2014-02-101-0/+2
| | | | | | | | | | | | | | OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) Notes: svn path=/head/; revision=343634
* Convert biology to MDOCS and MEXAMPLESAdam Weinberger2014-01-031-1/+4
| | | | Notes: svn path=/head/; revision=338550
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-5/+2
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - convert to the new perl5 frameworkAndrej Zverev2013-09-071-1/+2
| | | | | | | Approved by: portmgr (bapt@, blanket) Notes: svn path=/head/; revision=326575
* Update to 1.1.04Julien Laffaye2011-06-095-126/+35
| | | | | | | | | PR: ports/157527 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Approved by: bapt (mentor) Notes: svn path=/head/; revision=275282
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Velvet is a de novo genomic assembler specially designed for short readDmitry Marakasov2009-11-076-0/+243
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Notes: svn path=/head/; revision=243919
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