diff options
Diffstat (limited to 'biology')
35 files changed, 40 insertions, 20 deletions
diff --git a/biology/L-Breeder/Makefile b/biology/L-Breeder/Makefile index 39c96044318d..0c6fbc1f92c3 100644 --- a/biology/L-Breeder/Makefile +++ b/biology/L-Breeder/Makefile @@ -8,7 +8,7 @@ PORTNAME= LBreeder PORTVERSION= 1.0 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= biology MASTER_SITES= http://www.simonyi.ox.ac.uk/dawkins/software/yan/L-Breeder/ DISTNAME= ${PORTNAME}-source diff --git a/biology/adun/Makefile b/biology/adun/Makefile index 70118deea485..7491feeaedac 100644 --- a/biology/adun/Makefile +++ b/biology/adun/Makefile @@ -7,6 +7,7 @@ PORTNAME= adun PORTVERSION= 0.6 +PORTREVISION= 1 CATEGORIES= biology gnustep MASTER_SITES= http://download.gna.org/adun/ DISTNAME= Adun${PORTVERSION} diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile index c4998b28dd7c..ee85444fc5ef 100644 --- a/biology/artemis/Makefile +++ b/biology/artemis/Makefile @@ -7,7 +7,7 @@ PORTNAME= artemis PORTVERSION= 7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology java MASTER_SITES= http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/ DISTNAME= artemis_compiled_v${PORTVERSION}_${PORTREVISION} diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo index 804338297593..3355a8ea32d4 100644 --- a/biology/artemis/distinfo +++ b/biology/artemis/distinfo @@ -1,3 +1,3 @@ -MD5 (artemis_compiled_v7_1.tar.gz) = f81f52a99a7c7b40c2a5289e71e0ea03 -SHA256 (artemis_compiled_v7_1.tar.gz) = d770c48464be5903107379775765883f7827833be7339d90d3dc8e1430c0646e -SIZE (artemis_compiled_v7_1.tar.gz) = 4055125 +MD5 (artemis_compiled_v7_2.tar.gz) = f81f52a99a7c7b40c2a5289e71e0ea03 +SHA256 (artemis_compiled_v7_2.tar.gz) = d770c48464be5903107379775765883f7827833be7339d90d3dc8e1430c0646e +SIZE (artemis_compiled_v7_2.tar.gz) = 4055125 diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile index 92374d11797d..c49584bbd5cb 100644 --- a/biology/biococoa/Makefile +++ b/biology/biococoa/Makefile @@ -7,6 +7,7 @@ PORTNAME= biococoa PORTVERSION= 1.6.0 +PORTREVISION= 1 CATEGORIES= biology gnustep MASTER_SITES= ${MASTER_SITE_DEBIAN} MASTER_SITE_SUBDIR= pool/main/b/biococoa.app diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile index 5b27da842616..9d693b4d5072 100644 --- a/biology/biojava/Makefile +++ b/biology/biojava/Makefile @@ -7,6 +7,7 @@ PORTNAME= biojava DISTVERSION= 1.5-beta2 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology java MASTER_SITES= http://www.biojava.org/download/bj15b/all/:source \ diff --git a/biology/boinc-simap/Makefile b/biology/boinc-simap/Makefile index b765a9f23046..4c9da0ba6961 100644 --- a/biology/boinc-simap/Makefile +++ b/biology/boinc-simap/Makefile @@ -6,6 +6,7 @@ PORTNAME= boinc-simap PORTVERSION= ${SIMAP_VERSION}.${HMMER_VERSION} +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://boinc.bio.wzw.tum.de/boincsimap/download/ DISTNAME= ${SIMAP_BINARY} ${HMMER_BINARY} diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile index bdabee8ee1b0..93d67cee5f74 100644 --- a/biology/embassy/Makefile +++ b/biology/embassy/Makefile @@ -8,6 +8,7 @@ PORTNAME= embassy PORTVERSION= 3.0.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \ ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 2fdecddae40f..bc9016cc0d67 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -7,6 +7,7 @@ PORTNAME= emboss PORTVERSION= 3.0.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \ ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile index 7a6a15a906d3..210279060ebc 100644 --- a/biology/garlic/Makefile +++ b/biology/garlic/Makefile @@ -7,6 +7,7 @@ PORTNAME= garlic PORTVERSION= 1.5 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://garlic.mefos.hr/sources/garlic-${PORTVERSION}/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} diff --git a/biology/genpak/Makefile b/biology/genpak/Makefile index 7e71a07bd9c8..3ac7d7c088f2 100644 --- a/biology/genpak/Makefile +++ b/biology/genpak/Makefile @@ -8,7 +8,7 @@ PORTNAME= genpak PORTVERSION= 0.26 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology MASTER_SITES= http://www.bioinformatics.org/genpak/download/ DISTNAME= gp-${PORTVERSION} diff --git a/biology/gperiodic/Makefile b/biology/gperiodic/Makefile index e3d318199230..e49c771662a2 100644 --- a/biology/gperiodic/Makefile +++ b/biology/gperiodic/Makefile @@ -7,7 +7,7 @@ PORTNAME= gperiodic PORTVERSION= 2.0.8 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology MASTER_SITES= http://koti.welho.com/jfrantz/software/ diff --git a/biology/gperiodic/pkg-plist b/biology/gperiodic/pkg-plist index eaf00bcb6513..db8a172e1e3b 100644 --- a/biology/gperiodic/pkg-plist +++ b/biology/gperiodic/pkg-plist @@ -11,5 +11,3 @@ share/locale/pl/LC_MESSAGES/gperiodic.mo share/locale/sv/LC_MESSAGES/gperiodic.mo share/locale/tr/LC_MESSAGES/gperiodic.mo %%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrmtry share/locale/pl/LC_MESSAGES -@dirrmtry share/locale/pl diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile index 9596bb7d00e5..f7f974292de0 100644 --- a/biology/jalview/Makefile +++ b/biology/jalview/Makefile @@ -7,6 +7,7 @@ PORTNAME= jalview PORTVERSION= 2.07 +PORTREVISION= 1 CATEGORIES= biology java MASTER_SITES= http://www.jalview.org/source/ DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/} diff --git a/biology/kinemage/Makefile b/biology/kinemage/Makefile index 4cdf21027885..aaee515e2745 100644 --- a/biology/kinemage/Makefile +++ b/biology/kinemage/Makefile @@ -7,6 +7,7 @@ PORTNAME= kinemage PORTVERSION= 5.79 +PORTREVISION= 1 CATEGORIES= biology # There is no distfile to fetch here, just a dir of badly formatted sources #MASTER_SITES= ftp://kinemage.biochem.duke.edu/OPEN_SOURCE/ diff --git a/biology/lsysexp/Makefile b/biology/lsysexp/Makefile index 383d1e411121..dac8bf722cde 100644 --- a/biology/lsysexp/Makefile +++ b/biology/lsysexp/Makefile @@ -7,7 +7,7 @@ PORTNAME= lsysexp PORTVERSION= 0.67 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MASTER_SITES= http://coscorrosa.com/programs/${PORTNAME}/download/ \ http://freebsd.unixfreunde.de/sources/ diff --git a/biology/molden/Makefile b/biology/molden/Makefile index e3f721e4a781..1d8b3661b115 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -7,6 +7,7 @@ PORTNAME= molden PORTVERSION= 4.5 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/ DISTNAME= ${PORTNAME}${PORTVERSION} diff --git a/biology/molden/distinfo b/biology/molden/distinfo index 040963ee046e..7268a4f6579c 100644 --- a/biology/molden/distinfo +++ b/biology/molden/distinfo @@ -1,3 +1,3 @@ -MD5 (molden-4.5/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834 -SHA256 (molden-4.5/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7 -SIZE (molden-4.5/molden4.5.tar.Z) = 3605279 +MD5 (molden-4.5_1/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834 +SHA256 (molden-4.5_1/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7 +SIZE (molden-4.5_1/molden4.5.tar.Z) = 3605279 diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index 643c83de3c40..ba50ca954b8b 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -8,6 +8,7 @@ PORTNAME= ncbi-toolkit PORTVERSION= 2006.05.07 # containing BLAST v2.2.14 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile index ff7ae0854f05..868337eaa4da 100644 --- a/biology/p5-Bio-Das/Makefile +++ b/biology/p5-Bio-Das/Makefile @@ -7,6 +7,7 @@ PORTNAME= Bio-Das PORTVERSION= 1.03 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://www.biodas.org/download/Bio::Das/ \ ${MASTER_SITE_PERL_CPAN} diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile index 96d4d20471e8..3cd6454e72a8 100644 --- a/biology/p5-Bio-Phylo/Makefile +++ b/biology/p5-Bio-Phylo/Makefile @@ -7,6 +7,7 @@ PORTNAME= Bio-Phylo PORTVERSION= 0.15 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= ${MASTER_SITE_PERL_CPAN} MASTER_SITE_SUBDIR= Bio diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile index a5bedc037594..ec32aeaa90a4 100644 --- a/biology/p5-bioperl-devel/Makefile +++ b/biology/p5-bioperl-devel/Makefile @@ -7,6 +7,7 @@ PORTNAME= bioperl PORTVERSION= 1.5.1 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ PKGNAMEPREFIX= p5- diff --git a/biology/p5-bioperl-run-devel/Makefile b/biology/p5-bioperl-run-devel/Makefile index b6738ab318ac..10d10f59033b 100644 --- a/biology/p5-bioperl-run-devel/Makefile +++ b/biology/p5-bioperl-run-devel/Makefile @@ -7,6 +7,7 @@ PORTNAME= bioperl-run PORTVERSION= 1.5.1 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ PKGNAMEPREFIX= p5- @@ -14,7 +15,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= mauricio@arareko.net COMMENT= Wrapper modules for common bioinformatics tools (developer release) -BUILD_DEPENDS= p5-bioperl=1.5.1:${PORTSDIR}/biology/p5-bioperl-devel \ +BUILD_DEPENDS= p5-bioperl=1.5.1_1:${PORTSDIR}/biology/p5-bioperl-devel \ ${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff RUN_DEPENDS= ${BUILD_DEPENDS} diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile index 2e81e0d0d882..2decb02726d5 100644 --- a/biology/p5-bioperl-run/Makefile +++ b/biology/p5-bioperl-run/Makefile @@ -7,6 +7,7 @@ PORTNAME= bioperl-run PORTVERSION= 1.4 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ \ ${MASTER_SITE_PERL_CPAN} @@ -15,7 +16,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= mauricio@arareko.net COMMENT= Wrapper modules for common bioinformatics tools -BUILD_DEPENDS= p5-bioperl=1.4:${PORTSDIR}/biology/p5-bioperl \ +BUILD_DEPENDS= p5-bioperl=1.4_1:${PORTSDIR}/biology/p5-bioperl \ ${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff RUN_DEPENDS= ${BUILD_DEPENDS} diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile index ef6f01a65d10..7b2cbc1d6974 100644 --- a/biology/p5-bioperl/Makefile +++ b/biology/p5-bioperl/Makefile @@ -7,6 +7,7 @@ PORTNAME= bioperl PORTVERSION= 1.4 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ \ ${MASTER_SITE_PERL_CPAN} diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index bfd1b0407eb5..9e21481d7033 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -7,6 +7,7 @@ PORTNAME= phylip PORTVERSION= 3.66 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ \ diff --git a/biology/platon/Makefile b/biology/platon/Makefile index fe2338f4610c..2fa1e0481200 100644 --- a/biology/platon/Makefile +++ b/biology/platon/Makefile @@ -7,6 +7,7 @@ PORTNAME= platon PORTVERSION= 2007.01.09 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://xraysoft.chem.uu.nl/pub/unix/ DISTNAME= platon diff --git a/biology/povchem/Makefile b/biology/povchem/Makefile index 0536e1e852a8..b6e9d4d064fd 100644 --- a/biology/povchem/Makefile +++ b/biology/povchem/Makefile @@ -7,7 +7,7 @@ PORTNAME= povchem PORTVERSION= 1.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology graphics MASTER_SITES= http://www.chemicalgraphics.com/paul/PC_Dist/v1.00/ DISTFILES= povchem.c \ diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile index 39252c9bd9f7..dd40c86556d6 100644 --- a/biology/protomol/Makefile +++ b/biology/protomol/Makefile @@ -6,6 +6,7 @@ PORTNAME= protomol PORTVERSION= 2.0.3 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} MASTER_SITE_SUBDIR= ${PORTNAME} diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index cc0bf319a59d..77cc58f9e6f3 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -6,6 +6,7 @@ PORTNAME= pymol PORTVERSION= 0.99rc6 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} MASTER_SITE_SUBDIR= pymol diff --git a/biology/rasmol/Makefile b/biology/rasmol/Makefile index 93283da28967..bea4f4e3a1b6 100644 --- a/biology/rasmol/Makefile +++ b/biology/rasmol/Makefile @@ -7,6 +7,7 @@ PORTNAME= rasmol PORTVERSION= 2.7.2.1.1 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.bernstein-plus-sons.com/software/ DISTNAME= RasMol_${PORTVERSION} diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index e1b630d628b0..6cbc32c036b4 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -8,7 +8,7 @@ PORTNAME= seaview PORTVERSION= 2006.02.13 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ DISTNAME= ${PORTNAME}${PORTVERSION:S/.//g} diff --git a/biology/treeviewx/Makefile b/biology/treeviewx/Makefile index 5b835cd769a3..44d599a230a8 100644 --- a/biology/treeviewx/Makefile +++ b/biology/treeviewx/Makefile @@ -8,7 +8,7 @@ PORTNAME= treeviewx PORTVERSION= 0.5.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/${PORTVERSION:S/.1//}/ DISTNAME= tv-${PORTVERSION} diff --git a/biology/xdrawchem/Makefile b/biology/xdrawchem/Makefile index 3fe6f3d62af0..5d37c87ca9a8 100644 --- a/biology/xdrawchem/Makefile +++ b/biology/xdrawchem/Makefile @@ -7,7 +7,7 @@ PORTNAME= xdrawchem PORTVERSION= 1.9.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} MASTER_SITE_SUBDIR= xdrawchem diff --git a/biology/xmolwt/Makefile b/biology/xmolwt/Makefile index 0ce0b99716ff..519a59dcf0c8 100644 --- a/biology/xmolwt/Makefile +++ b/biology/xmolwt/Makefile @@ -6,7 +6,7 @@ PORTNAME= xmolwt PORTVERSION= 0.7 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= http://www.st.hirosaki-u.ac.jp/~rmiya/xmolwt/ |