diff options
Diffstat (limited to 'biology')
37 files changed, 37 insertions, 20 deletions
diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile index 3103c1deca8a..5a6f4d7bd69d 100644 --- a/biology/bedtools/Makefile +++ b/biology/bedtools/Makefile @@ -3,7 +3,7 @@ PORTNAME= bedtools DISTVERSIONPREFIX= v DISTVERSION= 2.27.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile index 015dc7462aca..ec9032be740a 100644 --- a/biology/bowtie/Makefile +++ b/biology/bowtie/Makefile @@ -3,7 +3,7 @@ PORTNAME= bowtie DISTVERSIONPREFIX= v DISTVERSION= 1.1.2 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 3cd943b2dfca..7bc1b98e114f 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -3,7 +3,7 @@ PORTNAME= canu DISTVERSIONPREFIX= v DISTVERSION= 1.8 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology java perl5 MAINTAINER= jwb@FreeBSD.org diff --git a/biology/cd-hit/Makefile b/biology/cd-hit/Makefile index 96dea56c5b9c..b2211b7f1f9a 100644 --- a/biology/cd-hit/Makefile +++ b/biology/cd-hit/Makefile @@ -2,7 +2,7 @@ PORTNAME= cd-hit PORTVERSION= 4.6.6 -PORTREVISION= 4 +PORTREVISION= 5 DISTVERSIONPREFIX= V CATEGORIES= biology diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile index bec15cc58359..5ae938d8eae5 100644 --- a/biology/checkm/Makefile +++ b/biology/checkm/Makefile @@ -3,6 +3,7 @@ PORTNAME= CheckM DISTVERSIONPREFIX= v DISTVERSION= 1.0.12 +PORTREVISION= 1 CATEGORIES= biology python MAINTAINER= yuri@FreeBSD.org diff --git a/biology/ddocent/Makefile b/biology/ddocent/Makefile index 552701cf244f..1608e3c3d1af 100644 --- a/biology/ddocent/Makefile +++ b/biology/ddocent/Makefile @@ -3,6 +3,7 @@ PORTNAME= dDocent DISTVERSIONPREFIX= v DISTVERSION= 2.2.25 +PORTREVISION= 1 CATEGORIES= biology java MAINTAINER= jwb@FreeBSD.org diff --git a/biology/fasttree/Makefile b/biology/fasttree/Makefile index de6b7a4f25ac..f58a6794c10c 100644 --- a/biology/fasttree/Makefile +++ b/biology/fasttree/Makefile @@ -2,7 +2,7 @@ PORTNAME= FastTree DISTVERSION= 2.1.10 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= http://www.microbesonline.org/fasttree/ EXTRACT_SUFX= .c diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile index cb7ade783bc5..28de1d68e915 100644 --- a/biology/freebayes/Makefile +++ b/biology/freebayes/Makefile @@ -3,6 +3,7 @@ PORTNAME= freebayes DISTVERSIONPREFIX= v DISTVERSION= 1.2.0 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/groopm/Makefile b/biology/groopm/Makefile index c336172c89da..e564a868a7f8 100644 --- a/biology/groopm/Makefile +++ b/biology/groopm/Makefile @@ -2,6 +2,7 @@ PORTNAME= GroopM DISTVERSION= 0.3.4 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 41fbf5bf9111..929337990983 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -2,6 +2,7 @@ PORTNAME= hyphy DISTVERSION= 2.3.14-16 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g3d88d3e6 CATEGORIES= biology diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile index 33023ead0e8f..25a9f782e2c6 100644 --- a/biology/iqtree/Makefile +++ b/biology/iqtree/Makefile @@ -3,6 +3,7 @@ PORTNAME= iqtree DISTVERSIONPREFIX= v DISTVERSION= 1.6.8 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile index d6b2964c808a..4624bdea99b3 100644 --- a/biology/jellyfish/Makefile +++ b/biology/jellyfish/Makefile @@ -2,7 +2,7 @@ PORTNAME= jellyfish PORTVERSION= 2.2.6 -PORTREVISION= 3 +PORTREVISION= 4 DISTVERSIONPREFIX= v CATEGORIES= biology diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 314ff3361c9d..7be076b61d49 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -3,7 +3,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.43.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/molden/Makefile b/biology/molden/Makefile index c8dbd154042a..de667ae4196d 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -3,6 +3,7 @@ PORTNAME= molden DISTVERSION= 5.8.2 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/ diff --git a/biology/mopac/Makefile b/biology/mopac/Makefile index cd032f63a06c..5633298d79aa 100644 --- a/biology/mopac/Makefile +++ b/biology/mopac/Makefile @@ -3,7 +3,7 @@ PORTNAME= mopac PORTVERSION= 7.${MOPAC_SUBVERSION} -PORTREVISION= 5 +PORTREVISION= 6 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://bioinformatics.org/ghemical/download/%SUBDIR%/ diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index aa16ea588af7..968e767c08fe 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -4,6 +4,7 @@ PORTNAME= mummer DISTVERSIONPREFIX= v DISTVERSION= 4.0.0beta2-2 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g277dac5 CATEGORIES= biology diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index 5524ca846356..71455c0afe9e 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -2,7 +2,7 @@ PORTNAME= ncbi-blast+ DISTVERSION= 2.7.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile index 0e49364492dd..e124db31ac60 100644 --- a/biology/ncbi-cxx-toolkit/Makefile +++ b/biology/ncbi-cxx-toolkit/Makefile @@ -2,6 +2,7 @@ PORTNAME= ncbi-cxx-toolkit DISTVERSION= 21_0_0 +PORTREVISION= 1 CATEGORIES= biology science devel MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2018/Apr_2_2018/ DISTNAME= ncbi_cxx--${DISTVERSION} diff --git a/biology/p5-transdecoder/Makefile b/biology/p5-transdecoder/Makefile index f5a7bc62e9dc..fc8a034f814d 100644 --- a/biology/p5-transdecoder/Makefile +++ b/biology/p5-transdecoder/Makefile @@ -3,6 +3,7 @@ PORTNAME= transdecoder DISTVERSIONPREFIX= TransDecoder-v DISTVERSION= 5.4.0 +PORTREVISION= 1 CATEGORIES= biology perl5 PKGNAMEPREFIX= p5- diff --git a/biology/pbbam/Makefile b/biology/pbbam/Makefile index c5bcc963076b..e98562004910 100644 --- a/biology/pbbam/Makefile +++ b/biology/pbbam/Makefile @@ -2,7 +2,7 @@ PORTNAME= pbbam DISTVERSION= g20180416 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/pbcopper/Makefile b/biology/pbcopper/Makefile index 420df60fef63..f02f7ade599c 100644 --- a/biology/pbcopper/Makefile +++ b/biology/pbcopper/Makefile @@ -2,7 +2,7 @@ PORTNAME= pbcopper DISTVERSION= g20180413 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/psi88/Makefile b/biology/psi88/Makefile index 1744fc89f3f5..ec6bcd2c40eb 100644 --- a/biology/psi88/Makefile +++ b/biology/psi88/Makefile @@ -3,7 +3,7 @@ PORTNAME= psi88 PORTVERSION= 1.0 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= biology MASTER_SITES= http://www.ccl.net/cca/software/SOURCES/FORTRAN/psi88/ DISTNAME= ${PORTNAME} diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile index 3e8a8957fe72..4849b4c9f991 100644 --- a/biology/py-biom-format/Makefile +++ b/biology/py-biom-format/Makefile @@ -2,6 +2,7 @@ PORTNAME= biom-format PORTVERSION= 2.1.7 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index ae46f598508c..ae944b19deeb 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -3,6 +3,7 @@ PORTNAME= biopython PORTVERSION= 1.72 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index a7433c704654..0220bdbde74d 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -4,6 +4,7 @@ PORTNAME= bx-python DISTVERSIONPREFIX= v DISTVERSION= 0.8.2 +PORTREVISION= 1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-gtfparse/Makefile b/biology/py-gtfparse/Makefile index 6150cebe39cc..32af223f74a7 100644 --- a/biology/py-gtfparse/Makefile +++ b/biology/py-gtfparse/Makefile @@ -2,6 +2,7 @@ PORTNAME= gtfparse DISTVERSION= 1.2.0 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-loompy/Makefile b/biology/py-loompy/Makefile index f485505b53dd..aa7e10532833 100644 --- a/biology/py-loompy/Makefile +++ b/biology/py-loompy/Makefile @@ -2,6 +2,7 @@ PORTNAME= loompy DISTVERSION= 2.0.16 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-macs2/Makefile b/biology/py-macs2/Makefile index 6794a65633af..1fd1faf302bc 100644 --- a/biology/py-macs2/Makefile +++ b/biology/py-macs2/Makefile @@ -2,7 +2,7 @@ PORTNAME= macs2 PORTVERSION= 2.1.0.p20170505 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-orange3-bioinformatics/Makefile b/biology/py-orange3-bioinformatics/Makefile index 2cc6436b8272..3674aa25e8ec 100644 --- a/biology/py-orange3-bioinformatics/Makefile +++ b/biology/py-orange3-bioinformatics/Makefile @@ -2,6 +2,7 @@ PORTNAME= orange3-bioinformatics DISTVERSION= 3.2.2 +PORTREVISION= 1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile index 74a0937f737a..2290c9126a11 100644 --- a/biology/py-orange3-single-cell/Makefile +++ b/biology/py-orange3-single-cell/Makefile @@ -2,6 +2,7 @@ PORTNAME= orange3-single-cell DISTVERSION= 0.8.2 +PORTREVISION= 1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile index 6a882e6fb888..12341e799135 100644 --- a/biology/pycogent/Makefile +++ b/biology/pycogent/Makefile @@ -3,7 +3,7 @@ PORTNAME= pycogent PORTVERSION= 1.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology python MAINTAINER= python@FreeBSD.org diff --git a/biology/pyfasta/Makefile b/biology/pyfasta/Makefile index 9f49320ad1b1..b5871a0fab0d 100644 --- a/biology/pyfasta/Makefile +++ b/biology/pyfasta/Makefile @@ -3,7 +3,7 @@ PORTNAME= pyfasta PORTVERSION= 0.5.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/seqan-apps/Makefile b/biology/seqan-apps/Makefile index 4d909dca3d88..f516828857c7 100644 --- a/biology/seqan-apps/Makefile +++ b/biology/seqan-apps/Makefile @@ -4,7 +4,7 @@ PORTNAME= seqan-apps DISTVERSIONPREFIX= seqan-v DISTVERSION= 2.4.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MAINTAINER= h2+fbsdports@fsfe.org diff --git a/biology/seqtools/Makefile b/biology/seqtools/Makefile index 3e0be761bbae..cb170b829c05 100644 --- a/biology/seqtools/Makefile +++ b/biology/seqtools/Makefile @@ -2,7 +2,7 @@ PORTNAME= seqtools PORTVERSION= 4.44.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/ diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile index 6f533cb5e6e1..2ccf32888998 100644 --- a/biology/stacks/Makefile +++ b/biology/stacks/Makefile @@ -2,7 +2,7 @@ PORTNAME= stacks DISTVERSION= 1.48 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile index 6bdefba3453b..20f6ae53139b 100644 --- a/biology/t_coffee/Makefile +++ b/biology/t_coffee/Makefile @@ -4,7 +4,7 @@ PORTNAME= t_coffee PORTVERSION= 9.03 DISTVERSIONSUFFIX= .r1318 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology MASTER_SITES= http://www.tcoffee.org/Packages/Stable/Version_${PORTVERSION}${DISTVERSIONSUFFIX}/ DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX} diff --git a/biology/unanimity/Makefile b/biology/unanimity/Makefile index 1db1dd6cce01..455e46550ab5 100644 --- a/biology/unanimity/Makefile +++ b/biology/unanimity/Makefile @@ -3,7 +3,7 @@ PORTNAME= unanimity DISTVERSIONPREFIX= v DISTVERSION= 3.1.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org |