diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/libsbml/Makefile | 2 | ||||
| -rw-r--r-- | biology/py-biom-format/Makefile | 10 | ||||
| -rw-r--r-- | biology/py-biopython/Makefile | 2 | ||||
| -rw-r--r-- | biology/py-bx-python/Makefile | 2 | ||||
| -rw-r--r-- | biology/py-cutadapt/Makefile | 2 | ||||
| -rw-r--r-- | biology/py-pysam/Makefile | 5 | ||||
| -rw-r--r-- | biology/pycogent/Makefile | 7 | ||||
| -rw-r--r-- | biology/pyfasta/Makefile | 1 | ||||
| -rw-r--r-- | biology/python-nexus/Makefile | 1 |
9 files changed, 15 insertions, 17 deletions
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 6ae00f67c805..4ef28a036795 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -27,7 +27,7 @@ OPTIONS_SUB= yes PLIST_SUB+= PORTVERSION=${PORTVERSION} PYTHON_BUILD_DEPENDS= swig2.0:devel/swig20 -PYTHON_USES= python +PYTHON_USES= python:2.7 PYTHON_CMAKE_ON= -DWITH_PYTHON:BOOL=ON \ -DPYTHON_INCLUDE_DIR:STRING="${PYTHON_INCLUDEDIR}" \ -DPYTHON_LIBRARY:STRING="${PYTHONBASE}/lib/lib${PYTHON_VERSION}.so" \ diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile index 03b3d210cc32..0c7c567cdafe 100644 --- a/biology/py-biom-format/Makefile +++ b/biology/py-biom-format/Makefile @@ -13,10 +13,10 @@ LICENSE= BSD3CLAUSE BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}h5py>=2.6.0:science/py-h5py \ - ${PYTHON_PKGNAMEPREFIX}click>=6.6:devel/py-click \ - ${PYTHON_PKGNAMEPREFIX}future>=0.15.2:devel/py-future \ - ${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy + ${PYTHON_PKGNAMEPREFIX}h5py>=2.6.0:science/py-h5py@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}click>=6.6:devel/py-click@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}future>=0.15.2:devel/py-future@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy@${FLAVOR} USE_GITHUB= yes GH_ACCOUNT= biocore @@ -27,7 +27,7 @@ USE_PYTHON= autoplist distutils .include <bsd.port.pre.mk> .if ${PYTHON_REL} < 3000 -RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pyqi>=0.2.0:devel/py-pyqi +RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pyqi>=0.2.0:devel/py-pyqi@${FLAVOR} .endif post-install: diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index c893687ef364..edc8c7a1e2ef 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -20,6 +20,6 @@ OPTIONS_DEFINE= REPORTLAB OPTIONS_DEFAULT= REPORTLAB REPORTLAB_DESC= PDF support in Bio.Graphics module -REPORTLAB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1 +REPORTLAB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1@${FLAVOR} .include <bsd.port.mk> diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index 89ccb9749a3e..0a11dd8824da 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -14,7 +14,7 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo + ${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo@${FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} USE_GITHUB= yes diff --git a/biology/py-cutadapt/Makefile b/biology/py-cutadapt/Makefile index 0d215ac15be5..863a1ee70ab2 100644 --- a/biology/py-cutadapt/Makefile +++ b/biology/py-cutadapt/Makefile @@ -12,7 +12,7 @@ COMMENT= Finds and removes adapter sequences, primers, poly-A tails, etc LICENSE= MIT -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen@${FLAVOR} USES= python USE_PYTHON= distutils diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 6bcbc6e2584e..afec069f8422 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -12,11 +12,8 @@ COMMENT= Python module for reading, manipulating and writing genomic data sets LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING -BUILD_DEPENDS= cython:lang/cython -RUN_DEPENDS= cython:lang/cython - USES= gmake python -USE_PYTHON= autoplist distutils +USE_PYTHON= autoplist distutils cython cython_run post-install: ${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/*.so diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile index f0725592332c..a70e2e31f00c 100644 --- a/biology/pycogent/Makefile +++ b/biology/pycogent/Makefile @@ -11,13 +11,12 @@ COMMENT= Toolkit for statistical analysis of biological sequences LICENSE= GPLv2 BUILD_DEPENDS= ${PYNUMPY} \ - ${LOCALBASE}/bin/cython:lang/cython \ - ${LOCALBASE}/bin/sphinx-build:textproc/py-sphinx \ - ${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=1.0.13:databases/py-sqlalchemy10 + ${LOCALBASE}/bin/sphinx-build:textproc/py-sphinx@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=1.0.13:databases/py-sqlalchemy10@${FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} USES= python:-2.7 USE_GITHUB= yes -USE_PYTHON= distutils autoplist +USE_PYTHON= distutils autoplist cython .include <bsd.port.mk> diff --git a/biology/pyfasta/Makefile b/biology/pyfasta/Makefile index 2c7d49cd2532..c06752787757 100644 --- a/biology/pyfasta/Makefile +++ b/biology/pyfasta/Makefile @@ -6,6 +6,7 @@ PORTVERSION= 0.5.2 PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Fast, memory-efficient, pythonic access to fasta sequence files diff --git a/biology/python-nexus/Makefile b/biology/python-nexus/Makefile index c55243d5e23a..bf0cb8d97943 100644 --- a/biology/python-nexus/Makefile +++ b/biology/python-nexus/Makefile @@ -5,6 +5,7 @@ PORTNAME= python-nexus PORTVERSION= 1.53 CATEGORIES= biology python MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Generic nexus file format reader for python |