diff --git a/biology/py-bcbio-gff/Makefile b/biology/py-bcbio-gff/Makefile index 325a33a56077..2a3b0260c9fd 100644 --- a/biology/py-bcbio-gff/Makefile +++ b/biology/py-bcbio-gff/Makefile @@ -1,19 +1,17 @@ PORTNAME= bcbio-gff DISTVERSION= 0.7.1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Read and write Generic Feature Format (GFF) with Biopython integration -WWW= https://pypi.org/project/bcbio-gff/ \ - https://biopython.org/wiki/GFF_Parsing \ - https://github.com/chapmanb/bcbb/tree/master/gff/ +WWW= https://github.com/chapmanb/bcbb/tree/master/gff/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= python USE_PYTHON= autoplist distutils .include diff --git a/biology/py-dna-features-viewer/Makefile b/biology/py-dna-features-viewer/Makefile index 906de191ad5d..faefb8faf5e8 100644 --- a/biology/py-dna-features-viewer/Makefile +++ b/biology/py-dna-features-viewer/Makefile @@ -1,23 +1,23 @@ PORTNAME= dna-features-viewer DISTVERSION= 3.1.3 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= dna_features_viewer-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Python library to visualize DNA features, e.g. GenBank or Gff files -WWW= https://pypi.python.org/project/dna-features-viewer/ +WWW= https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENCE.txt RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=3:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}bcbio-gff>0:biology/py-bcbio-gff@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} USES= python USE_PYTHON= autoplist distutils .include diff --git a/biology/py-dnaio/Makefile b/biology/py-dnaio/Makefile index 6dc8951da918..3baff38a1558 100644 --- a/biology/py-dnaio/Makefile +++ b/biology/py-dnaio/Makefile @@ -1,22 +1,22 @@ PORTNAME= dnaio DISTVERSION= 1.2.3 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Read and write FASTQ and FASTA -WWW= https://pypi.python.org/pypi/dnaio +WWW= https://github.com/marcelm/dnaio/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cython3>0:lang/cython3@${PY_FLAVOR} USES= python USE_PYTHON= autoplist pep517 .include diff --git a/biology/py-goatools/Makefile b/biology/py-goatools/Makefile index ef6eba5004f8..44c8f67d9ffd 100644 --- a/biology/py-goatools/Makefile +++ b/biology/py-goatools/Makefile @@ -1,31 +1,31 @@ PORTNAME= goatools DISTVERSION= 1.1.6 PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for processing and visualizing Gene Ontology terms -WWW= https://pypi.python.org/pypi/goatools +WWW= https://github.com/tanghaibao/goatools/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE # xlrd should be == 1.2.0 RUN_DEPENDS= ${PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}XlsxWriter>0:textproc/py-xlsxwriter@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>0:math/py-statsmodels@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xlrd>0:textproc/py-xlrd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}docopt>0:devel/py-docopt@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydot>0:graphics/py-pydot@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygraphviz>0:graphics/py-pygraphviz@${PY_FLAVOR} \ wget>0:ftp/wget USES= python USE_PYTHON= autoplist distutils .include diff --git a/biology/py-ont-fast5-api/Makefile b/biology/py-ont-fast5-api/Makefile index e154ea248556..9ead9df1cde1 100644 --- a/biology/py-ont-fast5-api/Makefile +++ b/biology/py-ont-fast5-api/Makefile @@ -1,44 +1,44 @@ PORTNAME= ont-fast5-api DISTVERSIONPREFIX= release_ DISTVERSION= 4.0.2 PORTREVISION= 1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Interface to HDF5 files in Oxford Nanopore .fast5 format -WWW= https://pypi.python.org/pypi/ont_fast5_api +WWW= https://github.com/nanoporetech/ont_fast5_api/ LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.md LIB_DEPENDS= libvbz_hdf_plugin.so:archivers/vbz-compression RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}progressbar>0:misc/py-progressbar@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>=0:devel/py-pip@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent distutils USE_GITHUB= yes GH_ACCOUNT= nanoporetech GH_PROJECT= ont_fast5_api NO_ARCH= yes NO_BUILD= yes post-patch: ${RM} ${WRKSRC}/ont_fast5_api/vbz_plugin/* pre-configure: @${REINPLACE_CMD} -e 's|progressbar33|progressbar|g' \ ${WRKSRC}/setup.py \ ${WRKSRC}/README.rst \ ${WRKSRC}/ont_fast5_api/conversion_tools/conversion_utils.py do-test: @cd ${WRKSRC} && ${PYTHON_CMD} ${PYDISTUTILS_SETUP} test .include diff --git a/biology/py-pybigwig/Makefile b/biology/py-pybigwig/Makefile index 76d160a9e818..2bdae8095d8b 100644 --- a/biology/py-pybigwig/Makefile +++ b/biology/py-pybigwig/Makefile @@ -1,22 +1,22 @@ PORTNAME= pyBigWig DISTVERSION= 0.3.22 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Python access to bigWig files using libBigWig -WWW= https://pypi.org/project/pyBigWig/ +WWW= https://github.com/deeptools/pyBigWig/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libcurl.so:ftp/curl USES= localbase python USE_PYTHON= autoplist distutils post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyBigWig*.so .include diff --git a/biology/py-pywgsim/Makefile b/biology/py-pywgsim/Makefile index 14bc3cbb17ba..e255e8a1fbc6 100644 --- a/biology/py-pywgsim/Makefile +++ b/biology/py-pywgsim/Makefile @@ -1,22 +1,22 @@ PORTNAME= pywgsim DISTVERSION= 0.5.2 PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Modified wgsim genomic data simulator -WWW= https://pypi.python.org/pypi/pywgsim +WWW= https://github.com/ialbert/pywgsim/ LICENSE= MIT RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}plac>=0:devel/py-plac@${PY_FLAVOR} USES= python USE_PYTHON= autoplist cython distutils post-configure: cython-${PYTHON_VER} ${WRKSRC}/pywgsim/wgsim_lib.pyx .include