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PORTNAME= pysam
DISTVERSIONPREFIX= v
DISTVERSION= 0.24.0
CATEGORIES= biology python
#MASTER_SITES= PYPI # no tests
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Python module for reading, manipulating and writing genomic data sets
WWW= https://github.com/pysam-developers/pysam
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/COPYING
LIB_DEPENDS= libhts.so:biology/htslib
RUN_DEPENDS= bcftools:biology/bcftools \
samtools:biology/samtools
USES= gmake python
USE_PYTHON= distutils autoplist cython cython_run pytest # 2 failed, 155 errors, see https://github.com/pysam-developers/pysam/issues/1284
USE_GITHUB= yes
GH_ACCOUNT= pysam-developers
BINARY_ALIAS= make=${GMAKE}
MAKE_ENV= HTSLIB_MODE=external \
HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \
HTSLIB_INCLUDE_DIR=${LOCALBASE}/include
TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
TEST_WRKSRC= ${WRKSRC}/tests
post-install:
@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_TAG}.so
# tests as of 0.23.0: 958 passed, 13 skipped, 1 warning in 502.60s (0:08:22)
# tests as of 0.24.0:
# Results (28.09s):
# 977 passed
# 16 skipped
.include <bsd.port.mk>
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