diff options
Diffstat (limited to 'biology/py-pysam')
| -rw-r--r-- | biology/py-pysam/Makefile | 27 | ||||
| -rw-r--r-- | biology/py-pysam/distinfo | 6 | ||||
| -rw-r--r-- | biology/py-pysam/files/patch-setup.py | 11 | ||||
| -rw-r--r-- | biology/py-pysam/pkg-descr | 2 |
4 files changed, 26 insertions, 20 deletions
diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 2b86675e98b7..745a4a165ed1 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -1,16 +1,35 @@ PORTNAME= pysam -DISTVERSION= 0.18.0 +DISTVERSIONPREFIX= v +DISTVERSION= 0.22.1 CATEGORIES= biology python -MASTER_SITES= CHEESESHOP +#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= ${WRKSRC}/COPYING -USES= gmake python:3.6-3.9 -USE_PYTHON= autoplist distutils cython cython_run +LIB_DEPENDS= libhts.so:biology/htslib +RUN_DEPENDS= bcftools:biology/bcftools \ + samtools:biology/samtools + +USES= gmake python +USE_PYTHON= distutils autoplist cython cython_run pytest # 2 failed, 155 errors, see https://github.com/pysam-developers/pysam/issues/1284 + +USE_GITHUB= yes +GH_ACCOUNT= pysam-developers + +BINARY_ALIAS= make=${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_EXT_SUFFIX}.so .include <bsd.port.mk> diff --git a/biology/py-pysam/distinfo b/biology/py-pysam/distinfo index b85394097108..f5f1e4268139 100644 --- a/biology/py-pysam/distinfo +++ b/biology/py-pysam/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1639969328 -SHA256 (pysam-0.18.0.tar.gz) = 1d6d49a0b3c626fae410a93d4c80583a8b5ddaacc9b46a080b250dbcebd30a59 -SIZE (pysam-0.18.0.tar.gz) = 3780010 +TIMESTAMP = 1714015094 +SHA256 (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6 +SIZE (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = 3885851 diff --git a/biology/py-pysam/files/patch-setup.py b/biology/py-pysam/files/patch-setup.py deleted file mode 100644 index d82a8bbbefcf..000000000000 --- a/biology/py-pysam/files/patch-setup.py +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py.orig 2017-04-19 05:48:10 UTC -+++ setup.py -@@ -60,7 +60,7 @@ def run_configure(option): - - - def run_make_print_config(): -- stdout = subprocess.check_output(["make", "-s", "print-config"]) -+ stdout = subprocess.check_output(["gmake", "-s", "print-config"]) - if IS_PYTHON3: - stdout = stdout.decode("ascii") - diff --git a/biology/py-pysam/pkg-descr b/biology/py-pysam/pkg-descr index 199ead088d20..6e0fa2bbf118 100644 --- a/biology/py-pysam/pkg-descr +++ b/biology/py-pysam/pkg-descr @@ -6,5 +6,3 @@ module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. - -WWW: https://github.com/pysam-developers/pysam |