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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2023-07-28 15:41:58 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2023-07-28 15:41:58 +0000 |
| commit | 505bb0df2b00b2e9a65545764cf39855eab6bfa5 (patch) | |
| tree | 07de74943e0439ab1c01386274e3522011b806e8 /biology | |
| parent | 4a76a74959d94be943e91b2921e2d555f381b031 (diff) | |
| download | ports-505bb0df2b00b2e9a65545764cf39855eab6bfa5.tar.gz ports-505bb0df2b00b2e9a65545764cf39855eab6bfa5.zip | |
biology/py-htseq: Python library for sequence analysis
HTSeq is a Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component
of HTSeq is htseq-count, a script to quantify gene expression in bulk
and single-cell RNA-Seq and similar experiments.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-htseq/Makefile | 30 | ||||
| -rw-r--r-- | biology/py-htseq/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-htseq/pkg-descr | 4 |
4 files changed, 38 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index ecb49b10cc6c..dc020b1fd61e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -171,6 +171,7 @@ SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits + SUBDIR += py-htseq SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy diff --git a/biology/py-htseq/Makefile b/biology/py-htseq/Makefile new file mode 100644 index 000000000000..2c5ff14011da --- /dev/null +++ b/biology/py-htseq/Makefile @@ -0,0 +1,30 @@ +PORTNAME= HTSeq +DISTVERSION= 2.0.3 +CATEGORIES= biology python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Python library to facilitate programmatic analysis of sequence data +WWW= https://pypi.python.org/project/htseq/ + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ + ${PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scipy>1.5.0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.1.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4:math/py-matplotlib@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist cython distutils pytest + +post-stage: + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/HTSeq/_StepVector.cpython-39.so + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/HTSeq/_HTSeq.cpython-39.so + +.include <bsd.port.mk> diff --git a/biology/py-htseq/distinfo b/biology/py-htseq/distinfo new file mode 100644 index 000000000000..88554006d541 --- /dev/null +++ b/biology/py-htseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1690498174 +SHA256 (HTSeq-2.0.3.tar.gz) = c7e7eb29bdc44e80d2d68e3599fa8a8f1d9d6475624dcf1b9644285a8a9c0fac +SIZE (HTSeq-2.0.3.tar.gz) = 394178 diff --git a/biology/py-htseq/pkg-descr b/biology/py-htseq/pkg-descr new file mode 100644 index 000000000000..afafda9c12f4 --- /dev/null +++ b/biology/py-htseq/pkg-descr @@ -0,0 +1,4 @@ +HTSeq is a Python library to facilitate programmatic analysis of data +from high-throughput sequencing (HTS) experiments. A popular component +of HTSeq is htseq-count, a script to quantify gene expression in bulk +and single-cell RNA-Seq and similar experiments. |