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biology/py-htseq: Python library for sequence analysis

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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.
This commit is contained in:
Jason W. Bacon 2023-07-28 10:41:58 -05:00
parent 4a76a74959
commit 505bb0df2b
4 changed files with 38 additions and 0 deletions
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1
biology/Makefile
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@ -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

30
biology/py-htseq/Makefile Normal file
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@ -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>

3
biology/py-htseq/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1690498174
SHA256 (HTSeq-2.0.3.tar.gz) = c7e7eb29bdc44e80d2d68e3599fa8a8f1d9d6475624dcf1b9644285a8a9c0fac
SIZE (HTSeq-2.0.3.tar.gz) = 394178

4
biology/py-htseq/pkg-descr Normal file
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@ -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.