git: 505bb0df2b00 - main - biology/py-htseq: Python library for sequence analysis

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=505bb0df2b00b2e9a65545764cf39855eab6bfa5

commit 505bb0df2b00b2e9a65545764cf39855eab6bfa5
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-07-28 15:41:58 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-07-28 15:41:58 +0000

    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.
---
 biology/Makefile           |  1 +
 biology/py-htseq/Makefile  | 30 ++++++++++++++++++++++++++++++
 biology/py-htseq/distinfo  |  3 +++
 biology/py-htseq/pkg-descr |  4 ++++
 4 files changed, 38 insertions(+)

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.