git: 5797d6a3298e - main - biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5797d6a3298ebfe3990db73084f34ed935911efa

commit 5797d6a3298ebfe3990db73084f34ed935911efa
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-13 13:34:09 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-08-13 13:34:09 +0000

    biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
    
    The ont_fast5_api is a simple interface to HDF5 files of the Oxford
    Nanopore .fast5 file format. It provides:
    
        o Implementation of the fast5 file schema using h5py library
        o Methods to interact with and reflect the fast5 file schema
        o Tools to convert between multi_read and single_read formats
        o Tools to compress/decompress raw data in files
---
 biology/Makefile                   |  1 +
 biology/py-ont-fast5-api/Makefile  | 42 ++++++++++++++++++++++++++++++++++++++
 biology/py-ont-fast5-api/distinfo  |  3 +++
 biology/py-ont-fast5-api/pkg-descr |  9 ++++++++
 4 files changed, 55 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 60ab10072e29..13f0cd294ee5 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -144,6 +144,7 @@
     SUBDIR += py-loompy
     SUBDIR += py-macs2
     SUBDIR += py-multiqc
+    SUBDIR += py-ont-fast5-api
     SUBDIR += py-orange3-bioinformatics
     SUBDIR += py-orange3-single-cell
     SUBDIR += py-pandas-charm
diff --git a/biology/py-ont-fast5-api/Makefile b/biology/py-ont-fast5-api/Makefile
new file mode 100644
index 000000000000..d998d68a0e04
--- /dev/null
+++ b/biology/py-ont-fast5-api/Makefile
@@ -0,0 +1,42 @@
+PORTNAME=	ont-fast5-api
+DISTVERSIONPREFIX=	release_
+DISTVERSION=	4.0.0
+CATEGORIES=	biology python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Interface to HDF5 files in Oxford Nanopore .fast5 format
+
+LICENSE=	MPL20
+LICENSE_FILE=	${WRKSRC}/LICENSE.md
+
+LIB_DEPENDS=	libvbz_hdf_plugin.so:archivers/vbz-compression
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}progressbar>0:misc/py-progressbar@${PY_FLAVOR}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pip>=0:devel/py-pip@${PY_FLAVOR}
+
+USES=		python
+USE_PYTHON=	autoplist distutils
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	nanoporetech
+GH_PROJECT=	ont_fast5_api
+
+NO_ARCH=	yes
+NO_BUILD=	yes
+
+post-patch:
+	${RM} ${WRKSRC}/ont_fast5_api/vbz_plugin/*
+
+pre-configure:
+	@${REINPLACE_CMD} -e 's|progressbar33|progressbar|g' \
+		${WRKSRC}/setup.py \
+		${WRKSRC}/README.rst \
+		${WRKSRC}/ont_fast5_api/conversion_tools/conversion_utils.py
+
+do-test:
+	@cd ${WRKSRC} && ${PYTHON_CMD} ${PYDISTUTILS_SETUP} test
+
+.include <bsd.port.mk>
diff --git a/biology/py-ont-fast5-api/distinfo b/biology/py-ont-fast5-api/distinfo
new file mode 100644
index 000000000000..9156cd8912ef
--- /dev/null
+++ b/biology/py-ont-fast5-api/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1628770827
+SHA256 (nanoporetech-ont_fast5_api-release_4.0.0_GH0.tar.gz) = 7f9b3fa0f814ff38c30e9cb21971ec61e2b3fd52fb166a8404c21bf25679e0ab
+SIZE (nanoporetech-ont_fast5_api-release_4.0.0_GH0.tar.gz) = 4081125
diff --git a/biology/py-ont-fast5-api/pkg-descr b/biology/py-ont-fast5-api/pkg-descr
new file mode 100644
index 000000000000..e8482d387fa0
--- /dev/null
+++ b/biology/py-ont-fast5-api/pkg-descr
@@ -0,0 +1,9 @@
+The ont_fast5_api is a simple interface to HDF5 files of the Oxford
+Nanopore .fast5 file format. It provides:
+
+    o Implementation of the fast5 file schema using h5py library
+    o Methods to interact with and reflect the fast5 file schema
+    o Tools to convert between multi_read and single_read formats
+    o Tools to compress/decompress raw data in files
+
+WWW: https://pypi.python.org/pypi/ont_fast5_api