Date: Fri, 13 Aug 2021 13:34:57 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5797d6a3298e - main - biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files Message-ID: <202108131334.17DDYvLH061371@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5797d6a3298ebfe3990db73084f34ed935911efa commit 5797d6a3298ebfe3990db73084f34ed935911efa Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-08-13 13:34:09 +0000 Commit: Jason W. Bacon <jwb@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@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
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