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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
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Jason W. Bacon
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Jason W. Bacon
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Aug 13, 2021
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PORTNAME= ont-fast5-api | ||
DISTVERSIONPREFIX= release_ | ||
DISTVERSION= 4.0.0 | ||
CATEGORIES= biology python | ||
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} | ||
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MAINTAINER= jwb@FreeBSD.org | ||
COMMENT= Interface to HDF5 files in Oxford Nanopore .fast5 format | ||
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LICENSE= MPL20 | ||
LICENSE_FILE= ${WRKSRC}/LICENSE.md | ||
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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} | ||
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USES= python | ||
USE_PYTHON= autoplist distutils | ||
USE_GITHUB= yes | ||
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GH_ACCOUNT= nanoporetech | ||
GH_PROJECT= ont_fast5_api | ||
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NO_ARCH= yes | ||
NO_BUILD= yes | ||
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post-patch: | ||
${RM} ${WRKSRC}/ont_fast5_api/vbz_plugin/* | ||
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pre-configure: | ||
@${REINPLACE_CMD} -e 's|progressbar33|progressbar|g' \ | ||
${WRKSRC}/setup.py \ | ||
${WRKSRC}/README.rst \ | ||
${WRKSRC}/ont_fast5_api/conversion_tools/conversion_utils.py | ||
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do-test: | ||
@cd ${WRKSRC} && ${PYTHON_CMD} ${PYDISTUTILS_SETUP} test | ||
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.include <bsd.port.mk> |
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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 |
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The ont_fast5_api is a simple interface to HDF5 files of the Oxford | ||
Nanopore .fast5 file format. It provides: | ||
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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 | ||
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WWW: https://pypi.python.org/pypi/ont_fast5_api |