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biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files

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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
This commit is contained in:
Jason W. Bacon 2021-08-13 08:34:09 -05:00
parent 6aeff2e8d1
commit 5797d6a329
4 changed files with 55 additions and 0 deletions
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1
biology/Makefile
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@ -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

42
biology/py-ont-fast5-api/Makefile Normal file
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@ -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>

3
biology/py-ont-fast5-api/distinfo Normal file
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@ -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

9
biology/py-ont-fast5-api/pkg-descr Normal file
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@ -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