diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2022-12-06 15:41:19 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2022-12-06 15:41:19 +0000 |
| commit | 29c79a3b6aee93dbe5b65e863bcb33e1bb773276 (patch) | |
| tree | 584502fe203f8011ea528a44f1eb237852fa3b5e | |
| parent | 2242eb825c0d5389b02c623938f427649d7fc34f (diff) | |
biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for genomes and metagenomes
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-pyrodigal/Makefile | 28 | ||||
| -rw-r--r-- | biology/py-pyrodigal/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-pyrodigal/pkg-descr | 18 |
4 files changed, 50 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 98b1f2663190..0622b83369d4 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -175,6 +175,7 @@ SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx + SUBDIR += py-pyrodigal SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile new file mode 100644 index 000000000000..7e6e5edb6414 --- /dev/null +++ b/biology/py-pyrodigal/Makefile @@ -0,0 +1,28 @@ +PORTNAME= pyrodigal +DISTVERSION= 2.0.2 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Python binding for Prodigal, an ORF finder for genomes and metagenomes +WWW= https://github.com/althonos/pyrodigal + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= python +USE_PYTHON= distutils cython concurrent autoplist pytest + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + +post-build: + @cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build_ext --inplace + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/_pyrodigal${PYTHON_EXT_SUFFIX}.so + +do-test: + @cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -vv + +.include <bsd.port.mk> diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo new file mode 100644 index 000000000000..02e6b0910a97 --- /dev/null +++ b/biology/py-pyrodigal/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1670316641 +SHA256 (pyrodigal-2.0.2.tar.gz) = 602c0fa5ec2db870d1eeca13b623610fe54cb8a2ad87e8b898b3b359379bbed5 +SIZE (pyrodigal-2.0.2.tar.gz) = 2616518 diff --git a/biology/py-pyrodigal/pkg-descr b/biology/py-pyrodigal/pkg-descr new file mode 100644 index 000000000000..c56d5dda28d0 --- /dev/null +++ b/biology/py-pyrodigal/pkg-descr @@ -0,0 +1,18 @@ +Pyrodigal is a Python module that provides bindings to Prodigal using Cython. + +Features: +The library now features everything from the original Prodigal CLI: +* run mode selection: Choose between single mode, using a training sequence to + count nucleotide hexamers, or metagenomic mode, using pre-trained data from + different organisms (prodigal -p). +* region masking: Prevent genes from being predicted across regions containing + unknown nucleotides (prodigal -m). +* closed ends: Genes will be identified as running over edges if they are larger + than a certain size, but this can be disabled (prodigal -c). +* training configuration: During the training process, a custom translation + table can be given (prodigal -g), and the Shine-Dalgarno motif search can be + forcefully bypassed (prodigal -n) +* output files: Output files can be written in a format mostly compatible with + the Prodigal binary, including the protein translations in FASTA format + (prodigal -a), the gene sequences in FASTA format (prodigal -d), or the + potential gene scores in tabular format (prodigal -s). |