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Tue, 6 Dec 2022 17:23:57 GMT (envelope-from git) Date: Tue, 6 Dec 2022 17:23:57 GMT Message-Id: <202212061723.2B6HNve6062000@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 29c79a3b6aee - main - biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for genomes and metagenomes List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 29c79a3b6aee93dbe5b65e863bcb33e1bb773276 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=29c79a3b6aee93dbe5b65e863bcb33e1bb773276 commit 29c79a3b6aee93dbe5b65e863bcb33e1bb773276 Author: Yuri Victorovich AuthorDate: 2022-12-06 15:41:19 +0000 Commit: Yuri Victorovich CommitDate: 2022-12-06 15:41:19 +0000 biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for genomes and metagenomes --- biology/Makefile | 1 + biology/py-pyrodigal/Makefile | 28 ++++++++++++++++++++++++++++ biology/py-pyrodigal/distinfo | 3 +++ biology/py-pyrodigal/pkg-descr | 18 ++++++++++++++++++ 4 files changed, 50 insertions(+) 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 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).