From owner-dev-commits-ports-main@freebsd.org Fri Aug 13 13:34:57 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id EF635657055; Fri, 13 Aug 2021 13:34:57 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4GmPgP6PXCz3p5l; Fri, 13 Aug 2021 13:34:57 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C3ED770B2; Fri, 13 Aug 2021 13:34:57 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 17DDYvjs061372; Fri, 13 Aug 2021 13:34:57 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17DDYvLH061371; Fri, 13 Aug 2021 13:34:57 GMT (envelope-from git) Date: Fri, 13 Aug 2021 13:34:57 GMT Message-Id: <202108131334.17DDYvLH061371@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 5797d6a3298e - main - biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 5797d6a3298ebfe3990db73084f34ed935911efa Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Aug 2021 13:34:58 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5797d6a3298ebfe3990db73084f34ed935911efa commit 5797d6a3298ebfe3990db73084f34ed935911efa Author: Jason W. Bacon AuthorDate: 2021-08-13 13:34:09 +0000 Commit: Jason W. Bacon 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 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