From owner-svn-ports-head@freebsd.org Tue Aug 7 07:50:41 2018 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 8B1BC1050B25; Tue, 7 Aug 2018 07:50:41 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 3E3DA8214E; Tue, 7 Aug 2018 07:50:41 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 1F52418E8A; Tue, 7 Aug 2018 07:50:41 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w777ofqT052903; Tue, 7 Aug 2018 07:50:41 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w777oecR052899; Tue, 7 Aug 2018 07:50:40 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201808070750.w777oecR052899@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Tue, 7 Aug 2018 07:50:40 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r476578 - in head/biology: . py-orange3-single-cell X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . py-orange3-single-cell X-SVN-Commit-Revision: 476578 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 07 Aug 2018 07:50:41 -0000 Author: yuri Date: Tue Aug 7 07:50:40 2018 New Revision: 476578 URL: https://svnweb.freebsd.org/changeset/ports/476578 Log: New port: biology/py-orange3-single-cell: Orange add-on for gene expression of single cell data Added: head/biology/py-orange3-single-cell/ head/biology/py-orange3-single-cell/Makefile (contents, props changed) head/biology/py-orange3-single-cell/distinfo (contents, props changed) head/biology/py-orange3-single-cell/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Aug 7 07:46:24 2018 (r476577) +++ head/biology/Makefile Tue Aug 7 07:50:40 2018 (r476578) @@ -106,6 +106,7 @@ SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics + SUBDIR += py-orange3-single-cell SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta Added: head/biology/py-orange3-single-cell/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-orange3-single-cell/Makefile Tue Aug 7 07:50:40 2018 (r476578) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= orange3-single-cell +DISTVERSION= 0.7.0 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Orange add-on for gene expression of single cell data + +LICENSE= AGPLv3+ + +RUN_DEPENDS= orange3>0:misc/orange3 \ + ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=0.20:math/py-pandas@${PY_FLAVOR} + +USES= python:3.4+ +USE_GITHUB= yes +GH_ACCOUNT= biolab +USE_PYTHON= distutils autoplist + +OPTIONS_DEFINE= DOCS + +DOCS_BUILD_DEPENDS= gmake:devel/gmake \ + ${PYTHON_PKGNAMEPREFIX}sphinx>0:textproc/py-sphinx@${PY_FLAVOR} + +pre-build-DOCS-on: + @cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${GMAKE} html htmlhelp SPHINXBUILD=${LOCALBASE}/bin/sphinx-build-${PYTHON_VER} + +pre-build-DOCS-off: + @${REINPLACE_CMD} "s|^ include_documentation| #include_documentation|" ${WRKSRC}/setup.py + +.include Added: head/biology/py-orange3-single-cell/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-orange3-single-cell/distinfo Tue Aug 7 07:50:40 2018 (r476578) @@ -0,0 +1,3 @@ +TIMESTAMP = 1533608220 +SHA256 (biolab-orange3-single-cell-0.7.0_GH0.tar.gz) = 73db7716d0e9f4c7d17a41770e2b72d94266a49b6ddbf79aba430c7bbcfa7753 +SIZE (biolab-orange3-single-cell-0.7.0_GH0.tar.gz) = 15862251 Added: head/biology/py-orange3-single-cell/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-orange3-single-cell/pkg-descr Tue Aug 7 07:50:40 2018 (r476578) @@ -0,0 +1,4 @@ +The Single Cell add-on for Orange3 adds functionality for analysis of single +cell data. + +WWW: https://singlecell.biolab.si/