From owner-svn-ports-head@freebsd.org Fri Dec 7 00:10:07 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 65EC31321716; Fri, 7 Dec 2018 00:10:07 +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 0DD4A6D2E6; Fri, 7 Dec 2018 00:10:07 +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 E2F4631AF; Fri, 7 Dec 2018 00:10:06 +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 wB70A6Y5063228; Fri, 7 Dec 2018 00:10:06 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wB70A6D7063225; Fri, 7 Dec 2018 00:10:06 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201812070010.wB70A6D7063225@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Fri, 7 Dec 2018 00:10:06 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r486812 - in head/biology: . groopm X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . groopm X-SVN-Commit-Revision: 486812 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 0DD4A6D2E6 X-Spamd-Result: default: False [-1.87 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-0.87)[-0.865,0]; NEURAL_HAM_LONG(-0.05)[-0.054,0]; NEURAL_HAM_SHORT(-0.95)[-0.950,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-Rspamd-Server: mx1.freebsd.org X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 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: Fri, 07 Dec 2018 00:10:07 -0000 Author: yuri Date: Fri Dec 7 00:10:05 2018 New Revision: 486812 URL: https://svnweb.freebsd.org/changeset/ports/486812 Log: New port: math/groopm: Metagenomic binning suite Added: head/biology/groopm/ head/biology/groopm/Makefile (contents, props changed) head/biology/groopm/distinfo (contents, props changed) head/biology/groopm/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Dec 7 00:04:10 2018 (r486811) +++ head/biology/Makefile Fri Dec 7 00:10:05 2018 (r486812) @@ -42,6 +42,7 @@ SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa + SUBDIR += groopm SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy Added: head/biology/groopm/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/groopm/Makefile Fri Dec 7 00:10:05 2018 (r486812) @@ -0,0 +1,24 @@ +# $FreeBSD$ + +PORTNAME= GroopM +DISTVERSION= 0.3.4 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Metagenomic binning suite + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.1.0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=0.10.1:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tables>=2.3:devel/py-tables@${PY_FLAVOR} + +USES= python +USE_PYTHON= distutils noflavors autoplist + +NO_ARCH= yes + +.include Added: head/biology/groopm/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/groopm/distinfo Fri Dec 7 00:10:05 2018 (r486812) @@ -0,0 +1,3 @@ +TIMESTAMP = 1544140602 +SHA256 (GroopM-0.3.4.tar.gz) = 48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080 +SIZE (GroopM-0.3.4.tar.gz) = 127707 Added: head/biology/groopm/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/groopm/pkg-descr Fri Dec 7 00:10:05 2018 (r486812) @@ -0,0 +1,7 @@ +GroopM is a metagenomic binning toolset. It leverages spatio-temoral +dynamics (differential coverage) to accurately (and almost automatically) +extract population genomes from multi-sample metagenomic datasets. + +GroopM is largely parameter-free. Use: groopm -h for more info. + +WWW: http://ecogenomics.github.io/GroopM/