From owner-svn-ports-all@freebsd.org Sun Feb 3 21:14:40 2019 Return-Path: Delivered-To: svn-ports-all@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 019C014B3B70; Sun, 3 Feb 2019 21:14:40 +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 TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 94E1087339; Sun, 3 Feb 2019 21:14:39 +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 8384D24328; Sun, 3 Feb 2019 21:14:39 +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 x13LEd6V020957; Sun, 3 Feb 2019 21:14:39 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x13LEcwK020950; Sun, 3 Feb 2019 21:14:38 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201902032114.x13LEcwK020950@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 3 Feb 2019 21:14:38 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r492079 - in head/biology: . figtree X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . figtree X-SVN-Commit-Revision: 492079 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 94E1087339 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_LONG(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.98)[-0.978,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 03 Feb 2019 21:14:40 -0000 Author: yuri Date: Sun Feb 3 21:14:38 2019 New Revision: 492079 URL: https://svnweb.freebsd.org/changeset/ports/492079 Log: New port: biology/figtree: Graphical viewer of phylogenetic trees Added: head/biology/figtree/ head/biology/figtree/Makefile (contents, props changed) head/biology/figtree/distinfo (contents, props changed) head/biology/figtree/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Feb 3 21:04:24 2019 (r492078) +++ head/biology/Makefile Sun Feb 3 21:14:38 2019 (r492079) @@ -36,6 +36,7 @@ SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit + SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic Added: head/biology/figtree/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/figtree/Makefile Sun Feb 3 21:14:38 2019 (r492079) @@ -0,0 +1,38 @@ +# $FreeBSD$ + +PORTNAME= figtree +DISTVERSIONPREFIX= v +DISTVERSION= 1.4.4 +CATEGORIES= biology java + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Graphical viewer of phylogenetic trees + +LICENSE= GPLv2 + +USE_JAVA= yes +USE_ANT= yes +USE_GITHUB= yes +GH_ACCOUNT= rambaut + +NO_ARCH= yes + +DESKTOP_ENTRIES="FigTree" "Phylogenetic tree viewer" "${PREFIX}/share/pixmaps/${PORTNAME}.png" "${PORTNAME}" \ + "Biology;Science;Education;" true + +PLIST_FILES= bin/${PORTNAME} \ + ${JAVAJARDIR}/${PORTNAME}-pdf.jar \ + ${JAVAJARDIR}/${PORTNAME}.jar \ + ${JAVAJARDIR}/figtreepanel.jar \ + share/pixmaps/${PORTNAME}.png \ + +do-install: + @(echo "#!/bin/sh"; \ + echo ""; \ + echo ${JAVA} -jar ${JAVAJARDIR}/${PORTNAME}.jar \ + ) > ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + @${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + ${INSTALL_DATA} ${WRKSRC}/dist/*.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/release/Linux/icons/${PORTNAME}.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png + +.include Added: head/biology/figtree/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/figtree/distinfo Sun Feb 3 21:14:38 2019 (r492079) @@ -0,0 +1,3 @@ +TIMESTAMP = 1549226829 +SHA256 (rambaut-figtree-v1.4.4_GH0.tar.gz) = 29a2e7fb2de0fa213aa0bb3003347fe278c28d8273bbc06f1d98cda9dda35d89 +SIZE (rambaut-figtree-v1.4.4_GH0.tar.gz) = 20994009 Added: head/biology/figtree/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/figtree/pkg-descr Sun Feb 3 21:14:38 2019 (r492079) @@ -0,0 +1,7 @@ +FigTree is designed as a graphical viewer of phylogenetic trees and as a program +for producing publication-ready figures. As with most of my programs, it was +written for my own needs so may not be as polished and feature-complete as a +commercial program. In particular it is designed to display summarized and +annotated trees produced by BEAST. + +WWW: http://tree.bio.ed.ac.uk/software/figtree/