From owner-svn-ports-head@freebsd.org Mon Jun 25 23:56:02 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 AFE4A10257F4; Mon, 25 Jun 2018 23:56:02 +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 6041473326; Mon, 25 Jun 2018 23:56:02 +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 416A546B8; Mon, 25 Jun 2018 23:56:02 +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 w5PNu2kj010377; Mon, 25 Jun 2018 23:56:02 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w5PNu1X6010369; Mon, 25 Jun 2018 23:56:01 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201806252356.w5PNu1X6010369@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 25 Jun 2018 23:56:01 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r473356 - in head/biology: . igv igv/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . igv igv/files X-SVN-Commit-Revision: 473356 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: 2.1.26 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: Mon, 25 Jun 2018 23:56:02 -0000 Author: yuri Date: Mon Jun 25 23:56:00 2018 New Revision: 473356 URL: https://svnweb.freebsd.org/changeset/ports/473356 Log: New port: biology/igv: Visualization tool for genomic datasets Added: head/biology/igv/ head/biology/igv/Makefile (contents, props changed) head/biology/igv/distinfo (contents, props changed) head/biology/igv/files/ head/biology/igv/files/igv.sh.in (contents, props changed) head/biology/igv/files/patch-build.xml (contents, props changed) head/biology/igv/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Jun 25 23:36:59 2018 (r473355) +++ head/biology/Makefile Mon Jun 25 23:56:00 2018 (r473356) @@ -43,6 +43,7 @@ SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy + SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree Added: head/biology/igv/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/Makefile Mon Jun 25 23:56:00 2018 (r473356) @@ -0,0 +1,46 @@ +# $FreeBSD$ + +PORTNAME= igv +DISTVERSIONPREFIX= v +DISTVERSION= 2.4.10 +CATEGORIES= biology java +MASTER_SITES= http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img +DISTFILES= tools.png:img +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Visualization tool for genomic datasets + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/license.txt + +BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel +RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel + +USES= gettext-runtime +USE_GITHUB= yes +GH_ACCOUNT= igvteam +USE_JAVA= yes +USE_ANT= yes +NO_ARCH= yes + +SUB_FILES= ${PORTNAME}.sh + +DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \ + "Biology;Science;" true + +PLIST_FILES= bin/${PORTNAME} \ + ${JAVAJARDIR}/batik-codec__V1.7.jar \ + ${JAVAJARDIR}/goby-io-igv__V1.0.jar \ + ${JAVAJARDIR}/${PORTNAME}.jar \ + share/pixmaps/igv.png + +do-install: + ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + ${INSTALL_DATA} ${WRKSRC}/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/batik-codec__V1.7.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/goby-io-igv__V1.0.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png + +.include Added: head/biology/igv/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/distinfo Mon Jun 25 23:56:00 2018 (r473356) @@ -0,0 +1,5 @@ +TIMESTAMP = 1529969906 +SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.4.10/tools.png) = 5139 +SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73 +SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902 Added: head/biology/igv/files/igv.sh.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/files/igv.sh.in Mon Jun 25 23:56:00 2018 (r473356) @@ -0,0 +1,9 @@ +#!/bin/sh +LANG=C +# phymem=$(free -m | awk '/^Mem:/{print $2}') +#igvmem=$(($phymem / 3)) +# ARGS=-Xmx${igvmem}m +java $ARGS \ + -Dapple.laf.useScreenMenuBar=true \ + -Djava.net.preferIPv4Stack=true \ + -jar %%JAVAJARDIR%%/igv.jar Added: head/biology/igv/files/patch-build.xml ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/files/patch-build.xml Mon Jun 25 23:56:00 2018 (r473356) @@ -0,0 +1,10 @@ +--- build.xml.orig 2018-06-25 21:00:29 UTC ++++ build.xml +@@ -177,6 +177,7 @@ + + + ++ + + + Added: head/biology/igv/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/pkg-descr Mon Jun 25 23:56:00 2018 (r473356) @@ -0,0 +1,6 @@ +The Integrative Genomics Viewer (IGV) is a high-performance visualization tool +for interactive exploration of large, integrated genomic datasets. It supports +a wide variety of data types, including array-based and next-generation sequence +data, and genomic annotations. + +WWW: https://software.broadinstitute.org/software/igv/