From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 60AC4138C9D for ; Fri, 17 Apr 2015 23:56:41 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EB134E088A; Fri, 17 Apr 2015 23:56:40 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 51F45E088A for ; Fri, 17 Apr 2015 23:56:40 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 97C233409B3 for ; Fri, 17 Apr 2015 23:56:39 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6C9C016272 for ; Fri, 17 Apr 2015 23:56:32 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1429310864.f5965a7c3727b476c3f8392bb1bec8eae7792f45.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/cgview-bin/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/cgview-bin/ChangeLog sci-biology/cgview-bin/cgview-bin-20131130.ebuild X-VCS-Directories: sci-biology/cgview-bin/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f5965a7c3727b476c3f8392bb1bec8eae7792f45 X-VCS-Branch: master Date: Fri, 17 Apr 2015 23:56:32 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: ea07330a-8025-4470-8646-2bd2adc26344 X-Archives-Hash: cc38f86882677473067882961bd2b187 commit: f5965a7c3727b476c3f8392bb1bec8eae7792f45 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Apr 17 22:47:44 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Apr 17 22:47:44 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5965a7c sci-biology/cgview-bin: fixed installation of perl-related files Package-Manager: portage-2.2.18 sci-biology/cgview-bin/ChangeLog | 4 ++++ sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 18 +++++++++++++----- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog index e3de215..3ab4181 100644 --- a/sci-biology/cgview-bin/ChangeLog +++ b/sci-biology/cgview-bin/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs + cgview-bin-20131130.ebuild: + sci-biology/cgview-bin: fixed installation of perl-related files + 18 Feb 2015; Justin Lecher cgview-bin-20131130.ebuild: sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild index 61141e3..74a9540 100644 --- a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild +++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild @@ -6,6 +6,9 @@ EAPI=5 inherit java-pkg-2 +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)" HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT" SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip" @@ -34,11 +37,16 @@ src_test(){ } src_install() { - echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview" + insinto /usr/share/${PN}/scripts + chmod a+x scripts/* # BUG: this does not work + doins scripts/* + echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview" echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview" doenvd "${S}/99cgview" - #export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin - #export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB" - - dobin bin/cgview.jar + perl_set_version + insinto ${VENDOR_LIB}/cgview + doins lib/perl_modules/Util/*.pm + # + # Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException + java-pkg_dojar bin/cgview.jar }