From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1PwLK7-0001B1-I3 for garchives@archives.gentoo.org; Sun, 06 Mar 2011 21:17:08 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A898AE061F; Sun, 6 Mar 2011 21:16:59 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 60B41E061F for ; Sun, 6 Mar 2011 21:16:58 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 6B4331B4060 for ; Sun, 6 Mar 2011 21:16:58 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id BFB2C8006E for ; Sun, 6 Mar 2011 21:16:57 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <96e413d2cda39af886222c35398a7d6f0db1c89f.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gap2caf/gap2caf-2.1.0.ebuild sci-biology/gap2caf/metadata.xml X-VCS-Directories: sci-biology/gap2caf/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 96e413d2cda39af886222c35398a7d6f0db1c89f Date: Sun, 6 Mar 2011 21:16:57 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 052a8da404f96f04cba3e8f292ff786c commit: 96e413d2cda39af886222c35398a7d6f0db1c89f Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Mar 6 21:09:46 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Mar 6 21:09:46 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D96e413d2 sci-biology/gap2caf-2.1.0: ebuild cleanup (Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit) --- sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 76 ++++++++++++++++++++++++= ++++++ sci-biology/gap2caf/metadata.xml | 9 ++++ 2 files changed, 85 insertions(+), 0 deletions(-) diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2c= af/gap2caf-2.1.0.ebuild new file mode 100644 index 0000000..5aae263 --- /dev/null +++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3D3 + +inherit eutils autotools + +DESCRIPTION=3D"GAP4 file format to CAF v2 format converter for genomic a= ssembly data" +HOMEPAGE=3D"http://www.sanger.ac.uk/resources/software/caf/" +SRC_URI=3D"ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.= 1.0.tar.gz + http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz" + +LICENSE=3D"as-is staden" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"" + +DEPEND=3D"" +RDEPEND=3D"${DEPEND}" + +DEPEND=3D"sci-biology/staden + >=3Ddev-lang/tcl-8.5" +RDEPEND=3D"${DEPEND}" + +#src_prepare(){ +# epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die +#} + +src_prepare(){ + sed -i 's:/include/tcl8.4:/include:' configure.ac || die + sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die + sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die + eaclocal + eautomake + eautoconf + sed -i 's:/include/tcl8.4:/include:' configure + sed -i 's:libtcl8.4:libtcl8.5:' configure +} + +src_configure(){ + # STADENROOT=3D/usr is used to find $STADENROOT/lib/staden/staden.profi= le and staden_config.h + # STADENSRC is used to locate gap4/IO.h + #CPPFLAGS=3D"$CPPFLAGS -I/home/mmokrejs/proj/staden/staden/trunk/src" \ + #LDFLAGS=3D"$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \ + # STADENROOT=3D/usr/share/staden \ + # STADENSRC=3D"${WORKDIR}"/staden-2.0.0b8-src \ + econf --with-stadenroot=3D/usr \ + --with-tcl=3D/usr \ + --with-stadensrc=3D"${WORKDIR}"/staden-2.0.0b8-src || die + #sed -i 's:prefix =3D /usr:prefix =3D $(DESTDIR)/usr:' Makefile || die + #sed -i 's:prefix =3D /usr:prefix =3D $(DESTDIR)/usr:' src/Makefile || = die + sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die + + # The below tricks in overall do not help, only for -ltk_utils somehow + sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden = -ltk_utils -rpath-link:' src/Makefile || die + sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap= :' src/Makefile || die + sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden= -lseq_utils:' src/Makefile || die +} + +# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME +# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install= the manpage files, +# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man do= es not help. +src_install(){ + # do not use upstream's install it just install shell wrapper into /usr= /bin/gap2caf + # calling "LD_LIBRARY_PATH=3D/usr/lib/staden /usr/lib/gap2caf/gap2caf $= @" + # emake install DESTDIR=3D"${D}" || die + # + # Instead, we rely on sci-biology/staden providind /etc/env.d/99staden = file providing LDPATH=3D/usr/lib/staden + dobin src/gap2caf + dodoc README || die +} + +# BUG #259848 +# A working ebuild which needs some files from staden source tree. That = is ugly, +# am sorting out with upstream how to get around in a clean way. diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metad= ata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/gap2caf/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +