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 1Pp1Tg-00058q-6Q for garchives@archives.gentoo.org; Mon, 14 Feb 2011 16:40:44 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A5C24E0A60; Mon, 14 Feb 2011 16:40:31 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 6330BE0A60 for ; Mon, 14 Feb 2011 16:40:31 +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 A4CB71B4024 for ; Mon, 14 Feb 2011 16:40:30 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 17C2D8006A for ; Mon, 14 Feb 2011 16:40:30 +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: <2edce2dbf5c139d4995cd7d1eadcb4d4f09139ca.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/estscan/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/estscan/estscan-3.0.3.ebuild sci-biology/estscan/metadata.xml X-VCS-Directories: sci-biology/estscan/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 2edce2dbf5c139d4995cd7d1eadcb4d4f09139ca Date: Mon, 14 Feb 2011 16:40:30 +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: 92539c4ba3d34e7740b0698f2c7a0ffb commit: 2edce2dbf5c139d4995cd7d1eadcb4d4f09139ca Author: Martin Mokrejs gentoo org> AuthorDate: Mon Feb 14 16:40:21 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Feb 14 16:40:21 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D2edce2db sci-biology/estscan: new package, something wrong with IUSE? (Portage version: 2.1.9.28/git/Linux i686, RepoMan options: --force, unsi= gned Manifest commit) --- sci-biology/estscan/estscan-3.0.3.ebuild | 103 ++++++++++++++++++++++++= ++++++ sci-biology/estscan/metadata.xml | 9 +++ 2 files changed, 112 insertions(+), 0 deletions(-) diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estsc= an/estscan-3.0.3.ebuild new file mode 100644 index 0000000..789dd09 --- /dev/null +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -0,0 +1,103 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils toolchain-funcs +inherit perl-module + +DESCRIPTION=3D"Predict coding regions in DNA/RNA sequences even in low-q= uality reads with frameshift-causing errors (supersedes ESTscan and ESTsc= an2)" +HOMEPAGE=3D"http://sourceforge.net/projects/estscan/" +SRC_URI=3D"http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz + http://downloads.sourceforge.net/estscan/At.smat.gz + http://downloads.sourceforge.net/estscan/Dm.smat.gz + http://downloads.sourceforge.net/estscan/Dr.smat.gz + http://downloads.sourceforge.net/estscan/Hs.smat.gz + http://downloads.sourceforge.net/estscan/Mm.smat.gz + http://downloads.sourceforge.net/estscan/Rn.smat.gz + http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf + http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" + +LICENSE=3D"estscan" +SLOT=3D"0" +KEYWORDS=3D"~x86 ~amd64" +IUSE=3D"icc ifc" + +DEPEND=3D"icc? ( dev-lang/icc ) + ifc? ( dev-lang/ifc )" + +RDEPEND=3D"" + +S=3D"${WORKDIR}" + +src_compile() { + # + sed -e 's/\\rm -f/rm -rf/' \ + -e 's/^ LDFLAGS =3D -lm/LDFLAGS =3D -lm/' -i "${P}"/Makefile || die "f= ailed to edit Makefile" + + # fix hard-coded paths + sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/ests= can.c || die + sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/ests= can.spec || die + + if ! use icc; then + sed -e 's/^ CFLAGS =3D -O2/#CFLAGS =3D ${CFLAGS}/' \ + -e 's/^ FFLAGS =3D -O2/#FFLAGS =3D ${FFLAGS}/' \ + -e "s/^ F77 =3D g77/F77 =3D $(tc-getF77)/" -i "${P}"/Makefile \ + || die "blah" + else + # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it give= s + # me gcc instead, same for $(tc-getF77) + # Moreover, the if/else logic here should separate users having only i= cc + # while not ifort (and vice-versa) from those having only + # gcc/gfortran/g77 + # + # FIXME: below as a dirty hack I force gfortran instead of ifort for + # my testing purposes. Didn't ebuild contain "PROVIDES" line? + # Same for FFLAGS. + sed -e "s:^# CC =3D icc:CC =3D icc:" \ + -e "s:^# CFLAGS =3D -O3 -ipo -axP:#CFLAGS =3D -O3 -ipo -axP:" \ + -e "s:^# FFLAGS =3D -O3 -ipo -axP:#FFLAGS =3D -O3 -ipo -axP:" \ + -e "s/^ CFLAGS =3D -O2/#CFLAGS =3D -O2/" \ + -e "s/^# F77 =3D ifort/F77 =3D gfortran/" \ + -e "s/^ FFLAGS =3D -O2/#FFLAGS =3D -O2/" \ + -e "s/^ CC =3D gcc/# CC =3D gcc/" \ + -e "s/^ F77 =3D g77/# F77 =3D g77/" -i "${P}"/Makefile || die "sed fa= iled to fix CFLAGS, FFLAGS, CC, F77" + fi + cd "${P}" || die "chdir "${P}" failed" + emake || die "emake failed" + + cd ../BTLib-0.19 || die "cd ../BTLib-0.19 failed" + perl Makefile.PL || die "perl Makefile.PL failed" +} + +src_install() { + # FIXME: Some kind of documentation is in {P}/estscan.spec + cd "${P}" + dobin build_model estscan evaluate_model extract_EST extract_UG_EST ext= ract_mRNA makesmat maskred prepare_data winsegshuffle || die "dobin faile= d" + # the file build_model_utils.pl should go into some PERL site-packages = dir + # see {P}/estscan.spec + + # install the doc (but is not in ${WORKDIR} because src_UNPACK() failed= on it + cd "${WORKDIR}" || die + insinto /usr/share/doc/ESTscan + # grab the file directly from ../distdir/ + doins ../distdir/user_guide_fev_07.pdf || die "failed to install user_g= uide_fev_07.pdf" + + # install the default precomputed matrices + cd "${WORKDIR}" || die + insinto /usr/share/ESTscan + doins *.smat || die "Failed to install matrices" + + # install BTlib (in perl) + cd BTLib-0.19 || die + dobin fetch indexer netfetch || die "dobin failed" + insinto /usr/share/ESTscan/ + doins fetch.conf || die "Failed to install fetch.conf" + + # FIXME: install the *.pm files from BTLib-0.19 + myinst=3D"DESTDIR=3D${D}" + perl-module_src_install || die "perl-module_src_install failed" + + einfo "Please edit /usr/share/ESTscan/fetch.conf to fit your local data= base layout." + einfo "Also create your own scoring matrices and place them into /usr/s= hare/ESTscan/." + einfo "You may follow the hints from http://estscan.sourceforge.net/" +} diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metad= ata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/estscan/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +