commit: b1b5577ab5e375948132c3dba0db7bde29968bf8 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed Sep 24 06:32:18 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Sep 24 06:32:18 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b1b5577a
sci-biology/estscan: Bump to EAPI=5 Package-Manager: portage-2.2.13 --- sci-biology/estscan/ChangeLog | 5 +++- sci-biology/estscan/estscan-3.0.3.ebuild | 50 +++++++++++++++----------------- 2 files changed, 28 insertions(+), 27 deletions(-) diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog index de16cc8..c19b120 100644 --- a/sci-biology/estscan/ChangeLog +++ b/sci-biology/estscan/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/estscan -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 24 Sep 2014; Justin Lecher <[email protected]> estscan-3.0.3.ebuild: + Bump to EAPI=5 + 03 Mar 2013; Justin Lecher <[email protected]> metadata.xml: Add local USE to metadata.xml diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild index a9a9de0..58514a3 100644 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -2,22 +2,22 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit eutils fortran-2 perl-module toolchain-funcs DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" -HOMEPAGE="http://sourceforge.net/projects/estscan/"; +HOMEPAGE="http://sourceforge.net/projects/${PN}/"; SRC_URI=" - http://downloads.sourceforge.net/estscan/estscan-3.0.3.tar.gz - http://downloads.sourceforge.net/estscan/At.smat.gz - http://downloads.sourceforge.net/estscan/Dm.smat.gz - http://downloads.sourceforge.net/estscan/Dr.smat.gz - http://downloads.sourceforge.net/estscan/Hs.smat.gz - http://downloads.sourceforge.net/estscan/Mm.smat.gz - http://downloads.sourceforge.net/estscan/Rn.smat.gz - http://downloads.sourceforge.net/estscan/user_guide_fev_07.pdf - http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz"; + http://downloads.sourceforge.net/${PN}/${P}.tar.gz + http://downloads.sourceforge.net/${PN}/At.smat.gz + http://downloads.sourceforge.net/${PN}/Dm.smat.gz + http://downloads.sourceforge.net/${PN}/Dr.smat.gz + http://downloads.sourceforge.net/${PN}/Hs.smat.gz + http://downloads.sourceforge.net/${PN}/Mm.smat.gz + http://downloads.sourceforge.net/${PN}/Rn.smat.gz + http://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf + http://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"; SLOT="0" LICENSE="estscan" @@ -25,10 +25,9 @@ KEYWORDS="~x86 ~amd64" IUSE="icc ifc" DEPEND=" - virtual/fortran + dev-perl/BTLib icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc ) - dev-perl/BTLib" + ifc? ( dev-lang/ifc )" RDEPEND="${DEPEND}" S="${WORKDIR}" @@ -40,8 +39,8 @@ src_prepare() { -i "${P}"/Makefile || die "failed to edit Makefile" # fix hard-coded paths - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.c || die - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/estscan.spec || die + sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die + sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die if ! use icc; then sed \ @@ -89,28 +88,27 @@ src_compile() { } src_install() { - # FIXME: Some kind of documentation is in {P}/estscan.spec + # FIXME: Some kind of documentation is in {P}/${PN}.spec cd ${P} || die "Failed to chdir to ${P}" dobin \ - build_model estscan evaluate_model extract_EST extract_UG_EST \ + build_model ${PN} evaluate_model extract_EST extract_UG_EST \ extract_mRNA makesmat maskred prepare_data winsegshuffle # the file build_model_utils.pl should go into some PERL site-packages dir - # see {P}/estscan.spec + # see {P}/${PN}.spec # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension - cd "${DISTDIR}" || die "Failed to chdir to ${DISTDIR}" - insinto /usr/share/doc/ESTscan + insinto /usr/share/doc/${PN} # grab the file directly from ../distdir/ doins "${DISTDIR}"/user_guide_fev_07.pdf # install the default precomputed matrices cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}" - insinto /usr/share/ESTscan + insinto /usr/share/${PN} doins *.smat # install BTlib (in perl) # dobin fetch indexer netfetch - insinto /usr/share/ESTscan/ + insinto /usr/share/${PN}/ # install the config file which is packed inside the BTLib tarball while is not # being installed by dev-perl/BTLib doins "${WORKDIR}"/BTLib-0.19/fetch.conf @@ -120,7 +118,7 @@ src_install() { # myinst="DESTDIR=${D}" # perl-module_src_install - einfo "Please edit /usr/share/ESTscan/fetch.conf to fit your local database layout." - einfo "Also create your own scoring matrices and place them into /usr/share/ESTscan/." - einfo "You may follow the hints from http://estscan.sourceforge.net/"; + einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout." + einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/." + einfo "You may follow the hints from http://${PN}.sourceforge.net/"; }
