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Diffstat (limited to 'sci-biology/estscan/estscan-3.0.3.ebuild')
| -rw-r--r-- | sci-biology/estscan/estscan-3.0.3.ebuild | 124 |
1 files changed, 0 insertions, 124 deletions
diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild deleted file mode 100644 index a0992b76b..000000000 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ /dev/null @@ -1,124 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit fortran-2 perl-module toolchain-funcs - -DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" -HOMEPAGE="https://sourceforge.net/projects/estscan/" -SRC_URI=" - https://downloads.sourceforge.net/${PN}/${P}.tar.gz - https://downloads.sourceforge.net/${PN}/At.smat.gz - https://downloads.sourceforge.net/${PN}/Dm.smat.gz - https://downloads.sourceforge.net/${PN}/Dr.smat.gz - https://downloads.sourceforge.net/${PN}/Hs.smat.gz - https://downloads.sourceforge.net/${PN}/Mm.smat.gz - https://downloads.sourceforge.net/${PN}/Rn.smat.gz - https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf - https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz" - -SLOT="0" -LICENSE="estscan" -KEYWORDS="~amd64 ~x86" -IUSE="icc ifc" - -DEPEND=" - dev-perl/BTLib - icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -src_prepare() { - default - sed \ - -e 's/\\rm -f/rm -rf/' \ - -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \ - -i "${P}"/Makefile || die "failed to edit Makefile" - - # fix hard-coded paths - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die - - if ! use icc; then - sed \ - -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die - fi - - if ! use ifc; then - sed \ - -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \ - -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \ - || die - fi - - if use icc; then - # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives - # me gcc instead, same for $(tc-getF77) - # Moreover, the if/else logic here should separate users having only icc - # while not ifort (and vice-versa) from those having only - # gcc/gfortran/g77 - # - # FIXME: below as a dirty hack I force gfortran instead of ifort for - # my testing purposes. Didn't ebuild contain "PROVIDES" line? - # Same for FFLAGS. - sed \ - -e "s:^# CC = icc:CC = icc:" \ - -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ - -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \ - -e "s/^ CC = gcc/# CC = gcc/" \ - -i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC" - - fi - - if use ifc; then - sed \ - -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \ - -e "s/^# F77 = ifort/F77 = gfortran/" \ - -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \ - -e "s/^ F77 = g77/# F77 = g77/" \ - -i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77" - fi -} - -src_compile() { - emake -C ${P} -} - -src_install() { - # FIXME: Some kind of documentation is in {P}/${PN}.spec - cd ${P} || die "Failed to chdir to ${P}" - dobin \ - build_model ${PN} evaluate_model extract_EST extract_UG_EST \ - extract_mRNA makesmat maskred prepare_data winsegshuffle - # the file build_model_utils.pl should go into some PERL site-packages dir - # see {P}/${PN}.spec - - # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension - insinto /usr/share/doc/${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 ${WORKDIR}" - insinto /usr/share/${PN} - doins *.smat - - # install BTlib (in perl) - # dobin fetch indexer netfetch - 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 - - # FIXME: install the *.pm files from BTLib-0.19 - # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19 - # myinst="DESTDIR=${D}" - # perl-module_src_install - - einfo "Please edit /usr/share/${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/" -} |