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# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit autotools emboss-r3 readme.gentoo-r1
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
SRC_URI="
ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz
https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz"
S="${WORKDIR}/${P^^}"
LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="minimal"
RDEPEND="
!dev-build/cons
!games-action/xbomber
"
PDEPEND="
!minimal? (
sci-biology/aaindex
sci-biology/cutg
sci-biology/primer3
sci-biology/prints
sci-biology/prosite
sci-biology/rebase
)"
PATCHES=(
"${WORKDIR}"/patches/${P}-fix-build-system.patch
"${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch
"${WORKDIR}"/patches/${P}-plplot-declarations.patch
"${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch
"${WORKDIR}"/patches/${P}-C99-bool.patch
"${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch
)
src_prepare() {
default
eautoreconf
}
src_install() {
emboss-r3_src_install
readme.gentoo_create_doc
# Install env file for setting libplplot and acd files path.
newenvd - 22emboss <<- EOF
# ACD files location
EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
EOF
# Remove useless dummy files
find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \
|| die "Failed to remove dummy files"
# Move the provided codon files to a different directory. This will avoid
# user confusion and file collisions on case-insensitive file systems (see
# bug #115446). This change is documented in "README.gentoo".
mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \
|| die "Failed to move CODON directory"
# collision with dev-texlive/texlive-latexextra, bug #927976
mv "${ED}"/usr/bin/{,emboss-}wordcount || die
}
pkg_postinst() {
readme.gentoo_print_elog
}
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