sci-biology/consed: Version bump to 29

* EAPI=6
* Allow for compiling with GCC 6
* [QA] Respect all user variables (CC, CXX, ...)
* [QA] Fix various C and C++ related warnings
* Fix perl shebangs to be portable

Package-Manager: portage-2.3.1

1 files changed, 111 insertions, 0 deletions

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
new file mode 100644
index 000000000000..159e10768847
--- /dev/null
+++ b/sci-biology/consed/consed-29.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="
+	${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+
+COMMON_DEPEND="
+	x11-libs/libX11
+	x11-libs/motif:0
+	sci-biology/samtools:0.1-legacy
+"
+DEPEND="
+	${COMMON_DEPEND}
+	virtual/pkgconfig
+"
+RDEPEND="
+	${COMMON_DEPEND}
+	dev-lang/perl
+	>=sci-biology/phred-071220-r1
+	>=sci-biology/phrap-1.080812-r2
+"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+PATCHES=(
+	"${FILESDIR}/${PN}-29-fix-build-system.patch"
+	"${FILESDIR}/${PN}-29-fix-c++14.patch"
+	"${FILESDIR}/${PN}-29-fix-qa.patch"
+	"${FILESDIR}/${PN}-29-fix-perl-shebang.patch"
+)
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
+	einfo "and place it in ${DISTDIR},"
+	einfo "obtain the file"
+	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	default
+
+	sed \
+		-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
+		-e "s:/usr/local/genome:${EPREFIX}/usr:" \
+		-e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \
+		-e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \
+		-i scripts/* contributions/* || die
+}
+
+src_configure() {
+	append-cflags -std=gnu99
+	append-lfs-flags
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}" \
+		CPPFLAGS="${CPPFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \
+		LIBS="-L${EPREFIX}/usr/$(get_libdir)" \
+		X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \
+		SAMTOOLS_LIBS="-lbam-0.1-legacy"
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/*
+
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq}
+
+	if use examples; then
+		insinto /usr/share/${PN}/examples
+		doins -r \
+			standard polyphred autofinish assembly_view 454_newbler \
+			align454reads align454reads_answer solexa_example \
+			solexa_example_answer selectRegions selectRegionsAnswer
+	fi
+
+	cat > 99consed <<-_EOF_ || die
+	CONSED_HOME=${EPREFIX}/usr
+	CONSED_PARAMETERS=${EPREFIX}/etc/consedrc
+	_EOF_
+	doenvd 99consed
+
+	dodoc README.txt *_announcement.txt
+}
+
+pkg_postinst() {
+	einfo "Package documentation is available at"
+	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}