sci-biology/consed: Import to tree; drop old EPAI=1 version, #526742

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 98 insertions, 73 deletions

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 61c95626d70c..b6e3c6c1be36 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/consed
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.7 2013/03/11 15:00:03 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.8 2014/10/26 16:13:23 jlec Exp $
+
+*consed-27 (26 Oct 2014)
+
+  26 Oct 2014; Justin Lecher <jlec@gentoo.org> -consed-19-r1.ebuild,
+  +consed-27.ebuild:
+  Import to tree; drop old EPAI=1 version, #526742
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/consed/consed-19-r1.ebuild b/sci-biology/consed/consed-19-r1.ebuild
deleted file mode 100644
index 18bd330c7e66..000000000000
--- a/sci-biology/consed/consed-19-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.4 2012/10/24 19:30:07 ulm Exp $
-
-EAPI=1
-
-inherit toolchain-funcs
-
-DESCRIPTION="Consed: a genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-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_unpack() {
-	unpack ${A}
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq}
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME=/usr' > "${S}/99consed"
-	doenvd "${S}/99consed" || die
-	dodoc README.txt *_announcement.txt
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
new file mode 100644
index 000000000000..b56fccd7213b
--- /dev/null
+++ b/sci-biology/consed/consed-27.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="
+	${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+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 ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+	sed -i \
+		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
+	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+	sed \
+		-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+		-i "${S}"/scripts/* || die
+}
+
+src_compile() {
+	emake
+	emake -C misc/mktrace
+	emake -C misc/phd2fasta
+	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
+	dobin scripts/* contributions/*
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq}
+	insinto /usr/share/${PN}/examples
+	doins -r \
+		standard polyphred autofinish assembly_view 454_newbler \
+		align454reads align454reads_answer solexa_example \
+		solexa_example_answer selectRegions selectRegionsAnswer
+	echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
+	echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
+	mkdir -p "${ED}"/etc/consedrc || die
+	touch "${ED}"/etc/consedrc || die
+	doenvd "${S}/99consed" || die
+	sed \
+		-e "s#/usr/local/genome#${EPREFIX}/usr#" \
+		-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
+	sed \
+		-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
+		-i "${ED}"/usr/bin/phredPhrap || die
+	sed \
+		-e 's#/wt1/gordon/genome#/usr/bin#' \
+		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
+	dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+	einfo "Package documentation is available at"
+	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}