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

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 119 insertions, 80 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/Manifest b/sci-biology/consed/Manifest
index e06858128ab9..8f477970ddea 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,16 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089
 DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3
-EBUILD consed-19-r1.ebuild 2224 SHA256 af6b072465f5ad98b0d6b4028b4d9e9f75bfbfaeb0a5819a8457546fea3501f5 SHA512 46d345cf86dddc3dd2097a0c499d8463dad45a0b27ab18d4c199379e8bb47b3fbdf6ed7bee27baf7f30fa26b041e34f2e00159acee4739f7f22b68a5cb7c1172 WHIRLPOOL a15dce3322db2972ae4b4c65c7705e01992118a27372e7a87555bba6392b01d5afaf612da48dda0f83461f3aebe1db7179d9c42d832574e9b086c21ffdfed877
+DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
+DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
 EBUILD consed-19-r2.ebuild 2247 SHA256 f126517211157449839927993dbfd31f1fe90528a48e64c65adfeba2a163eefd SHA512 505c20fa8f8b7dde1f321ef6204db6b7841e1080f34d6508761a22d028897e5962555483ed85994464772a2b3477aded23303f16a65f659ed6f0717b0ddb933c WHIRLPOOL e9f4e0d796934255d715df94f35ece626b02e0af1f72aefbed6729ec049f10eb8aafff88693050a78ca3c8a0fb629b22c713052120e08a3a612811de41d3c016
-MISC ChangeLog 1382 SHA256 9e5d985ecd7fe21610b98f6907a682b1ba8ca656d235a0a0751fd9dd3148e223 SHA512 30a348e5e76fd436a2d039010f08749ff4cba43882c2484315f18e3da815a550d45a135c8a68adc3417357c6e6f9d453365dcb8733dfd6e20fb3a0de1edb0577 WHIRLPOOL 249e8420f438c7439b98d032c5f34621374b959c1a9dbece8f606fe620d6724e0f02621dcea2321aadfe1be10178988984cd2cc4c147a320c411e7d460ad3d10
+EBUILD consed-27.ebuild 2823 SHA256 e3db2662e23ab2adefe466e59cdd36c050dc8d7d2b35481fde86cced1ed281ff SHA512 c33d903ef50567003d55f69b7edac7711f99edf4e7fa4cd7e96b56dbe0724a2a9b13cc2dfc8fde680eba41b2d16fd65ee1529ca5bc1ccc0f77766c5208526997 WHIRLPOOL e03e63b187f4d3f9d868afff3955e0680d4c3dbccc0cd4cb55dbdd8f0c05e4f327ef003665350125c0a297b785989bbacfe4074f52b9f68fc78f75bd229f3bc2
+MISC ChangeLog 1550 SHA256 e110efe81735bbf632bf4a714561ab23dd49b8c03e0e34e0d062041e95ccd3f5 SHA512 f75dcb91ca84cdc363871da94fdb50369bc213f76e3d0e97ee2efbe352721e7994ffe53e92e96f326af5a552eb8edd1d895f839939be7e27f91e5cc5d230ae14 WHIRLPOOL a09fa21234435824b67947e0db03020e18fc6621ca9303478200849f5fe503369c7efb8fcfffcceec89998b971e49cb40ec92db40d6515fbc174eb3c45822c9f
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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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"
+}