sci-biology/mgblast: initial ebuild but while it needs an old version of ncbi-tools source tree to build ... it is not tested yet

4 files changed, 67 insertions, 0 deletions

diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog
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+# ChangeLog for sci-biology/mgblast
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mgblast-0.1 (24 Mar 2014)
+
+  24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +mgblast-0.1.ebuild, +metadata.xml:
+  initial ebuild but while it needs an old version of ncbi-tools source tree to
+  build ... it is not tested yet
+
diff --git a/sci-biology/mgblast/Manifest b/sci-biology/mgblast/Manifest
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+++ b/sci-biology/mgblast/Manifest
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+DIST mgblast.tar.gz 22904 SHA256 eb790a0e3979b511f289e440f8bc381788509e80a214792315356a23af151cf2
diff --git a/sci-biology/mgblast/metadata.xml b/sci-biology/mgblast/metadata.xml
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+++ b/sci-biology/mgblast/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
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index 000000000..8b7011a15
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+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
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+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Customized version of megablast from TIGR Gene Indices project used by tgicl and gicl utilities"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="" # upstream binary is provided by sci-biology/tgicl currently
+#KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sci-biology/ncbi-tools"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}
+
+# mgblast needs old version of ncbi-tools unpacked and compiled during its own compilation
+# from newer tools you need to include blfmtutl.h but the next error is no go for me:
+#   mgblast.c:2205: error: too few arguments to function ‘BXMLBuildOneQueryIteration’
+
+# Quoting from mgblast/README: the present package was built and tested only with the release 20060507
+
+src_prepare(){
+	# mgblast cannot be compiled against newer ncbi-tools but let's try
+	mv mgblast/makefile mgblast/Makefile 2>/dev/null || true
+	sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' mgblast/Makefile
+	sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile
+	sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' mgblast/Makefile
+	sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
+	sed -i "s#-I-#-iquote#" mgblast/Makefile
+}
+
+src_compile(){
+	cd ${S}/mgblast || die
+	emake || die "mgblast really needs an older ncbi-toolkit version so we are out of luck, install the binary provided by upstream instead from mgblast-bin package"
+}
+
+src_install(){
+	cd ${S}/mgblast || die
+	dobin mgblast || die
+}