[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/

[Martin Mokrejs]

commit:     2c576304e6b594c5423610448a39bb68e75d47ea
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 11:53:41 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 11:53:41 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c576304

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

---
 sci-biology/mgblast/ChangeLog          | 11 ++++++++
 sci-biology/mgblast/metadata.xml       |  9 +++++++
 sci-biology/mgblast/mgblast-0.1.ebuild | 46 ++++++++++++++++++++++++++++++++++
 3 files changed, 66 insertions(+)

diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog
new file mode 100644
index 0000000..5b62270
--- /dev/null
+++ b/sci-biology/mgblast/ChangeLog
@@ -0,0 +1,11 @@
+# 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@×××××××××××××××.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/metadata.xml b/sci-biology/mgblast/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/mgblast/metadata.xml
@@ -0,0 +1,9 @@
+<?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@×××××××××××××××.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
new file mode 100644
index 0000000..8b7011a
--- /dev/null
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -0,0 +1,46 @@
+# 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
+}