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 <mmokr...@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/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>mmokr...@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 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 +}
