commit: aada253938880482eb9e52d146948e062aaea848 Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org> AuthorDate: Tue Sep 16 16:24:23 2014 +0000 Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> CommitDate: Tue Sep 16 16:24:23 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aada2539
clean up Package-Manager: portage-2.2.8-r1 --- sci-biology/mgblast/ChangeLog | 4 +++- sci-biology/mgblast/mgblast-0.1.ebuild | 20 ++++++++++---------- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog index 5b62270..8a87f81 100644 --- a/sci-biology/mgblast/ChangeLog +++ b/sci-biology/mgblast/ChangeLog @@ -2,10 +2,12 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Sep 2014; Christoph Junghans <[email protected]> mgblast-0.1.ebuild: + clean up + *mgblast-0.1 (24 Mar 2014) 24 Mar 2014; Martin Mokrejs <[email protected]> +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/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild index 8b7011a..4638e9b 100644 --- a/sci-biology/mgblast/mgblast-0.1.ebuild +++ b/sci-biology/mgblast/mgblast-0.1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 DESCRIPTION="Customized version of megablast from TIGR Gene Indices project used by tgicl and gicl utilities" HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"; @@ -17,7 +17,7 @@ IUSE="" DEPEND="sci-biology/ncbi-tools" RDEPEND="${DEPEND}" -S=${WORKDIR} +S="${WORKDIR}" # mgblast needs old version of ncbi-tools unpacked and compiled during its own compilation # from newer tools you need to include blfmtutl.h but the next error is no go for me: @@ -28,19 +28,19 @@ S=${WORKDIR} 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 + sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' mgblast/Makefile || die + sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile || die + sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' mgblast/Makefile || die + sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile || die # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ ! + sed -i "s#-I-#-iquote#" mgblast/Makefile || die } src_compile(){ - cd ${S}/mgblast || die + cd "${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 ${S}/mgblast || die - dobin mgblast || die + cd "${S}"/mgblast || die + dobin mgblast }
