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authorIan Stakenvicius <axs@gentoo.org>2016-04-19 16:34:54 -0400
committerIan Stakenvicius <axs@gentoo.org>2016-04-19 16:34:54 -0400
commitcd5113534b40b92c4b055c9a12c52e105e22828a (patch)
tree525edff033d86189e4ea51deeb6888635fcea38d
parentfix <pkg/> reference in metadata.xml (diff)
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sci-biology/hmmer: cheamup of 2.3.2 version
* Bumped EAPI * Merged KEYWORDS between 2.3.2-r1 and 2.3.2-r2 * dropped IUSE="pvm" as package was dropped 5 years ago * fixed metadata.xml to match Package-Manager: portage-2.2.26
-rw-r--r--sci-biology/hmmer/hmmer-2.3.2-r1.ebuild51
-rw-r--r--sci-biology/hmmer/hmmer-2.3.2-r3.ebuild (renamed from sci-biology/hmmer/hmmer-2.3.2-r2.ebuild)28
-rw-r--r--sci-biology/hmmer/metadata.xml4
3 files changed, 15 insertions, 68 deletions
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
deleted file mode 100644
index 7b1fbba5e07..00000000000
--- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
-HOMEPAGE="http://hmmer.janelia.org/"
-SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ia64 ~ppc ~sparc x86"
-
-DEPEND="pvm? ( sys-cluster/pvm )"
-
-src_compile() {
- ./configure \
- --host=${CHOST} \
- --prefix="${D}"/usr \
- --exec_prefix="${D}"/usr \
- --mandir="${D}"/usr/share/man \
- --enable-lfs \
- $(use_enable pvm) \
- $(use_enable threads) || die
- emake || die
-}
-
-src_install() {
- einstall || die
-
- cd src
- dolib libhmmer.a
- insinto /usr/include/hmmer
- doins *.h
-
- cd ../squid
- dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
- dolib libsquid.a
- insinto /usr/include/hmmer
- doins *.h
-
- cd ..
- dodoc NOTES
- newdoc 00README README
- insinto /usr/share/doc/${PF}
- doins Userguide.pdf
-}
-
-src_test() {
- make check
-}
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
index 64fa5003007..9868ec14eaa 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
@@ -1,45 +1,47 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
+EAPI=6
+
DESCRIPTION="Sequence analysis using profile hidden Markov models"
LICENSE="GPL-2"
HOMEPAGE="http://hmmer.janelia.org/"
SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86"
+IUSE="threads test"
+KEYWORDS="~alpha amd64 ia64 ~ppc ppc64 ~sparc x86"
-DEPEND="pvm? ( sys-cluster/pvm )"
+DEPEND=""
+RDEPEND=""
-src_compile() {
+src_configure() {
econf \
--host=${CHOST} \
--prefix="${D}"/usr \
--exec_prefix="${D}"/usr \
--mandir="${D}"/usr/share/man \
--enable-lfs \
- $(use_enable pvm) \
- $(use_enable threads) || die
- emake || die
+ $(use_enable threads)
}
src_install() {
- einstall || die
+ emake DESTDIR="${D}" install
- cd src
+ pushd src >/dev/null || die
dolib libhmmer.a
insinto /usr/include/hmmer
doins *.h
+ popd >/dev/null || die
- cd ../squid
+ pushd squid >/dev/null || die
dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
dolib libsquid.a
insinto /usr/include/hmmer
doins *.h
+ popd >/dev/null || die
- cd ..
dodoc NOTES
newdoc 00README README
insinto /usr/share/doc/${PF}
@@ -47,5 +49,5 @@ src_install() {
}
src_test() {
- make check
+ emake check
}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index a6a17ef2582..8417d1580d4 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -5,8 +5,4 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <use>
- <flag name="pvm">Add support for parallel virtual machine
- (<pkg>sys-cluster/pvm</pkg>)</flag>
- </use>
</pkgmetadata>