[gentoo-commits] repo/gentoo:master commit in: sci-biology/mummer/

[David Seifert]

commit:     7b5460f041d22383cf26a2d7cd5b3d784eb68133
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 15 16:16:27 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jan 15 16:20:52 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b5460f0

sci-biology/mummer: Version bump to 3.9.4_alpha

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/mummer/Manifest                  |  1 +
 sci-biology/mummer/mummer-3.9.4_alpha.ebuild | 83 ++++++++++++++++++++++++++++
 2 files changed, 84 insertions(+)

diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
index 5e45695..8089124 100644
--- a/sci-biology/mummer/Manifest
+++ b/sci-biology/mummer/Manifest
@@ -1,3 +1,4 @@
 DIST MUMmer3.20.tar.gz 3155446 SHA256 
9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 SHA512 
7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd
 WHIRLPOOL 
a08af35aee960bcd6274d3a00b1c1819d23367c81a72fd41c652c3579253b0aeeb5ef66f6dcfed60b4987c3a40830d04cd81745dce8a274cc3de0663dd54ae6f
 DIST MUMmer3.21.tar.gz 3155965 SHA256 
7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 SHA512 
61d49e5451e1697003f7acaac690f2ede7ab71766208d3218954527c48be76ddb78d60ff40ae1bdcd4b93d3efaf21b5bd027da3722eab1ae3fa399ee726bc96e
 WHIRLPOOL 
50c7b0d7c00bf85aa8e0f8b80bf55186f8c0a53d26c3e50d2149120bc46f3632de4cb861a4d4265c1e3be731dffb71940344b238fd3e977412134b0e401cb95e
 DIST MUMmer3.22.tar.gz 3156338 SHA256 
429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da SHA512 
37bbb368c679d2e98fa9b9ef10c18008c173c25ee79183eb30e34125b1dc9cd10f005b7bd7c648335a8025509d8e3456fcc7ce497c95fa71c3c5d3ed3685665f
 WHIRLPOOL 
487333ca38a9c59984ed059e8dd620ad3c0a5ae1a537e500c7b8b2d58213ac88960a13c0f25e6e0490d1209c9e73cfe8df0f8a43dbae9fd6a3e9fe3ce42da453
+DIST mummer-3.9.4_alpha.tar.gz 956517 SHA256 
fb2f03c729cd078d526d6318f91061f8832c2e8bd0d519ddf3c0b6e656029cfa SHA512 
f0b962a69df6918afc7d163b30bcf5bd9eb2be663c8ac685b5e06317953cf12b9d240df8a5bfe8a9410b65cf88176cc7a71eecfc460e51df7ad1b27dc3a10fc2
 WHIRLPOOL 
8443cde87f868136eaa005db2b5b461a822097778d4c36448602a5cda058dc1dfa10daa08883248ffaba79a1d33240170b94b96548ebb56a01eaa27838d4afd6

diff --git a/sci-biology/mummer/mummer-3.9.4_alpha.ebuild 
b/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
new file mode 100644
index 00000000..c949000
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.9.4_alpha.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+
+inherit perl-functions python-r1 toolchain-funcs
+
+MY_PV=${PV//_/}
+
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/";
+SRC_URI="https://github.com/gmarcais/${PN}/releases/download/v${MY_PV}/${PN}-${MY_PV}.tar.gz
 -> ${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="openmp perl python"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+       python? (
+               ${PYTHON_DEPS}
+               dev-lang/swig:0
+       )"
+RDEPEND="
+       app-shells/tcsh
+       dev-lang/perl:=
+       python? ( ${PYTHON_DEPS} )"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S=${WORKDIR}/${PN}-${MY_PV}
+
+pkg_pretend() {
+       [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+       [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+       use python && preamble="python_foreach_impl run_in_build_dir"
+}
+
+src_configure() {
+       perl_set_version
+       configure() {
+               local pythonconf
+               if use python; then
+                       
pythonconf="--enable-python-binding=$(python_get_sitedir)"
+               else
+                       pythonconf="--disable-python-binding"
+               fi
+
+               ECONF_SOURCE="${S}" econf \
+                       --disable-static \
+                       --disable-ruby-binding \
+                       $(use_enable perl perl-binding "${VENDOR_LIB}") \
+                       $(use_enable openmp) \
+                       $(use_enable python swig) \
+                       "${pythonconf}"
+       }
+       ${preamble} configure
+}
+
+src_compile() {
+       ${preamble} default
+}
+
+src_install() {
+       ${preamble} default
+       einstalldocs
+
+       # avoid file collision
+       mv "${ED%/}"/usr/bin/{,mummer-}annotate || die
+
+       # move perl module into right place
+       mkdir -p "${D%/}${VENDOR_LIB}" || die
+       mv "${ED%/}"/usr/$(get_libdir)/mummer/Foundation.pm 
"${D%/}${VENDOR_LIB}" || die
+
+       # no static libs, can purge .la files
+       find "${D}" -name '*.la' -delete || die
+}