commit: 4dddd0bce4418af8c0ae000928d0107ab093a8fa
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 5 15:22:24 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 5 15:22:24 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4dddd0bc
sci-biology/mira: version bump, note that >=gcc-4.9.1 is needed since 4.9.x
Package-Manager: portage-2.2.18
sci-biology/mira/ChangeLog | 130 +++++++++++++++++++++
.../mira/files/mira-3.4.0.2-boost-1.50.patch | 24 ++++
sci-biology/mira/files/mira-4.9.5-cout.patch | 16 +++
sci-biology/mira/metadata.xml | 5 +
sci-biology/mira/mira-4.9.5.ebuild | 79 +++++++++++++
5 files changed, 254 insertions(+)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
new file mode 100644
index 0000000..4255505
--- /dev/null
+++ b/sci-biology/mira/ChangeLog
@@ -0,0 +1,130 @@
+# ChangeLog for sci-biology/mira
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.31
2015/04/07 14:33:30 jlec Exp $
+
+ 25 Jan 2015; Justin Lecher <j...@gentoo.org> mira-4.0.2.ebuild,
+ +files/mira-4.0.2-cout.patch:
+ Build fix for newer gcc, #537564
+
+*mira-4.0.2 (23 Jan 2015)
+
+ 23 Jan 2015; Justin Lecher <j...@gentoo.org> +mira-4.0.2.ebuild:
+ Version Bump, thanks Martin Mokrejš for the work
+
+ 23 Jan 2015; Justin Lecher <j...@gentoo.org> mira-3.9.18.ebuild:
+ Add workaroung for m4 dir location, #536172
+
+ 14 Jan 2014; Justin Lecher <j...@gentoo.org> -mira-3.2.1.ebuild:
+ Drop old
+
+ 14 Jan 2014; Agostino Sarubbo <a...@gentoo.org> mira-3.9.18.ebuild:
+ Stable for x86, wrt bug #497218
+
+ 12 Jan 2014; Pacho Ramos <pa...@gentoo.org> mira-3.9.18.ebuild:
+ amd64 stable, bug #497218
+
+ 06 Jan 2014; Justin Lecher <j...@gentoo.org> mira-3.2.1.ebuild:
+ Punt base.eclass
+
+ 06 Jan 2014; Justin Lecher <j...@gentoo.org> -mira-3.2.1-r1.ebuild,
+ -mira-3.4.0.2.ebuild:
+ Drop old
+
+*mira-3.9.18 (07 Jul 2013)
+
+ 07 Jul 2013; Justin Lecher <j...@gentoo.org> +mira-3.9.18.ebuild:
+ Version Bump; fixed compilation with dev-libs/boost-1.53.0 and some libtool
+ versions, #450322; thanks Martin Mokrejs for all his work
+
+ 11 Mar 2013; Justin Lecher <j...@gentoo.org> metadata.xml:
+ Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+*mira-3.4.0.2 (07 Nov 2012)
+
+ 07 Nov 2012; Justin Lecher <j...@gentoo.org> mira-3.2.1.ebuild,
+ mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild,
+ +files/mira-3.4.0.2-boost-1.50.patch:
+ Version Bump, #377807
+
+*mira-3.2.1-r1 (07 Nov 2012)
+
+ 07 Nov 2012; Justin Lecher <j...@gentoo.org> mira-3.2.1.ebuild,
+ +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch:
+ Fix for boost >1.50, #425468
+
+ 08 Jul 2012; Justin Lecher <j...@gentoo.org> -mira-3.0.5.ebuild,
+ -mira-3.2.0.ebuild:
+ Drop old
+
+ 25 Jun 2012; Jeff Horelick <jdh...@gentoo.org> mira-3.2.1.ebuild:
+ marked x86 per bug 418439
+
+ 24 Jun 2012; Agostino Sarubbo <a...@gentoo.org> mira-3.2.1.ebuild:
+ Stable for amd64, wrt bug #418439
+
+ 23 Jun 2012; Kacper Kowalik <xarthisius...@gmail.com> mira-3.2.1.ebuild:
+ Don't install docs that are no longer there, thanks to David Abbott for the
+ patch
+
+*mira-3.2.1 (21 May 2011)
+
+ 21 May 2011; Andrey Kislyuk <wea...@gentoo.org> +mira-3.2.1.ebuild:
+ Version bump and fix bug 367921
+
+ 11 Feb 2011; Markos Chandras <hwoar...@gentoo.org> mira-3.2.0.ebuild:
+ Stable on amd64 wrt bug #353568
+
+ 07 Feb 2011; Pawel Hajdan jr <phajdan...@gentoo.org> mira-3.2.0.ebuild:
+ x86 stable wrt bug #353568
+
+ 17 Oct 2010; Andrey Kislyuk <wea...@gentoo.org> mira-3.2.0.ebuild:
+ Remove doc USE flag and dependency, workaround for bug 340419
+
+*mira-3.2.0 (26 Sep 2010)
+
+ 26 Sep 2010; Andrey Kislyuk <wea...@gentoo.org> -mira-3.0.0.ebuild,
+ -mira-3.0.3.ebuild, +mira-3.2.0.ebuild:
+ Version bump, drop old
+
+ 28 Jun 2010; Justin Lecher <j...@gentoo.org> mira-3.0.0.ebuild,
+ mira-3.0.3.ebuild, mira-3.0.5.ebuild:
+ Prepared for prefix, #325929
+
+*mira-3.0.5 (05 May 2010)
+
+ 05 May 2010; Andrey Kislyuk <wea...@gentoo.org> +mira-3.0.5.ebuild:
+ Version bump
+
+*mira-3.0.3 (18 Mar 2010)
+
+ 18 Mar 2010; Andrey Kislyuk <wea...@gentoo.org> -mira-3.0.2.ebuild,
+ +mira-3.0.3.ebuild:
+ Hotfix from upstream
+
+*mira-3.0.2 (10 Mar 2010)
+
+ 10 Mar 2010; Andrey Kislyuk <wea...@gentoo.org> -mira-3.0.1.ebuild,
+ +mira-3.0.2.ebuild:
+ Hotfix from upstream
+
+*mira-3.0.1 (06 Mar 2010)
+
+ 06 Mar 2010; Andrey Kislyuk <wea...@gentoo.org> +mira-3.0.1.ebuild:
+ Version bump (bugfix release)
+
+ 25 Feb 2010; Samuli Suominen <ssuomi...@gentoo.org> mira-3.0.0.ebuild,
+ +files/mira-3.0.0-asneeded.patch:
+ Fix ax_lib_expat.m4 macro to not use LDFLAGS for passing libraries wrt
+ #305547 by Kacper Kowalik.
+
+ 03 Feb 2010; Andrey Kislyuk <wea...@gentoo.org> mira-3.0.0.ebuild:
+ add eautoreconf
+
+ 03 Feb 2010; Andrey Kislyuk <wea...@gentoo.org> mira-3.0.0.ebuild:
+ Install 3rd party files
+
+*mira-3.0.0 (02 Feb 2010)
+
+ 02 Feb 2010; Andrey Kislyuk <wea...@gentoo.org> +metadata.xml,
+ +mira-3.0.0.ebuild:
+ New package, ebuild written by me
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
new file mode 100644
index 0000000..4271922
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
@@ -0,0 +1,24 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 1ac06af..5b7be93 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+ for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so*
$BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e
's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib";
AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system";
AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ if test "x$link_regex" != "xyes"; then
+ for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}*
2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e
's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib";
AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system";
AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ fi
diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch
b/sci-biology/mira/files/mira-4.9.5-cout.patch
new file mode 100644
index 0000000..14feb02
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.9.5-cout.patch
@@ -0,0 +1,16 @@
+ src/progs/quirks.C | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/progs/quirks.C b/src/progs/quirks.C
+index 47e5ee8..060b6f3 100644
+--- a/src/progs/quirks.C
++++ b/src/progs/quirks.C
+@@ -25,6 +25,8 @@
+
+ #include <boost/filesystem.hpp>
+
++#include <iostream>
++
+ // make the "tcmalloc: large alloc" messages from TCMallom disappear
+ // by setting the reporting environment variable to a very large value
+ // see:
http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/mira/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.9.5.ebuild
b/sci-biology/mira/mira-4.9.5.ebuild
new file mode 100644
index 0000000..e643b5b
--- /dev/null
+++ b/sci-biology/mira/mira-4.9.5.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.2
2015/01/25 17:04:35 jlec Exp $
+
+EAPI=5
+
+MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived)
to mira-4.0rc2 (upstream fromat)
+
+inherit autotools eutils multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454
and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html";
+SRC_URI="
+
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
+
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+#
http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
+#
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+#
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc"
+
+CDEPEND="
+ dev-libs/boost
+ dev-util/google-perftools"
+DEPEND="${CDEPEND}
+ app-editors/vim-core
+ dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
+
+# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i
's/flex++/flex -+/' || die
+ epatch \
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
+ "${FILESDIR}"/${P}-cout.patch
+
+ sed \
+ -e "s:-O[23]::g" \
+ -e "s:-funroll-loops::g" \
+ -i configure.ac || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+# base_src_compile
+# # TODO: resolve docbook incompatibility for building docs
+# if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+ default
+ dodoc ${DOCS[@]}
+
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+ dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo
"http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html";
+}
