From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
Date: Wed, 18 May 2011 16:10:52 +0000 (UTC) [thread overview]
Message-ID: <71511493b0866f094c9b7a11490facd09df27c86.mmokrejs@gentoo> (raw)
commit: 71511493b0866f094c9b7a11490facd09df27c86
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed May 18 16:10:34 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May 18 16:10:34 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=71511493
sci-biology/mira-3.2.1-r1: added an extra patch for traceinfo off-by-one error
(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)
---
sci-biology/mira/files/mira-3.0.0-asneeded.patch | 56 ++++++++++++++++++++
.../mira/files/mira_left_clip.readpool.C.patch | 36 +++++++++++++
sci-biology/mira/metadata.xml | 9 +++
sci-biology/mira/mira-3.2.1-r1.ebuild | 55 +++++++++++++++++++
sci-biology/mira/mira-3.2.1.17-r1.ebuild | 55 +++++++++++++++++++
5 files changed, 211 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
new file mode 100644
index 0000000..9bbd267
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
@@ -0,0 +1,56 @@
+http://bugs.gentoo.org/show_bug.cgi?id=305547
+
+--- config/m4/ax_lib_expat.m4
++++ config/m4/ax_lib_expat.m4
+@@ -96,6 +99,7 @@
+
+ EXPAT_CFLAGS=""
+ EXPAT_LDFLAGS=""
++ EXPAT_LIBS=""
+ EXPAT_VERSION=""
+
+ dnl
+@@ -105,7 +109,8 @@
+
+ if test -n "$expat_prefix"; then
+ expat_include_dir="$expat_prefix/include"
+- expat_lib_flags="-L$expat_prefix/lib -lexpat"
++ expat_lib_flags="-L$expat_prefix/lib"
++ expat_libs="-lexpat"
+ run_expat_test="yes"
+ elif test "$expat_requested" = "yes"; then
+ if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
+@@ -126,6 +131,8 @@
+ saved_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $expat_lib_flags"
+
++ saved_LIBS="$LIBS"
++ LIBS="$LIBS $expat_libs"
+ dnl
+ dnl Check Expat headers
+ dnl
+@@ -171,7 +178,8 @@
+ ]]
+ )],
+ [
+ EXPAT_LDFLAGS="$expat_lib_flags"
++ EXPAT_LIBS="$expat_libs"
+ expat_lib_found="yes"
+ AC_MSG_RESULT([found])
+ ],
+@@ -185,6 +193,7 @@
+
+ CPPFLAGS="$saved_CPPFLAGS"
+ LDFLAGS="$saved_LDFLAGS"
++ LIBS="$saved_LIBS"
+ fi
+
+ AC_MSG_CHECKING([for Expat XML Parser])
+@@ -194,6 +203,7 @@
+
+ AC_SUBST([EXPAT_CFLAGS])
+ AC_SUBST([EXPAT_LDFLAGS])
++ AC_SUBST([EXPAT_LIBS])
+
+ HAVE_EXPAT="yes"
+ else
diff --git a/sci-biology/mira/files/mira_left_clip.readpool.C.patch b/sci-biology/mira/files/mira_left_clip.readpool.C.patch
new file mode 100644
index 0000000..12977dd
--- /dev/null
+++ b/sci-biology/mira/files/mira_left_clip.readpool.C.patch
@@ -0,0 +1,36 @@
+*** src/mira/readpool.C.ori 2010-11-21 11:42:29.000000000 -0600
+--- src/mira/readpool.C 2011-01-13 10:20:38.000000000 -0600
+***************
+*** 1751,1757 ****
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : {
+! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str()));
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : {
+--- 1751,1757 ----
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : {
+! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())-1);
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : {
+***************
+*** 1759,1765 ****
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : {
+! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str()));
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : {
+--- 1759,1765 ----
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : {
+! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())-1);
+ break;
+ }
+ case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : {
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/mira/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>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r1.ebuild
new file mode 100644
index 0000000..020876c
--- /dev/null
+++ b/sci-biology/mira/mira-3.2.1-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+MIRA_3RDPARTY_PV="17-04-2010"
+
+inherit autotools base 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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+
+CDEPEND=">=dev-libs/boost-1.41.0-r3"
+DEPEND="${CDEPEND}
+ dev-libs/expat"
+RDEPEND="${CDEPEND}
+ sci-biology/smalt-bin
+ sci-biology/ssaha2-bin"
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+ epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
+ # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
+ epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ AT_M4DIR="config/m4" eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-thread=boost_thread-mt
+}
+
+src_compile() {
+ base_src_compile
+ # TODO: resolve docbook incompatibility for building docs
+ if use doc; then emake -C doc clean docs || die; fi
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
+ find doc/docs/man -type f | xargs doman
+ find doc/docs/texinfo -type f | xargs doinfo
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
new file mode 100644
index 0000000..020876c
--- /dev/null
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+MIRA_3RDPARTY_PV="17-04-2010"
+
+inherit autotools base 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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+
+CDEPEND=">=dev-libs/boost-1.41.0-r3"
+DEPEND="${CDEPEND}
+ dev-libs/expat"
+RDEPEND="${CDEPEND}
+ sci-biology/smalt-bin
+ sci-biology/ssaha2-bin"
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+ epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
+ # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
+ epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ AT_M4DIR="config/m4" eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-thread=boost_thread-mt
+}
+
+src_compile() {
+ base_src_compile
+ # TODO: resolve docbook incompatibility for building docs
+ if use doc; then emake -C doc clean docs || die; fi
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
+ find doc/docs/man -type f | xargs doman
+ find doc/docs/texinfo -type f | xargs doinfo
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
next reply other threads:[~2011-05-18 16:11 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-05-18 16:10 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2011-06-23 15:04 [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/ Martin Mokrejs
2011-12-08 1:39 Martin Mokrejs
2013-02-22 0:37 Martin Mokrejs
2015-06-05 15:23 Martin Mokrejs
2015-07-21 9:02 Martin Mokrejs
2020-09-22 11:12 Aisha Tammy
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