* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2011-05-18 16:10 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2011-05-18 16:10 UTC (permalink / raw
To: gentoo-commits
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}
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2011-06-23 15:04 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2011-06-23 15:04 UTC (permalink / raw
To: gentoo-commits
commit: 73f514811fefcf2be4be2a75d8018426660f6d5e
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 15:04:37 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 15:04:37 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=73f51481
sci-biology/mira: libtool.m4 fix so we can safely run eautoreconf and a version bump
(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)
---
sci-biology/mira/files/libtool.m4.patch | 13 +++++++++++++
sci-biology/mira/mira-3.2.1-r2.ebuild | 1 +
sci-biology/mira/mira-3.2.1.17-r1.ebuild | 5 ++---
.../{mira-3.2.1-r2.ebuild => mira-3.2.1.18.ebuild} | 4 +++-
4 files changed, 19 insertions(+), 4 deletions(-)
diff --git a/sci-biology/mira/files/libtool.m4.patch b/sci-biology/mira/files/libtool.m4.patch
new file mode 100644
index 0000000..9cfaeef
--- /dev/null
+++ b/sci-biology/mira/files/libtool.m4.patch
@@ -0,0 +1,13 @@
+--- config/m4/libtool.m4.ori 2011-06-22 12:28:14.000000000 +0200
++++ config/m4/libtool.m4 2011-06-22 12:28:39.000000000 +0200
+@@ -88,10 +88,6 @@
+ # This can be used to rebuild libtool when needed
+ LIBTOOL_DEPS="$ltmain"
+
+-# Always use our own libtool.
+-LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+-AC_SUBST(LIBTOOL)dnl
+-
+ _LT_SETUP
+
+ # Only expand once:
diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild
index a4de8cc..c110959 100644
--- a/sci-biology/mira/mira-3.2.1-r2.ebuild
+++ b/sci-biology/mira/mira-3.2.1-r2.ebuild
@@ -31,6 +31,7 @@ src_prepare() {
epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ epatch "${FILESDIR}"/libtool.m4.patch
AT_M4DIR="config/m4" eautoreconf
}
diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
index 9fe96ff..04b3767 100644
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -16,9 +16,7 @@ SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
LICENSE="GPL-2"
SLOT="0"
IUSE=""
-KEYWORDS=""
-# masked because of 'libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
CDEPEND=">=dev-libs/boost-1.41.0-r3
dev-util/google-perftools"
@@ -33,6 +31,7 @@ src_prepare() {
epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ epatch "${FILESDIR}"/libtool.m4.patch
AT_M4DIR="config/m4" eautoreconf
}
diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1.18.ebuild
similarity index 87%
copy from sci-biology/mira/mira-3.2.1-r2.ebuild
copy to sci-biology/mira/mira-3.2.1.18.ebuild
index a4de8cc..3ea8ce1 100644
--- a/sci-biology/mira/mira-3.2.1-r2.ebuild
+++ b/sci-biology/mira/mira-3.2.1.18.ebuild
@@ -31,7 +31,9 @@ src_prepare() {
epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ epatch "${FILESDIR}"/libtool.m4.patch
AT_M4DIR="config/m4" eautoreconf
+ #epatch "${FILESDIR}"/libtool.patch
}
src_configure() {
@@ -44,7 +46,7 @@ src_configure() {
src_compile() {
base_src_compile
# TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die; fi
+ if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi
}
src_install() {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2011-12-08 1:39 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2011-12-08 1:39 UTC (permalink / raw
To: gentoo-commits
commit: 2b33defb28660b66594a4ca772f7a87d6a487089
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 8 01:38:57 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 8 01:38:57 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b33defb
sci-biology/mira: version bump
(Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit)
---
sci-biology/mira/ChangeLog | 13 +++++
sci-biology/mira/files/mira-3.4.0.1-asneeded.patch | 29 ++++++++++
sci-biology/mira/mira-3.4.0.1.ebuild | 57 ++++++++++++++++++++
3 files changed, 99 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
new file mode 100644
index 0000000..0982f99
--- /dev/null
+++ b/sci-biology/mira/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/mira
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mira-3.4.0.1 (08 Dec 2011)
+
+ 08 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +mira-3.4.0.1.ebuild, +files/mira-3.4.0.1-asneeded.patch:
+ version bump and dropped the expat patch for --as-needed CFLAGS as upstream
+ fixed that in a different way, the still applicable part of the patch is
+ however provided under files/ but is just a cosmetic change (hence not really
+ needed)
+
diff --git a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch b/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch
new file mode 100644
index 0000000..4184323
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch
@@ -0,0 +1,29 @@
+--- config/m4/ax_lib_expat.m4.ori 2011-12-08 01:59:42.000000000 +0100
++++ config/m4/ax_lib_expat.m4 2011-12-08 02:00:08.000000000 +0100
+@@ -108,7 +108,8 @@
+
+ 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 "$expat_lib_flags"; then
+@@ -129,6 +130,8 @@
+ saved_LDFLAGS="$LDFLAGS"
+ LIBS="$LDFLAGS $expat_lib_flags"
+
++ saved_LIBS="$LIBS"
++ LIBS="$LIBS $expat_libs"
+ dnl
+ dnl Check Expat headers
+ dnl
+@@ -188,6 +191,7 @@
+
+ CPPFLAGS="$saved_CPPFLAGS"
+ LDFLAGS="$saved_LDFLAGS"
++ LIBS="$saved_LIBS"
+ fi
+
+ AC_MSG_CHECKING([for Expat XML Parser])
diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
new file mode 100644
index 0000000..78d1cc3
--- /dev/null
+++ b/sci-biology/mira/mira-3.4.0.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+MIRA_3RDPARTY_PV="09-09-2011"
+
+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
+ dev-util/google-perftools"
+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
+ # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
+ epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
+ epatch "${FILESDIR}"/libtool.m4.patch
+ AT_M4DIR="config/m4" eautoreconf
+ #epatch "${FILESDIR}"/libtool.patch
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
+ --with-boost-thread=boost_thread-mt
+}
+
+src_compile() {
+ base_src_compile
+ # TODO: resolve docbook incompatibility for building docs
+ if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet."; fi
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
+ find doc/docs/man -type f | xargs doman
+ find doc/docs/texinfo -type f | xargs doinfo
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2013-02-22 0:37 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2013-02-22 0:37 UTC (permalink / raw
To: gentoo-commits
commit: c2386356030a1cee494636d114a52a59714fb10c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 22 00:36:44 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 22 00:36:44 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c2386356
sci-biology/mira: current stable and development version bumps
Package-Manager: portage-2.1.11.38
---
sci-biology/mira/ChangeLog | 11 +++-
.../mira/files/mira-3.4.0.2-boost-1.50.patch | 24 ++++++++
sci-biology/mira/mira-3.4.1.1.ebuild | 61 ++++++++++++++++++++
sci-biology/mira/mira-3.9.9.ebuild | 61 ++++++++++++++++++++
4 files changed, 155 insertions(+), 2 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 4cd234f..68b66f6 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,7 +1,15 @@
# ChangeLog for sci-biology/mira
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mira-3.4.1.1 (22 Feb 2013)
+*mira-3.9.9 (22 Feb 2013)
+
+ 22 Feb 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/mira-3.4.0.2-boost-1.50.patch, +mira-3.4.1.1.ebuild,
+ +mira-3.9.9.ebuild:
+ sci-biology/mira: current stable and development version bumps
+
22 May 2012; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r2.ebuild,
-mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild:
Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop
@@ -15,4 +23,3 @@
fixed that in a different way, the still applicable part of the patch is
however provided under files/ but is just a cosmetic change (hence not really
needed)
-
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/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild
new file mode 100644
index 0000000..5260ee1
--- /dev/null
+++ b/sci-biology/mira/mira-3.4.1.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+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="
+ http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/${P}.tar.gz
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+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 )
+
+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
+ 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() {
+ base_src_install
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}
diff --git a/sci-biology/mira/mira-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild
new file mode 100644
index 0000000..0deeb87
--- /dev/null
+++ b/sci-biology/mira/mira-3.9.9.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+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="
+ http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+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 )
+
+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
+ 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() {
+ base_src_install
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2015-06-05 15:23 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-06-05 15:23 UTC (permalink / raw
To: gentoo-commits
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 <jlec@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 <jlec@gentoo.org> +mira-4.0.2.ebuild:
+ Version Bump, thanks Martin Mokrejš for the work
+
+ 23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild:
+ Add workaroung for m4 dir location, #536172
+
+ 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1.ebuild:
+ Drop old
+
+ 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> mira-3.9.18.ebuild:
+ Stable for x86, wrt bug #497218
+
+ 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> mira-3.9.18.ebuild:
+ amd64 stable, bug #497218
+
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild:
+ Punt base.eclass
+
+ 06 Jan 2014; Justin Lecher <jlec@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 <jlec@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 <jlec@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 <jlec@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 <jlec@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 <jlec@gentoo.org> -mira-3.0.5.ebuild,
+ -mira-3.2.0.ebuild:
+ Drop old
+
+ 25 Jun 2012; Jeff Horelick <jdhore@gentoo.org> mira-3.2.1.ebuild:
+ marked x86 per bug 418439
+
+ 24 Jun 2012; Agostino Sarubbo <ago@gentoo.org> mira-3.2.1.ebuild:
+ Stable for amd64, wrt bug #418439
+
+ 23 Jun 2012; Kacper Kowalik <xarthisius.kk@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 <weaver@gentoo.org> +mira-3.2.1.ebuild:
+ Version bump and fix bug 367921
+
+ 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> mira-3.2.0.ebuild:
+ Stable on amd64 wrt bug #353568
+
+ 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mira-3.2.0.ebuild:
+ x86 stable wrt bug #353568
+
+ 17 Oct 2010; Andrey Kislyuk <weaver@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 <weaver@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 <jlec@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 <weaver@gentoo.org> +mira-3.0.5.ebuild:
+ Version bump
+
+*mira-3.0.3 (18 Mar 2010)
+
+ 18 Mar 2010; Andrey Kislyuk <weaver@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 <weaver@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 <weaver@gentoo.org> +mira-3.0.1.ebuild:
+ Version bump (bugfix release)
+
+ 25 Feb 2010; Samuli Suominen <ssuominen@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 <weaver@gentoo.org> mira-3.0.0.ebuild:
+ add eautoreconf
+
+ 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild:
+ Install 3rd party files
+
+*mira-3.0.0 (02 Feb 2010)
+
+ 02 Feb 2010; Andrey Kislyuk <weaver@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"
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2015-07-21 9:02 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-07-21 9:02 UTC (permalink / raw
To: gentoo-commits
commit: e5b4b8f74ae97147b52041ed4a8c1c9b03952a07
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 21 09:00:57 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 21 09:00:57 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5b4b8f7
sci-biology/mira-4.9.5: fix missing AND in Makefile; install config files for staden and consed viewers/editors (maybe use config protect?)
Package-Manager: portage-2.2.18
sci-biology/mira/ChangeLog | 5 +++++
.../mira-4.9.5-fix-miramer-symlink-error.patch | 22 ++++++++++++++++++++++
sci-biology/mira/mira-4.9.5.ebuild | 16 +++++++++++++++-
3 files changed, 42 insertions(+), 1 deletion(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 8e61af5..68522a6 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,11 @@
# 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 $
+ 21 Jul 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/mira-4.9.5-fix-miramer-symlink-error.patch, mira-4.9.5.ebuild:
+ sci-biology/mira-4.9.5: fix missing AND in Makefile; install config files for
+ staden and consed viewers/editors (maybe use config protect?)
+
08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/mira: Updating remote-id in metadata.xml
diff --git a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
new file mode 100644
index 0000000..6bdda94
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
@@ -0,0 +1,22 @@
+--- mira-4.9.5/src/progs/Makefile.in.ori 2015-07-21 00:55:09.860884698 +0200
++++ mira-4.9.5/src/progs/Makefile.in 2015-07-21 00:55:29.660884750 +0200
+@@ -717,7 +717,7 @@
+ rm -f mirabait$(EXEEXT) && \
+ $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
+ rm -f miraconvert$(EXEEXT) && \
+- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
++ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
+ rm -f miramer$(EXEEXT) && \
+ $(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
+
+--- mira-4.9.5/src/progs/Makefile.am.ori 2015-07-21 01:30:09.580890184 +0200
++++ mira-4.9.5/src/progs/Makefile.am 2015-07-21 01:30:24.590890223 +0200
+@@ -51,7 +51,7 @@
+ rm -f mirabait$(EXEEXT) && \
+ $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
+ rm -f miraconvert$(EXEEXT) && \
+- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
++ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
+ rm -f miramer$(EXEEXT) && \
+ $(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
+
diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild
index e643b5b..ebd9e14 100644
--- a/sci-biology/mira/mira-4.9.5.ebuild
+++ b/sci-biology/mira/mira-4.9.5.ebuild
@@ -42,7 +42,8 @@ src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
epatch \
"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
- "${FILESDIR}"/${P}-cout.patch
+ "${FILESDIR}"/${P}-cout.patch \
+ "${FILESDIR}"/${P}-fix-miramer-symlink-error.patch
sed \
-e "s:-O[23]::g" \
@@ -71,6 +72,19 @@ src_install() {
dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+
+ # if sci-biology/staden is installed, ideally use configprotect?
+ if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
+ if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
+ cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
+ insinto /usr/share/staden/etc/
+ doins "${WORKDIR}"/GTAGDB
+ fi
+ fi
+ if [ -e "/etc/consedrc/" ]; then
+ insinto /etc/consedrc
+ doins "${S}"/src/support/consedtaglib.txt
+ fi
}
pkg_postinst() {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 7+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
commit: 0406b0d1d4a8a775323fed57801dedf70517cc5b
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:07:36 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:07:36 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0406b0d1
sci-biology/mira: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
.../mira/files/mira-3.4.0.2-boost-1.50.patch | 24 ------
sci-biology/mira/files/mira-4.9.5-cout.patch | 16 ----
.../mira-4.9.5-fix-miramer-symlink-error.patch | 22 ------
sci-biology/mira/metadata.xml | 11 ---
sci-biology/mira/mira-4.9.5.ebuild | 92 ----------------------
5 files changed, 165 deletions(-)
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
deleted file mode 100644
index 427192294..000000000
--- a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- 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$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
- [link_regex="no"])
- done
- fi
diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch
deleted file mode 100644
index 14feb0284..000000000
--- a/sci-biology/mira/files/mira-4.9.5-cout.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/progs/quirks.C | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/progs/quirks.C b/src/progs/quirks.C
-index 47e5ee8..060b6f3 100644
---- a/src/progs/quirks.C
-+++ b/src/progs/quirks.C
-@@ -25,6 +25,8 @@
-
- #include <boost/filesystem.hpp>
-
-+#include <iostream>
-+
- // make the "tcmalloc: large alloc" messages from TCMallom disappear
- // by setting the reporting environment variable to a very large value
- // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
diff --git a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
deleted file mode 100644
index 6bdda946a..000000000
--- a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- mira-4.9.5/src/progs/Makefile.in.ori 2015-07-21 00:55:09.860884698 +0200
-+++ mira-4.9.5/src/progs/Makefile.in 2015-07-21 00:55:29.660884750 +0200
-@@ -717,7 +717,7 @@
- rm -f mirabait$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
- rm -f miraconvert$(EXEEXT) && \
-- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
-+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
- rm -f miramer$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
-
---- mira-4.9.5/src/progs/Makefile.am.ori 2015-07-21 01:30:09.580890184 +0200
-+++ mira-4.9.5/src/progs/Makefile.am 2015-07-21 01:30:24.590890223 +0200
-@@ -51,7 +51,7 @@
- rm -f mirabait$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
- rm -f miraconvert$(EXEEXT) && \
-- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
-+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
- rm -f miramer$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
-
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
deleted file mode 100644
index 65cad0432..000000000
--- a/sci-biology/mira/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">mira-assembler</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild
deleted file mode 100644
index 7c888a5e7..000000000
--- a/sci-biology/mira/mira-4.9.5.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${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"
-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 \
- "${FILESDIR}"/${P}-fix-miramer-symlink-error.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 "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-
- # if sci-biology/staden is installed, ideally use configprotect?
- if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
- if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
- cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
- insinto /usr/share/staden/etc/
- doins "${WORKDIR}"/GTAGDB
- fi
- fi
- if [ -e "/etc/consedrc/" ]; then
- insinto /etc/consedrc
- doins "${S}"/src/support/consedtaglib.txt
- fi
-}
-
-pkg_postinst() {
- einfo "Documentation is no longer built, you can find it at:"
- einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread
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2020-09-22 11:12 Aisha Tammy
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