[gentoo-commits] proj/sci:master commit in: sci-biology/embassy-mira/files/, sci-biology/embassy-mira/

["Justin Lecher" <jlec@gentoo.org>]

commit:     81c51e7195ef67d762fb851feaabacf70f642b1d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 11:39:15 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 11:39:15 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=81c51e71

Move to new embassy-ng.eclass

(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-biology/embassy-mira/ChangeLog                 |   33 +++++++
 .../embassy-mira/embassy-mira-2.8.2-r2.ebuild      |   10 ++
 .../embassy-mira/files/embassy-mira-2.8.2-r2.patch |   99 ++++++++++++++++++++
 sci-biology/embassy-mira/metadata.xml              |    5 +
 4 files changed, 147 insertions(+), 0 deletions(-)

diff --git a/sci-biology/embassy-mira/ChangeLog b/sci-biology/embassy-mira/ChangeLog
new file mode 100644
index 0000000..db0fe61
--- /dev/null
+++ b/sci-biology/embassy-mira/ChangeLog
@@ -0,0 +1,33 @@
+# ChangeLog for sci-biology/embassy-mira
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mira/ChangeLog,v 1.5 2010/01/15 22:46:25 fauli Exp $
+
+*embassy-mira-2.8.2-r2 (10 Mar 2011)
+
+  10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-mira-2.8.2-r2.ebuild,
+  +files/embassy-mira-2.8.2-r2.patch, +metadata.xml:
+  Move to new embassy-ng.eclass
+
+  15 Jan 2010; Christian Faulhammer <fauli@gentoo.org>
+  embassy-mira-2.8.2-r1.ebuild:
+  Transfer Prefix keywords
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Giving up maintainership of this package.
+
+*embassy-mira-2.8.2-r1 (01 Sep 2009)
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-mira-2.8.2-r1.ebuild:
+  Updated version for EMBASSY 6.1.0.
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  embassy-mira-2.8.2.ebuild:
+  Stabilised on amd64 and x86.
+
+*embassy-mira-2.8.2 (27 Aug 2008)
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +embassy-mira-2.8.2.ebuild:
+  Initial import for EMBASSY 6.0.1.
+

diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild
new file mode 100644
index 0000000..041b297
--- /dev/null
+++ b/sci-biology/embassy-mira/embassy-mira-2.8.2-r2.ebuild
@@ -0,0 +1,10 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mira/embassy-mira-2.8.2-r1.ebuild,v 1.2 2010/01/15 22:46:25 fauli Exp $
+
+EBOV="6.3.1"
+EBOV_DESCRIPTION="Fragment assembly add-on package"
+
+inherit embassy-ng
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-mira/files/embassy-mira-2.8.2-r2.patch b/sci-biology/embassy-mira/files/embassy-mira-2.8.2-r2.patch
new file mode 100644
index 0000000..c44a80f
--- /dev/null
+++ b/sci-biology/embassy-mira/files/embassy-mira-2.8.2-r2.patch
@@ -0,0 +1,99 @@
+diff --git a/Makefile.am b/Makefile.am
+index 7bc74b2..2f4b19c 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,5 +1,6 @@
+ #
+ 
++ACLOCAL_AMFLAGS = -I m4
+ SUBDIRS = src emboss_acd emboss_doc
+ 
+ EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
+diff --git a/configure.in b/configure.in
+index 2e11775..19d82d0 100644
+--- a/configure.in
++++ b/configure.in
+@@ -187,15 +187,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+ 
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" != "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+ 
+ dnl Check for header files
+ AC_PATH_XTRA
+@@ -250,8 +241,8 @@ AX_LIB_POSTGRESQL
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+ 
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+ 
+ 
+ dnl "Export" these variables for PCRE
+@@ -388,9 +379,30 @@ AC_ARG_ENABLE(systemlibs,
+    AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
+ if test "${enable_systemlibs}" = "yes" ; then
+     have_systemlibs=yes
++    DEFINE_USE_SYSTEM_PCRE="#define"
++    PKG_CHECK_MODULES([PLPLOT], [plplotd])
++    PKG_CHECK_MODULES([ZLIB], [zlib])
++else
++    dnl X11 is only used by plplot
++    dnl Intel MacOSX 10.6 puts X11 in a non-standard place
++    if test "${with_x}" != "no" ; then
++    if test "`uname -a | grep Darwin`"; then
++    OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++    if test ${OSXX} '>' '10.4'; then
++    CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++    fi
++    fi
++    fi
++    if test "${with_x}" != "no" ; then
++    LF_EMBOSS_PATH_XLIB
++    fi
++     AC_MSG_NOTICE(USING bundled LIBS)
+ fi          
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+ 
+ 
+ 
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 2968b79..78d83db 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,9 @@ INCLUDES = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++INCLUDES = -I${embprefix}/include $(PLPLOT_CFLAGS) \
++	$(NLINCLUDES) -I${embprefix}/include/emboss \
++	-I${embprefix}/include/pcre
+ endif
+ 
+ if ISSHARED
+@@ -58,6 +58,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	../../../plplot/libeplplot.la \
+ 	$(XLIB)
+ else
+-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
++        -lajax -lpcre $(NLADD) $(PLPLOT_LIBS) $(XLIB)
+ endif

diff --git a/sci-biology/embassy-mira/metadata.xml b/sci-biology/embassy-mira/metadata.xml
new file mode 100644
index 0000000..d464821
--- /dev/null
+++ b/sci-biology/embassy-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>