reinit the tree, so we can have metadata

4 files changed, 134 insertions, 0 deletions

diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
new file mode 100644
index 000000000000..fd6bbeeca444
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2860 SHA256 21b6a87a19f37745f76fe9c45837d9a5bab6420dafcb9f50aa3899b88b3cd322 SHA512 6b1c8a2915c9c48ec203bc131461b9acecc3948da79f36941e2fd97a22bf044a35ee717e0be0b13f46d8a6f81148c29faa1e048ed4066cf768dbc705141a772d WHIRLPOOL 00b3a809502d22dfe01a3f5b12db5a62914753b81aaa4d4450c9506a1afcef65c9fa58706da6ca367de077395226aeb5ecb341cc5cb448aa0373a00569c9a778
+DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54
+EBUILD embassy-clustalomega-1.1.0.660.ebuild 384 SHA256 65cae24f4b0267a64896197967e01222c4f70fa67e8907ae566625e4759ae170 SHA512 8504bb9294da8a76c23114476fc16a011c45380b5f0f243bcf5a3bc68db6fd71fb7156f450ee14f78ec7825f8ecd46f4b0a7d0764c3dfd7ba1a2939026b123a4 WHIRLPOOL 7775f060bc5590ab9ac9cd99f734b445ca5cef7e9c2b4862ac50b59954884b91c3d8a6b5ba0a287dcad4c8f31fbc331b317e85b6ba876da46fdb87a27f22ba54
+MISC ChangeLog 3469 SHA256 4c77683d03e44a19a3a917d792b3fbf57524d874cc0e9c39f67e14c1db309dca SHA512 9b11c405c970db09f55c466ac67b7961062a05ef3d3e3b85aed5b865eb4bcc8834a782ba0d7b48a753da980ba21519e3c3d980915a379951fd2d53ce31bb8a09 WHIRLPOOL 8a6734e22cfc7aca3ff914962cbb001212e1bf1b9676831838d3793f332f4813d3446e0c889e95a6979186400a921e8862a26ea0925a959ee2feb9736a031bdc
+MISC ChangeLog-2015 799 SHA256 b9f70f99fb963c9ccf78c43e36ac262753b16438a4b1fb7589d83c5796c010fc SHA512 2bbe112471e0e8042f170d73ac947b0d202cbbc86cefb596c97046bd1fd0319d15f24c17b99a6f69f8e1c346d44fa71ce039e0aee5e6829a8dc9b5c66e767ca4 WHIRLPOOL 99fe0031d3a5b19e5dfc757bb06764a705f063d0a71461cd735b04e95680b40ea9bc8a85f24b48fce2feb0228b96e3980a6119c3831ccf02c1f28a9942d17871
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild
new file mode 100644
index 000000000000..2d2a2c62632c
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+RDEPEND="sci-biology/clustal-omega"
+
+S="${WORKDIR}/CLUSTALOMEGA-1.1.0"
+PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch )
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
new file mode 100644
index 000000000000..5525d79b525f
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f12ed19..b143922 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+ 
+ 
+ 
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 9135679..c201149 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/metadata.xml
@@ -0,0 +1,11 @@
+<?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">emboss</remote-id>
+  </upstream>
+</pkgmetadata>