reinit the tree, so we can have metadata

4 files changed, 134 insertions, 0 deletions

diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
new file mode 100644
index 000000000000..5021cd8b5caa
--- /dev/null
+++ b/sci-biology/embassy-meme/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-meme-4.7.650_fix-build-system.patch 2860 SHA256 928eb90afbc7b70f69fd4bb7f1090bbd4ea2bd3d7a286b56c947dd481156b5b6 SHA512 c44b219c75e67d17fcfd56145ae3709053bda38b8690141d1e9b846e4e4a9cab135f0dc9c5399e4712cf030ad562dd075f45c393e78157a2c1b92d80903b3d1c WHIRLPOOL 4e93c672ee6026ee7b2e2ff6c8771a375049629f5e24e2e6cf9afa72cced5fc62d21f49c161fb5ffe55f0637ffe14baf78df15c1c95e0a42d3495a1619365141
+DIST embassy-meme-4.7.660.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51
+EBUILD embassy-meme-4.7.660.ebuild 381 SHA256 a89b8707e8bb0bf2f7d291d9223c97553b15ee50dd8cde2932bbcab0afface8b SHA512 b31045a88106d64ddbdd91cb85d06328b99b57eb490aa9f74f9cbf2464e3ed6485ca5e54ebd8146df8aacf0d44ee8f6f1d68cbb7a9e9dd3f2f46d637e2a8404b WHIRLPOOL dc87425fad3902502e290f228885500a6cba050a235a54f4831d138609a3d3c72fdd65e26e7b830bed4e146fbfc0317a5ace53f448f3c7718133fd0fae4a487f
+MISC ChangeLog 3427 SHA256 bda42da0f155e2b202a1ac73eb0c3201d0721f1bb00ea253971ef2bf3fc2a4b3 SHA512 04340e39cd3f9676a9cac7b9137a1b62b83dfd1f9e5dc6cbfc01a5dde8d061c05ae242151b60364b5639254a6a4fd8b689ca822dd2659d9927600caaaa049b42 WHIRLPOOL db9cf3c9002291ec6679c0c9a2e05dba1ac5f883faecb4380b673874723bdb6e34f0c608db65a62cb0a1ad6fa460c9cf2dadd2f79ca2f765acceb95a224178f7
+MISC ChangeLog-2015 750 SHA256 dd4f3a12304e509ea4abd9caa5a5e1b68b2bc1df56b9c3cd26233de0531fea4a SHA512 0b079723cd9c0a825cae54d654e4ccc7f051242ec7eb399de0265e2ce43960b57d7854825535a2300a0b96ac70d735b6d23fe086a13192108b14addd4f3605c0 WHIRLPOOL af77519eb83320b982ed520d1d2b7a81edf88d4971a731c8964bca1080c2c4a9b4202a1f16addd68bca4893699a08b4419bc504fb34a4e0552d809646f272bd9
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild
new file mode 100644
index 000000000000..8752e78d8fc9
--- /dev/null
+++ b/sci-biology/embassy-meme/embassy-meme-4.7.660.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="MEME - Multiple Em for Motif Elicitation"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sci-biology/meme"
+
+S="${WORKDIR}/MEME-4.7.650"
+PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
new file mode 100644
index 000000000000..56f5814e1efa
--- /dev/null
+++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 391989f..d921f25 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1600399..9f28162 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -60,5 +58,5 @@ 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-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-meme/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>