reinit the tree, so we can have metadata

4 files changed, 142 insertions, 0 deletions

diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest
new file mode 100644
index 000000000000..a1f17bf5ac50
--- /dev/null
+++ b/sci-biology/embassy-topo/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-topo-2.0.650_fix-build-system.patch 3167 SHA256 d78bcacee455ab12fdb482fa760eb89716da3bac9dbf5ace0f9bba37f2585dbf SHA512 bacff621e9d80d39a4e415736e1524cf69dd86b0253f65fb52ad2dda200cafe8e14af296897c3f695bbe360f2a56862a40dec6b8b0d0e597310f065e191ae770 WHIRLPOOL 09ffc786288a0b428f349cf74973729a9dea8d8ed2078897538b97b59ef41cd48053e0763c6665310a770c6410b28726fe9c09b0ada9543d6fd8054b1e99b24f
+DIST embassy-topo-2.0.660.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55
+EBUILD embassy-topo-2.0.660.ebuild 342 SHA256 07b735f534f885f651c75d4135d45d15417fcb97340ff25cf4ba4e03612b7595 SHA512 c2a0822f7d20ae5c2bb78aa2f3705517fa7371b154a16395d7b13b5835980a11dce9364cb6d0a90f47a39cc729692b4567ceb5085022b3c0ed41535a3a8ab067 WHIRLPOOL ef6c670b13175f0f99d48aa7b978757c7ff1bf6e2984909f6ba8a48de5f4c2d79145c2dfecaf6e3a6f90dda93fbb7942ac38f6db69707e69bc943e8b0822c28f
+MISC ChangeLog 3671 SHA256 7e5217f1daaad28f1c3c4137c619bbf5075360217fe9ad443a32c7a61e8e94fc SHA512 7399a29b68d4b9d974c463aed165882eb8ea32c48ae8297dc2856cea08d032db73579aec4d243f31032df947cd560cc00b6d7c17a3596b9edccca0f693d4f45c WHIRLPOOL d4c5cf7abeab2f3e68ef0c12e8eb48e2a76a653f07481fd9aea955a159c68eaa09dd86108b9181c3965eaf504c4fea191296a5142727926d864c61d718d66db7
+MISC ChangeLog-2015 5212 SHA256 9bf176f777b2a7325026c20377fe46465c1f29f96a1af3e78ac3721a511bb30f SHA512 c7c527494cba100183d37b40b97913f3b4d401de0d990ccc1bda92288deb994e25f8daac07ea14b18287435a3409ec81a489bdf2be333d21ace00db07f1835f7 WHIRLPOOL 05b8f8040075da4b7e2277547af92019562d3a744b7370c2e9dc98df7d43d36a3972e88ef96295831c95f23d0b2c4027ba3f6ceda25304699c4be490c2c06f3f
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild
new file mode 100644
index 000000000000..009adfe73914
--- /dev/null
+++ b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="Transmembrane protein display"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}/TOPO-2.0.650"
+PATCHES=( "${FILESDIR}"/${PN}-2.0.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..3c37879de8c8
--- /dev/null
+++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 8eeb8ca..4fd28ac 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1cdb0b1..0e86a4b 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-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-topo/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>