reinit the tree, so we can have metadata

4 files changed, 132 insertions, 0 deletions

diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest
new file mode 100644
index 000000000000..fc4349289add
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2860 SHA256 e44b11ca5a40404db741838ce87a68c536723bb81b3729dc1ef021c050d59b7b SHA512 9c8dfdd2e6c7f8542a989118dad6c70159c55a7f56593800b9d1896fb717b0c28ea100f5884f3284823ad1e92da6e5fe307e798028475e29d353edfe52b62865 WHIRLPOOL b02d9f774e807bca06b4a16d1438a5970c412868309333f35b39db5c067821a30a37affc9b74b44c8dcd458969f9dc1aa4ad07835b9660020bf10f26ed421fd5
+DIST embassy-domainatrix-0.1.660.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0
+EBUILD embassy-domainatrix-0.1.660.ebuild 345 SHA256 da2c8c3ae8e45af225e9b28ae00ca3112aac955ccd21a1d55b3e4dd1488fd691 SHA512 0438a817780278fb85fbd6ba9135725e5b6a850318f8b8e95a504b388e649f7a19fc8472145ced331193d64addbaa1603c3c89e0272872f8795a13cf44d0288f WHIRLPOOL 130580891b28786330c204a7132386b7fbc8dd578a28fb05c14399f5a76840804dcff9709d7f535ff5c08bc4772a27e07e1f13cf2bebf56c42b96dd65258de33
+MISC ChangeLog 3740 SHA256 355fa6e17b11140fbb3bddb902bd9a089b9852abddadcec48092136a5bfbc619 SHA512 dcd955932cf92a35a24fe3afb5e9c69472108aeb13bae65349e81b89b82ae8f46f90a00e8d4834ea71e6c1ce4cf1e4f3ca13f9ccfff73f74682cbc7319a780f4 WHIRLPOOL 887058d56ab82ab7565a4e87cbc5b3df6e5d23a10a4402bade4e14a2acb1f10adfd8f509e95b66c18e1f958999b87e814b2000d1dc132d9eb6080748b20b1c1f
+MISC ChangeLog-2015 5803 SHA256 519cb6863e78ea24aef1f05084802a891f4eef60ae9394eb7fa2c59fcda781c4 SHA512 1c79388eca11496a9d09b96de8324d4fc7041e7ee08a7813d8b81f1fc7084c808b348f2ebb3d3e66aaa948c23546ebdb16122aa2beedd58db1a077c2b9a88d9c WHIRLPOOL 9baf95d3dfe1d5abdc100a4a772f17e193374f493e3a0bbac20b54d499040814c5239694601ba91a9c043cbff7fbbd2ad07af3fe899a273edefefbb9ac9826c3
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild
new file mode 100644
index 000000000000..4607d87fdc17
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.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="Protein domain analysis add-on package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/DOMAINATRIX-0.1.650"
+PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..a932e1ebe21e
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index d16cc02..d327a0d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index d405d00..54be7ca 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -64,5 +62,5 @@ 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-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/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>