reinit the tree, so we can have metadata

4 files changed, 132 insertions, 0 deletions

diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest
new file mode 100644
index 000000000000..b57c08dbe610
--- /dev/null
+++ b/sci-biology/embassy-domsearch/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-domsearch-0.1.650_fix-build-system.patch 2890 SHA256 8b6901b6126ec5642c08ff114b2401d2b498b6912e2c58e0767156d775d0a166 SHA512 3f012a5646751b43ec66d006df04cbe8fa880d0acd62723962dbb0e1817c5f5db2bd4879c25cf932114aa43291bc70816afef6664088532222e11135f0ab5603 WHIRLPOOL 11cb26d3dcab609c43d404afaeca56f44439fe84bf4d25b05bdd98c4838e11d19753f2f3390af93c7d9b9141226e02804190cd8a8f0061dd7d67bd0e0d989644
+DIST embassy-domsearch-0.1.660.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111
+EBUILD embassy-domsearch-0.1.660.ebuild 341 SHA256 3e25fee23debf35e06c6e2c1a1f1d31f1913d7a2782165fb86d71f60da8111d1 SHA512 b7719faa5c0b7fd20379351f41930926cdea99e5c1b26e23aec3f7aceae12e1db885997782b2c4ca89e0bc5d92e17261e990d644ba04da36d9c219c0e5732afa WHIRLPOOL adc45d6d31b88003d7395fd1dd570b1f7ae90dd68015bb83d02431f8a929c54e51cc8681febff2b3b387ed20f26c3b7283627f1b0bcdf4ec3cfd06a903419103
+MISC ChangeLog 3722 SHA256 a46008601cf02935daa424c5201e812f1e86c00db5ff3325ff9853a7c16a10b7 SHA512 4116820109aa24ceca048ebe8875aff64095991a881d8d9026b86eb84736df6bc9b7e4d3015b32d6da2a5ea1baed072ff78a515246efc176e2f52dcbd71e72f7 WHIRLPOOL 22dbd4538aa426a57006b95a340f00e7a2e2b101d340e2bd3c4ab04f2ddf91e61e8139a7c243f7c63c4343a1a2fdb82e0e1fee0c0cacae15a261c86ced661dcd
+MISC ChangeLog-2015 3869 SHA256 bd705086afad7fdfa6045c3d7fca59e2b3036b2d65d2a43585e1add5bb13cd58 SHA512 0914a10689fc1d3d6e44cdfe75158e275b56362a700aec1ba2ab7ceaf4e6e212d5881c7fa38ee774da39e5d858d44574ff625c2996b03d6843453703d298184c WHIRLPOOL 03fbac60078932d22105d1c3b113ab5acc1cb916da773efe0cd2fada41b1ef5d686c8208135168e327749a2102a7d9c77a01c21bd1d2360dc1e52185bd51746c
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild
new file mode 100644
index 000000000000..a47adcfb8457
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-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 search add-on package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/DOMSEARCH-0.1.650"
+PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..d24857c8386d
--- /dev/null
+++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f0f97fa..d419d7d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 9829ebd..433a5c5 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${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 \
+ 	../../../plplot/libeplplot.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-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-domsearch/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>