reinit the tree, so we can have metadata

4 files changed, 142 insertions, 0 deletions

diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest
new file mode 100644
index 000000000000..ad9e72cf33d4
--- /dev/null
+++ b/sci-biology/embassy-cbstools/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 3167 SHA256 8b73cb6b96e5afb0baced7ac7259addfb67b684d3c3035fa195f800bb264f08c SHA512 0ec7317d719da5466f02813105184d44c18f5ec668e0cdc1e120324216070009da4e38ce34dffb320b438665926f4506437e60757c3103fb03a526c46ca042d8 WHIRLPOOL ce99924dd94eee2df05665c8760efa2f9f2d374c896c526a0383875028e750f950004e79959c257aeecf750265fbd6b996de05b6fda7aa3a338e6d43cdf1672f
+DIST embassy-cbstools-1.0.0.660.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a
+EBUILD embassy-cbstools-1.0.0.660.ebuild 352 SHA256 04797dc5f89cdc030290c805d730a301ad72acdeb956a8e292abcb2b78a237e5 SHA512 f85c1ecdd7c16e13c8e1a08441b73a76f66ff770a3ca75eeb745f31b46aa5e2b74172f20de4b520e64e0ed167cf50b55d01ab78b760c9fbfde8ecee689f2703a WHIRLPOOL e41fadc600afcf81a49a4794f630d49bbbff49a6c5ab01c1a3453af074791e97f36b9d32b6cb5020a87c5055937431edf21b4e1d6cf70508aff33a9f94462308
+MISC ChangeLog 3712 SHA256 c3834418e0b0538c112851f6ccc138110748e0df3fa7f196a61c03508b862d1a SHA512 2f62c48e531025a873833d04af1585a19122b6648d0e6e3bb0db647043f48c76e04ed60562e2b877b51e9383884a75f4f218106fd19d7591f2c2a62c1cf8daf9 WHIRLPOOL 1b9a2e4a734599e52d586207e0c850747b450916dcd6774e9e1bb0550216a1a95a1b926feb60a076d001e9c751e77901fb5af0c5b41a089d1c2afb1d74246613
+MISC ChangeLog-2015 1799 SHA256 409f049c1e7d5031d8ddeeec23f2069e45b3e006a1098c24e07c2be2859bb212 SHA512 deb61b1a12f4790cab05ce0905cfb07e43648a9b38d914d10a4eeb6f5aadcc3a55b5a0291fe3df9bc5d2053a2ed838448d09d2b0bd6fdd62f714c0e62dc37f2b WHIRLPOOL 8e2256d7fcc4643b6108af8791f6ab7e362b97d89838954c596f0dbaf64a2dbd05c9c2e660f34372b88c8af33736ded26f91b111956797718e9d8c7a3aee24d2
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild
new file mode 100644
index 000000000000..6104a470f3f7
--- /dev/null
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.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="Applications from the CBS group"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}/CBSTOOLS-1.0.0.650"
+PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..d29310efcb47
--- /dev/null
+++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index a70d4d2..b8f5e79 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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 824a03c..9db171d 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -19,9 +19,7 @@ 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
+@@ -65,5 +63,5 @@ 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-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-cbstools/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>