reinit the tree, so we can have metadata

4 files changed, 132 insertions, 0 deletions

diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest
new file mode 100644
index 000000000000..70ea7d7dabe5
--- /dev/null
+++ b/sci-biology/embassy-signature/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-signature-0.1.650_fix-build-system.patch 2860 SHA256 768fe1c2740827007d475f31451195090032b907e0ed5b36b9201504d6eb4df2 SHA512 54a6027b2fb1d17eff98b7c1e9adc61578a2845b30be3b7c40551b4291950ce11900798dbf7d54e1fc9421743a8d313fc42a14cfa39976735ac8cfae5a297954 WHIRLPOOL a272e7679d14c883fb76d83e78e429582c776364c590738f4bb6b3e793f54c95bd0bb42b263fc6ca5569a34a9be2e84a2dc62cb67efe05ad451ac0513102c2d8
+DIST embassy-signature-0.1.660.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3
+EBUILD embassy-signature-0.1.660.ebuild 337 SHA256 f6f54e84e70866656557e64974fc3d6773e9c62a3541e4e94e254446e14cdafa SHA512 ce592d367c64428911a735a5ecc3a24000a5b1e8c3b3fcaf466e5005a962deaf113416cd161039eb445a1a41f7296ca7376531396bed019047c0d97c86296585 WHIRLPOOL f0c8b7d716026c97fc01f50ece571de4d13c522832c1e2f65aa1f57cc7ac0a3ada05ded0996f2822e31141cf5be19779ae4c928ef947c6e7749145775d8be929
+MISC ChangeLog 3722 SHA256 535090c557eb13db1501c464a1ca480e81081ac6a447d8f9b60898fff0aac43f SHA512 21cf306716bc2071f5344c7e7a89380eaaeb696d4689fcc4e26844f50f0ab170806cee5949896d6365a86f21dbdf16517e6eec6c03720726192b3ec58b685d62 WHIRLPOOL a4e86701782c8a8f9f557d979f9d6ea383df0c95438843623b295740aa81776af5af7c3314374aa76c08e936e5e511b20c9198a1090bbebaf4ff7af5270b4428
+MISC ChangeLog-2015 3864 SHA256 27b743af18ee8d2fc1420f1dcb7aba01c65211fb4c7ac965a2926f141fa8428a SHA512 220fd9e7da3a4c4a306631d4460b39431de1e5d29af32257071e0cb35c680541eea139825c5bfe1760e7313df2b4695b2cbe7850fe2fc916f3cb50c66cfd50e3 WHIRLPOOL a1596d167902201f0fc6f735186372d6c0f5de529106f524af11bfb8de08e9d1dc518a0984936c4873f03d062a43b6e5a168ea2eba10a16edcaf83cced3fdfd1
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild
new file mode 100644
index 000000000000..c0ea3e302504
--- /dev/null
+++ b/sci-biology/embassy-signature/embassy-signature-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 signature add-on package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/SIGNATURE-0.1.650"
+PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..32e4d684cbb3
--- /dev/null
+++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 2f5ddd0..827543f 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index d77e43c..849f17a 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -68,5 +66,5 @@ 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-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-signature/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>