Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #335603

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

13 files changed, 346 insertions, 41 deletions

diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog
index 8a98140f81ad..6996907cd24b 100644
--- a/sci-biology/embassy-cbstools/ChangeLog
+++ b/sci-biology/embassy-cbstools/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-cbstools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.7 2011/10/20 08:56:48 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.8 2015/03/28 17:35:00 jlec Exp $
+
+*embassy-cbstools-1.0.0.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-cbstools-1.0.0.650.ebuild,
+  +files/embassy-cbstools-1.0.0.650_fix-build-system.patch, metadata.xml:
+  Import latest changes from science overlay, thanks Ted Tanberry for the work;
+  fixes #335603
 
   20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org>
   embassy-cbstools-1.0.0.ebuild, embassy-cbstools-1.0.0-r1.ebuild:
@@ -32,4 +40,3 @@
   27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +embassy-cbstools-1.0.0.ebuild:
   Initial import for EMBASSY 6.0.1.
-
diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest
index 4d3dfdd02a31..8a69f0032818 100644
--- a/sci-biology/embassy-cbstools/Manifest
+++ b/sci-biology/embassy-cbstools/Manifest
@@ -1,28 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
-DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
-DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
-DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 RMD160 0653dd66127f4865478b777e5a4bf97cc6e90c0c SHA1 3d8190ce5a9cb9ed10aad0bd4d70c5f4226b4cf3 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693
-DIST embassy-6.1.0-cbstools-1.0.0.tar.gz 356429 RMD160 f6f153cc55a87f127918c7707685ff09ed0aa931 SHA1 b6c8b2b799c981ccae78de590fce275a35ab5091 SHA256 de9e39838ee142ba4bb30a499c3326b35a1b86f07bcf1a6848f3f957fae69262
-EBUILD embassy-cbstools-1.0.0-r1.ebuild 544 RMD160 d1c416b904ece7c0eac371a1caa51ecb2bd9b813 SHA1 71790f220205dd3cf4b93885a8522a666e71a90f SHA256 9db4ff135b24e86fae98683e88d66bfc80b0204f0c29a1e3926037d56f1d50a1
-EBUILD embassy-cbstools-1.0.0.ebuild 504 RMD160 11d183a54862233158fb7a69684180b9965f2f3a SHA1 aef059c4bf6c8310dac95f30641dd4c9c82119eb SHA256 71a95a9654810371b8e2520b4565df719bf8b83361cd3be05274bf880fa8621f
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-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 2586 SHA256 15692e00271d3d473d0591e7ee46eadca450b002188b795e22826f7e73ebb66f SHA512 38e4fbba5246a44d63b3ac695d8ed45ab6d0902fbe482007b0e206e7a61c0e2429108dbcbbfc1fed161571280a7d7656d6c385bd9cf85ea5a7bfa958e187c6fb WHIRLPOOL 37c54e3d75d457b8539f9e99c04bbb78eea1e1bfc4b31c012062bf8ff8956a78788ae5b93e15c0149745303ff837f7d81562bab69a98b813c417169a1258847c
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693
+DIST embassy-6.1.0-cbstools-1.0.0.tar.gz 356429 SHA256 de9e39838ee142ba4bb30a499c3326b35a1b86f07bcf1a6848f3f957fae69262
+DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a
+EBUILD embassy-cbstools-1.0.0-r1.ebuild 544 SHA256 9db4ff135b24e86fae98683e88d66bfc80b0204f0c29a1e3926037d56f1d50a1 SHA512 8b5f1f55daa97e181f23590e51189749af77e2fb40ec36caf4c492a84bed36d09e3e353e8267016f0a2d40d303bcbaca83edf5af7da27dbece3fd8d865695b9a WHIRLPOOL 0304ed650785ff9af4213bdf03b31cf29bdc015fd74904269e278308d30f3ab575499f954a0928d349594bfc4589ff9af3313d0a7f43bfa0b3c64263fda1d70f
+EBUILD embassy-cbstools-1.0.0.650.ebuild 461 SHA256 43fc26e1a1f29d3ee96eed2e5cdeb952479cfcd94b39ae21b58bb93dd270c79f SHA512 9d3eaa981851c18547d6c90527a8561e1da08fa3ba39e1164f8d5a7e2239b6b5b63767fe2cd0b0cccd6019cf4bdec11cc802b6ba107344e46f0838d8ab49cd4d WHIRLPOOL ab4638036733586c3b5df12b4bc0e4ea6e7fb883ab8e2c4268545740ee5f30418e42cd68d4d16ae5fc0e375b5228649b5fb3f6543f1c85ff7cc486ba125ca155
+EBUILD embassy-cbstools-1.0.0.ebuild 504 SHA256 71a95a9654810371b8e2520b4565df719bf8b83361cd3be05274bf880fa8621f SHA512 ab1b7aeedcb9470bc5e280f9803d3f9b8fc71daae758f36a64ef5bb15038143f49020984ade3369ed4ede377c46b81951d3c5a3e793710df220050f61b0915f1 WHIRLPOOL 2994eada7616e524ecbd5bc0e1c31400cb668d73b89858f3125cd91c789548462aa45b0cbb09162625e61e7caddaab5d92711778178a1cc30db9820e68979d39
+MISC ChangeLog 1508 SHA256 8513871a24824a3c0590926e806a2c83f6dca6872735b5b324cb0b12da08d987 SHA512 2286fca698ffacdc4a30d6e7271e1f270422624be2720bab28271d7ce02693e0a9727e67acdc2c7310fdf3c4d9e16da6149a8dca9aecf640b4254c88a5a41a75 WHIRLPOOL 7f471a2eda3d2bb57a9ef7a2d61ed019fc9b673963a42e6dff88616a58d8e705b14bad29113376fe2d0d431415898cc429965c54e3a172ec5b77287e86660d37
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0
 
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diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
new file mode 100644
index 000000000000..462183789f05
--- /dev/null
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild,v 1.1 2015/03/28 17:35:00 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="applications from the CBS group"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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..63c67a1601d1
--- /dev/null
+++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,97 @@
+--- CBSTOOLS-1.0.0.650/configure.ac
++++ CBSTOOLS-1.0.0.650/configure.ac
+@@ -635,33 +635,6 @@
+ 
+ 
+ 
+-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${with_x}" != "xno"],
+@@ -737,21 +710,6 @@
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,11 @@
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- CBSTOOLS-1.0.0.650/src/Makefile.am
++++ CBSTOOLS-1.0.0.650/src/Makefile.am
+@@ -19,9 +19,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${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 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+--- CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am
++++ CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-cbstools/metadata.xml
+++ b/sci-biology/embassy-cbstools/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
index 87bff755f767..7e72f7989961 100644
--- a/sci-biology/embassy-clustalomega/Manifest
+++ b/sci-biology/embassy-clustalomega/Manifest
@@ -1,5 +1,27 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2383 SHA256 42b1e713f2e987226ec6a9ce4177755139e573a752d7b16ed8dddfe6732a7230 SHA512 e0b517d5e6a5969d7428b8dfb72f71e9dd871383827db36a0bc9149c3fc4aa90638e7e9b0752927b1a081eae3ac62d2d8d0feb9aaa5c5434a1d09dc42f4104ef WHIRLPOOL d62e8e6888e09fcc592a0d5fc7383a76611f6ca09113726d4e744452ffe66c5359e843a5b4009969d59cc543b9a3e9d9003f1b7a6fe8a67091570dd9c597f769
 DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54
-EBUILD embassy-clustalomega-1.1.0.ebuild 390 SHA256 74257039492f6d0010aa70d61770636a521b4789f34409be647900317a96c37a SHA512 56962c8e4d6e6e687711c078cf7101ce13f17a76839b93d6bde519ea1ea7d278bbca8ea35d9fd4290fe530f8b75c4d8fca47fd33eb843963656e88666b0fe219 WHIRLPOOL da84aae8accd3c79318ad8a519c7be7a3aba7605b72de51fcf43ee38a26d792967368310165c93402b92f1471922fa85cd30fb93a4ea3e560c5a223bf3286f6f
-MISC ChangeLog 432 SHA256 0c1bfc6bece0d5cdb7c2bd61ef43ae03727e3c3b108e2223f1ad97b8c4addc7f SHA512 089d3d73c734b54d7bd809fe6b3eb1f7524c8012375ef8919c411cdeea6b9246484cd50ae9c2994639108583aec32717e28ede200558b0cc78a26134dbf89bd1 WHIRLPOOL 197985f7959fdfe9b61376435e34802f2ed8a1d9ddfacb617ea6ca6e9a2cd79cecae4d11cea7540e18597e488e954e780db5ec546d47849b51f246e9e20f016b
+EBUILD embassy-clustalomega-1.1.0.ebuild 516 SHA256 f62578afcd4c7dc08febd9b63c07a4ba427472cf18b8576f054b3877f25f54c9 SHA512 01b48231d892d25ada2112a5ca9b4a402115dc12cce0913a963ae7f63a90c55fb3cb0d8ad5863f2e191dea020824452b59cd25a8ffb61a78abd845b3cb863ca5 WHIRLPOOL 9c004bf3744fb81b13d5c06cf5f43dfc79c03342482697be8b8919dbb40898200a664b34f629185fa8d7b676cd4b793d3929505ed2acdf286fa2e8b4ab2a7b75
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 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
new file mode 100644
index 000000000000..ca0d19435299
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild,v 1.1 2015/03/28 17:33:53 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+=" sci-biology/clustal-omega"
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
new file mode 100644
index 000000000000..7847da78ac4a
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
@@ -0,0 +1,90 @@
+--- CLUSTALOMEGA-1.1.0/configure.ac
++++ CLUSTALOMEGA-1.1.0/configure.ac
+@@ -635,33 +635,6 @@
+ 
+ 
+ 
+-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${with_x}" != "xno"],
+@@ -737,21 +710,6 @@
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,11 @@
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- CLUSTALOMEGA-1.1.0/src/Makefile.am
++++ CLUSTALOMEGA-1.1.0/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${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 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog
index bd6b1008fd01..edaaffccfb53 100644
--- a/sci-biology/embassy/ChangeLog
+++ b/sci-biology/embassy/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/embassy
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.35 2011/04/05 08:06:56 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.36 2015/03/28 17:38:39 jlec Exp $
+
+*embassy-6.6.0 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-6.6.0.ebuild,
+  metadata.xml:
+  Import latest changes from science overlay, thanks Ted Tanberry for the work;
+  fixes #335603
 
   05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-4.0.0.ebuild:
   Dropped old, due to unsatisfied deps
diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest
index b5fb57be2cc9..60f78412fb8c 100644
--- a/sci-biology/embassy/Manifest
+++ b/sci-biology/embassy/Manifest
@@ -1,14 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
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-EBUILD embassy-6.1.0.ebuild 1121 RMD160 75aca3b740307acd8519fc98cdec830fde3213c9 SHA1 50fc4b3656e7fff6739d3f20c7c019f22ff9f1fd SHA256 09e481e48cd9365291e757fa4892812eb4df475bf8864365dbcf3dac076c2f6c
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+EBUILD embassy-6.0.1.ebuild 1144 SHA256 e0cb11917f6852ebcff2a76781ae6a19f9d61dd3d7ebdb7e0bf4c8c25232f449 SHA512 dea7bac8927f96403898322b5a3cd491e5810bf6b67fa1ef784acddbb638333fe839d2f10d63fe8d2150ef9787693fe53cc5b32963ab3be0fc59c524e8d89171 WHIRLPOOL b9be1dbffc095bbd3a531fbce791b3559f02abd1339e5431ec17febe82e68427859e76ed9580fcb824cd63d740bafa9eb62bdaa54db2088901c81f6247a10b3e
+EBUILD embassy-6.1.0.ebuild 1121 SHA256 09e481e48cd9365291e757fa4892812eb4df475bf8864365dbcf3dac076c2f6c SHA512 b290ce86e0e293baa68893ec875368426dd5aca0a556be5d9ff1a71db88e4bf5e6884b12bc7321f3494110032da503f60d478a10952f0e9eb0763cc25446de72 WHIRLPOOL 0bdb646790e0b3a2b52d79a6612481c37af72a075699c702d825432458f95ed502ae449ad070b5d36ab7f9f1e103ba10993a2b42fd2ff084405bcf93c1ae7de1
+EBUILD embassy-6.6.0.ebuild 1088 SHA256 4ee702cf346f514a357940c8611f346d807e07d1228e5200c6453c1892c1325b SHA512 b8c7fb65734f15f78c4d6e1d17345147e9ec121da2e4b97ca47010c72fe54ff714249d4b4b29996c384435ff71d60fb59eae70aaceb8ce0c860877debb53ac81 WHIRLPOOL a69922e7850401572da62980abbbccdde6bdedaee88d957d9764b962fb866115aa9ee69e63ab12a557a48d5fd088fa16f7881bb2ede86c21057efb2dcc7d618d
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diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild
new file mode 100644
index 000000000000..0e60ce04f87d
--- /dev/null
+++ b/sci-biology/embassy/embassy-6.6.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/embassy-6.6.0.ebuild,v 1.1 2015/03/28 17:38:39 jlec Exp $
+
+EAPI=5
+
+DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
+HOMEPAGE="http://emboss.sourceforge.net/embassy/"
+
+LICENSE+=" freedist"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+="
+	>=sci-biology/embassy-cbstools-1.0.0.650
+	>=sci-biology/embassy-clustalomega-1.1.0
+	>=sci-biology/embassy-domainatrix-0.1.650
+	>=sci-biology/embassy-domalign-0.1.650
+	>=sci-biology/embassy-domsearch-0.1.650
+	>=sci-biology/embassy-emnu-1.05.650
+	>=sci-biology/embassy-esim4-1.0.0.650
+	>=sci-biology/embassy-hmmer-2.3.2.650
+	>=sci-biology/embassy-iprscan-4.3.1.650
+	>=sci-biology/embassy-meme-4.7.650
+	>=sci-biology/embassy-mse-3.0.0.650
+	>=sci-biology/embassy-phylipnew-3.69.650
+	>=sci-biology/embassy-signature-0.1.650
+	>=sci-biology/embassy-structure-0.1.650
+	>=sci-biology/embassy-topo-2.0.650
+	>=sci-biology/embassy-vienna-1.7.2.650
+"
diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy/metadata.xml
+++ b/sci-biology/embassy/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
+  <herd>sci-biology</herd>
 </pkgmetadata>