reinit the tree, so we can have metadata

8 files changed, 689 insertions, 0 deletions

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
new file mode 100644
index 000000000000..3e260fbd1307
--- /dev/null
+++ b/sci-biology/emboss/Manifest
@@ -0,0 +1,10 @@
+AUX README.gentoo 1522 SHA256 3cbb20ef948613f07698ab17c2b432e3aeab0ade6499a965c538d4feae8440d2 SHA512 a5441a056ebb11d24b83b8bfb9182f0753b85ec5ba126a123eb97c55fc665dadff2cc5f16c8e4314535f1b6a206c200324c0c5d5db6af109c841ee68ac76bb07 WHIRLPOOL b659d2c08416786ce4bdd0de0d61da49c1e6be4524e19c4b262a81a6455bf6b3e24ca0f1c7b5414c5fda35a006827fc5e229411821247b76bc26afda5a0a21d8
+AUX emboss-6.6.0_FORTIFY_SOURCE-fix.patch 417 SHA256 317bff2c29f321afe7274babba8db554420a26744cef6aa73885b18e7434e89f SHA512 9873504675825613c913fbd8c03d919c5d70ad7f15e3983ae9dc5ecd04e57d1086c303a4f38efd29def4f089099b24449014bbe965816c7f8b37a5d4ffa13469 WHIRLPOOL b23ea76326c732d5c25429589bed6301d0a6e9342523275a40c225c2af0e25eb2b6279905c52633b35eb3208bf43b7f4a1307c5f66bf95e81e8c8097d967d801
+AUX emboss-6.6.0_fix-build-system.patch 12599 SHA256 9ff77b03a1b1d5d28ae7720a6e61ddf226337d04aaf4da69e3c9a5918dcea7de SHA512 60dbb50967b0b855fabd68f2df7713da81007cb84aeb3f2d7510d13e533e3b19ed3d07e012010ebb1b2af04522f6f2142fbef405b9b580740a6bb5d30319b67b WHIRLPOOL 938e9208888fcb180177585c777465b1b2e82588a4a06588b79e85b76f53509c0ce04db6e03258bcb3ccc131c6d815a07b8933474bf98a2ecbe1359595b9892e
+AUX emboss-6.6.0_plplot-declarations.patch 1562 SHA256 d0146d519f23c0bee9c2b13cde1c8f6b4e2ae333740672623620d5236e58326d SHA512 fc27b7c1d518b5cdacf1964d56219c6574f43d18dc324e41b9dcdfd1afef17a784f2b209b62c366fb902ba57a50f438a1b328eb2118ee9463ce82b36039bc0bb WHIRLPOOL d23b7a061d1fa41c8319fd9f00168153022a70575148b6c23cd41d9fa9cf393caddb3d26a4ebcf94b66892998bd356b2ea391f448306706e364603bdbe809153
+AUX emboss-6.6.0_qa-implicit-declarations.patch 1324 SHA256 87de58d0a6225ba7f4644edd802d8c8658d59bd8140b48771da86b849e725b96 SHA512 15c303fe48a438f50f1c9a0efd7e8fcbcb4102151fc182feb8e0d74c47c3435385a1e44436cebd3c2017c97dd89b82832258748f28f3740e511a92b088f539fb WHIRLPOOL d1aeee505672c1ec596afc547052324144f4b72f397722d9e387d94c1940b30f81b8f265d9cd1ef902dea083f628ae79a3a3e5f65bb2342eb54c57fa169ca60a
+DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
+EBUILD emboss-6.6.0-r1.ebuild 1648 SHA256 74dc9b874d2cd6a49e18b9f354c011e4ccffd2a256903115872d404a9ff55efb SHA512 3ff85cc699f9ccfaf68d8335b8631a7f976ad69e82a8bd0be70123fb61ab90c50250691c1e507b2ba891a07b5e6693612209d44780afe35ceef4e2c431f9d265 WHIRLPOOL 98bcab5a9f8c285d9c00d0c08784e060ac65913668dcd2bb36fa30e311c367454fb3b7610eeb233bd44a0b0314b53a8e8af65f6e297dc3d423191cf3b17514ce
+MISC ChangeLog 5649 SHA256 6d655b59592dd57123b0bde406c08fcc5e4f63943e7918d4e24563f3bb55c9cc SHA512 1666627eab0475e700adef75869d76c0e5aa2fcb7a8487fecb9905dbc422b9272dac58f837c90aba126bda8f44dd6de4d4022d34ed0de987be10e35bbcec8645 WHIRLPOOL bfbc42764b3c95c3ad99ffa52ce5be9fdb43994ac2956961471fc626ce1ec2cd6df835fb9e0a339a963e53d3d2bb2ba4818560073f15d947d83a4e496c96ba44
+MISC ChangeLog-2015 13162 SHA256 48e1aa2076b5f4cb4177bfcb0133c424d7e1ee9a3cedc9b11eee74e426bed4bb SHA512 104d3b3f33162d1f22e0136b4cbbec298decbfe386ab5bc2f4e46e900fb8017ab36665b8dc00bdf6e20326f54131f16ce43b7863a4801b277c7517c8bd44e813 WHIRLPOOL 45b332443d0ba23f278ef2d58087e7c1f9d14123b704f633cc67ff9fe16e9a54e0b2d8e06c5a52cae6cb4acce1943693fc69f484da2addf2268df2bfbd9f641a
+MISC metadata.xml 1107 SHA256 a4a887fdc78fba3c2f9e9da6b8187ce74f0914ec57fdecd292abdfe9c6147d84 SHA512 b39a7f8b99f837b49190a19ee3b3f1b79cad8e93d3d5c88e5bfe30a009268d7255fd09f7f0eb3c4b574bed89acf5884ba981b146bd9706f4e0666acdac82c429 WHIRLPOOL 7088e789d13fb2b5b19d193ab29aeebfaf22c11b5f7eabf0cbdcfa2809680071686d18bd4e2fb9ba2dc89707f1705018b1b26ef3135517dcd573d75d77078662
diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
new file mode 100644
index 000000000000..2aa5aa9bc5c9
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2 readme.gentoo-r1
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
+
+RDEPEND="
+	!games-action/xbomber
+	!sys-devel/cons"
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/primer3
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+	)"
+
+S="${WORKDIR}/${P^^}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}_fix-build-system.patch
+	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+	"${FILESDIR}"/${P}_plplot-declarations.patch
+	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
+)
+
+src_install() {
+	emboss-r2_src_install
+
+	readme.gentoo_create_doc
+
+	# Install env file for setting libplplot and acd files path.
+	cat > 22emboss <<- EOF || die
+		# ACD files location
+		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
+	EOF
+	doenvd 22emboss
+
+	# Remove useless dummy files
+	find "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files"
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.gentoo".
+	mv "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \
+		|| die "Failed to move CODON directory"
+}
+
+pkg_postinst() {
+	readme.gentoo_print_elog
+}
diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo
new file mode 100644
index 000000000000..d1879bd0811c
--- /dev/null
+++ b/sci-biology/emboss/files/README.gentoo
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+	# cd ${EPREFIX}/usr/share/EMBOSS/data
+	# ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+	# cd ${EPREFIX}/usr/share/EMBOSS/data
+	# ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
new file mode 100644
index 000000000000..7704873e9d26
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
@@ -0,0 +1,11 @@
+--- EMBOSS-6.6.0/emboss/embossversion.c
++++ EMBOSS-6.6.0/emboss/embossversion.c
+@@ -415,7 +415,7 @@
+ 	ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING);
+ #endif
+ #ifdef _FORTIFY_SOURCE
+-	ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE);
++	ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL);
+ #endif
+ 	ajFmtPrintF(outfile, "\n");
+ 	ajFmtPrintF(outfile, "Sizes (bytes):\n");
diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
new file mode 100644
index 000000000000..266bddd95a37
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
@@ -0,0 +1,411 @@
+ Makefile.am               |  9 +++---
+ ajax/Makefile.am          |  4 +--
+ ajax/acd/Makefile.am      |  8 +++--
+ ajax/ajaxdb/Makefile.am   |  6 ++--
+ ajax/core/Makefile.am     |  6 ++--
+ ajax/core/ajreg.h         |  7 ++--
+ ajax/ensembl/Makefile.am  |  6 ++--
+ ajax/graphics/Makefile.am |  8 +++--
+ configure.ac              | 82 ++++++++++++++++++++++++++---------------------
+ emboss/Makefile.am        | 13 +++++---
+ jemboss/lib/Makefile.am   |  2 +-
+ m4/idxdbs.m4              | 17 +++-------
+ nucleus/Makefile.am       |  8 +++--
+ 13 files changed, 100 insertions(+), 76 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 177dec5..18dd99a 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -12,8 +12,11 @@ LICENSE \
+ ONEWS \
+ PROBLEMS
+ 
+-SUBDIRS = \
+-plplot \
++SUBDIRS =
++if !ESYSTEMLIBS
++SUBDIRS += plplot
++endif
++SUBDIRS += \
+ ajax \
+ nucleus \
+ emboss \
+@@ -33,5 +36,3 @@ dist-hook:
+ 	tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
+ 	tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
+ 
+-install-exec-hook:
+-	$(bindir)/embossupdate
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index f27472c..de34e17 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,7 +1,7 @@
+ ## Process this file with automake to produce Makefile.in
+ 
+-SUBDIRS  = pcre
++SUBDIRS  =
+ if !ESYSTEMLIBS
+-SUBDIRS += expat zlib
++SUBDIRS += pcre expat zlib
+ endif
+ SUBDIRS += core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 9f0f700..3295a1d 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -3,16 +3,20 @@
+ lib_LTLIBRARIES = libacd.la
+ 
+ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
+ 
+ libacd_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ajaxdb
++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ if !ESYSTEMLIBS
++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++libacd_la_CFLAGS   += $(PLPLOT_CFLAGS)
++endif
+ libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ 
+ libacd_la_LDFLAGS  = -version-info 6:5:0
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index c2b0c00..9de14fe 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -3,14 +3,16 @@
+ lib_LTLIBRARIES = libajaxdb.la
+ 
+ libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
+ 
+ libajaxdb_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ensembl
+-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
+ libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ 
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index 2906837..3189c34 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -3,13 +3,15 @@
+ lib_LTLIBRARIES = libajax.la
+ 
+ libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
+ 
+-libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
++libajax_la_CPPFLAGS  =
+ if !ESYSTEMLIBS
++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 1623c82..5d928cf 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -39,9 +39,8 @@
+ #include "ajdefine.h"
+ #include "ajstr.h"
+ 
+-#include "pcre_config.h"
+-#include "pcre_internal.h"
+-#include "pcreposix.h"
++#include <pcre.h>
++#include <pcreposix.h>
+ 
+ AJ_BEGIN_DECLS
+ 
+@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
+ 
+ typedef struct AjSRegexp
+ {
+-    real_pcre *pcre;
++    struct real_pcre *pcre;
+     pcre_extra *extra;
+     int *ovector;
+     const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index 0d1250b..5484c02 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -3,13 +3,15 @@
+ lib_LTLIBRARIES = libensembl.la
+ 
+ libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libensembl_la_LIBADD = ../core/libajax.la
+ 
+-libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
++libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ 
+ libensembl_la_LDFLAGS  = -version-info 6:5:0
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index a4f202b..1114c2c 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -3,12 +3,16 @@
+ lib_LTLIBRARIES = libajaxg.la
+ 
+ libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS)
+ 
+-libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
++libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+-endif
+ libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++libajaxg_la_CFLAGS   += $(PLPLOT_CFLAGS)
++endif
+ libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ 
+ libajaxg_la_LDFLAGS  = -version-info 6:5:0
+diff --git a/configure.ac b/configure.ac
+index a7bd9c6..9ba3121 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -629,32 +629,6 @@ AS_CASE([${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 Define where the EMBOSS package is located
+ AC_SUBST([AJAX_FIXED_ROOT])
+ AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
+@@ -743,17 +717,7 @@ 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])
+ 
+ 
+ 
+@@ -849,7 +813,53 @@ 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([PCRE], [libpcre])
++  PKG_CHECK_MODULES([EXPAT], [expat])
++  PKG_CHECK_MODULES([ZLIB], [zlib])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++    [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++    )
++],
++[
++dnl using bundled libraries
++  dnl PCRE library definitions - see the MAJOR and MINOR values
++  dnl to see which version's configure.ac 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 "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])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 89ada78..f987d40 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -28,15 +28,18 @@ endif
+ 
+ AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
++if !ESYSTEMLIBS
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+-if !ESYSTEMLIBS
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+-AM_CPPFLAGS += -I$(top_srcdir)/nucleus
+ AM_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++AM_CFLAGS   += $(PLPLOT_CFLAGS)
++endif
++AM_CPPFLAGS += -I$(top_srcdir)/nucleus
+ AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
+ AM_CPPFLAGS += $(JAVA_CPPFLAGS)
+ 
+@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
+ if !ESYSTEMLIBS
+ LDADD += ../ajax/zlib/libezlib.la
+ LDADD += ../ajax/expat/libeexpat.la
+-endif
+ LDADD += ../ajax/pcre/libepcre.la
+ LDADD += ../plplot/libeplplot.la
++else
++LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS)
++endif
+ LDADD += $(XLIB)
+ 
+ #if PURIFY
+diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
+index 5f7e21e..8b45ce2 100644
+--- a/jemboss/lib/Makefile.am
++++ b/jemboss/lib/Makefile.am
+@@ -12,7 +12,7 @@ mail.jar \
+ jalviewApplet.jar \
+ jemboss.jar
+ 
+-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
+ if JAVA_BUILD
+ 	$(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
+ endif
+diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
+index 0ca7ea9..9b54f2a 100644
+--- a/m4/idxdbs.m4
++++ b/m4/idxdbs.m4
+@@ -1,17 +1,8 @@
+ AC_DEFUN([CHECK_IDXDBS],
+ [
+-AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
+ 
+-
+-if test -f ./emboss/index/edam.xac; then
+-AC_MSG_RESULT(yes)
+-else
+-AC_MSG_RESULT(no)
+-echo ""
+-echo "Pre-indexed edam, taxon + drcat databases not found."
+-echo "Please download them from within this directory using:"
+-echo "    rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
+-echo "and then repeat the configure step."
+-exit 1
+-fi
++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
++	[],
++	[AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
+ ])
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index 37b8543..5819c89 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
+@@ -3,6 +3,7 @@
+ lib_LTLIBRARIES = libnucleus.la
+ 
+ libnucleus_la_CFLAGS  = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libnucleus_la_LIBADD  = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
+ 
+ if ISSHARED
+ if ISAIXIA64
+@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
+ endif
+ endif
+ 
+-libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/plplot
+-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
++else
++libnucleus_la_CFLAGS   += $(PLPLOT_CFLAGS)
+ endif
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
new file mode 100644
index 000000000000..15f5f967a07d
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
@@ -0,0 +1,61 @@
+--- EMBOSS-6.6.0/ajax/graphics/ajgraph.c
++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c
+@@ -49,7 +49,7 @@
+ 
+ #define GRAPH_DEBUG 1
+ 
+-#include "plplotP.h"
++#include <plplotP.h>
+ 
+ 
+ static void     GraphArray(ajuint numofpoints,
+@@ -964,10 +964,10 @@
+     if(!thys->ready)
+     {
+ #if GRAPH_DEBUG
+-        ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
++        ajDebug("=g= plsfnam ('%S')\n", txt);
+ #endif
+ 
+-        plxsfnam(ajStrGetPtr(txt), ext);
++        plsfnam(ajStrGetPtr(txt));
+         ajStrAssignS(&graphBasename, txt);
+         ajStrAssignC(&graphExtension, ext);
+         if(ajStrGetCharFirst(graphExtension) == '.')
+@@ -1213,10 +1213,10 @@
+ void ajGraphicsSetPenwidth(float penwidth)
+ {
+ #if GRAPH_DEBUG
+-    ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
++    ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth);
+ #endif
+ 
+-    plwid((PLINT)penwidth);
++    c_plwidth((PLINT)penwidth);
+ 
+     return;
+ }
+@@ -1538,10 +1538,10 @@
+ static void GraphSetPen(ajint colour)
+ {
+ #if GRAPH_DEBUG
+-    ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
++    ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
+ #endif
+ 
+-    plcol((PLINT)colour);
++    plcol0((PLINT)colour);
+ 
+     return;
+ }
+--- EMBOSS-6.6.0/ajax/graphics/ajgraph.h
++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h
+@@ -32,7 +32,7 @@
+ /* ========================================================================= */
+ 
+ #include "ajdefine.h"
+-#include "plplot.h"
++#include <plplot.h>
+ #include "ajgraphstruct.h"
+ #include "ajdefine.h"
+ #include "ajstr.h"
diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
new file mode 100644
index 000000000000..eff10b2e6700
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
@@ -0,0 +1,74 @@
+--- EMBOSS-6.6.0/ajax/core/ajfeatread.c
++++ EMBOSS-6.6.0/ajax/core/ajfeatread.c
+@@ -45,6 +45,7 @@
+ 
+ #include <limits.h>
+ #include <math.h>
++#include <string.h>
+ #include <errno.h>
+ 
+ #ifdef WIN32
+--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
++++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
+@@ -43,7 +43,7 @@
+ 
+ #include <limits.h>
+ #include <math.h>
+-
++#include <string.h>
+ 
+ static AjPRegexp featoutRegUfoFmt = NULL;
+ static AjPRegexp featoutRegUfoFile = NULL;
+--- EMBOSS-6.6.0/ajax/core/ajpdbio.c
++++ EMBOSS-6.6.0/ajax/core/ajpdbio.c
+@@ -37,7 +37,7 @@
+ 
+ #include <limits.h>
+ #include <math.h>
+-
++#include <string.h>
+ 
+ 
+ 
+--- EMBOSS-6.6.0/ajax/core/ajreg.c
++++ EMBOSS-6.6.0/ajax/core/ajreg.c
+@@ -32,6 +32,7 @@
+ #include "ajlib.h"
+ 
+ #include "ajreg.h"
++#include <string.h>
+ 
+ 
+ 
+--- EMBOSS-6.6.0/ajax/core/ajseqtype.c
++++ EMBOSS-6.6.0/ajax/core/ajseqtype.c
+@@ -32,7 +32,7 @@
+ #include "ajfeat.h"
+ #include "ajfile.h"
+ #include "ajreg.h"
+-
++#include <string.h>
+ 
+ 
+ 
+--- EMBOSS-6.6.0/nucleus/embindex.c
++++ EMBOSS-6.6.0/nucleus/embindex.c
+@@ -35,6 +35,7 @@
+ #include "ajnam.h"
+ 
+ #include <errno.h>
++#include <string.h>
+ 
+ #define BTENTRYFILE     ".ent"
+ #define KWLIMIT 12
+--- EMBOSS-6.6.0/nucleus/embword.c
++++ EMBOSS-6.6.0/nucleus/embword.c
+@@ -36,7 +36,7 @@
+ #include "ajutil.h"
+ 
+ #include <math.h>
+-
++#include <string.h>
+ 
+ 
+ 
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
new file mode 100644
index 000000000000..9a479025456e
--- /dev/null
+++ b/sci-biology/emboss/metadata.xml
@@ -0,0 +1,24 @@
+<?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>
+  <longdescription>
+		EMBOSS is "The European Molecular Biology Open Software Suite".
+		EMBOSS is a free Open Source software analysis package specially
+		developed for the needs of the molecular biology (e.g. EMBnet) user
+		community. The software automatically copes with data in a variety
+		of formats and even allows transparent retrieval of sequence data
+		from the web. Also, as extensive libraries are provided with the
+		package, it is a platform to allow other scientists to develop and
+		release software in true open source spirit. EMBOSS also integrates
+		a range of currently available packages and tools for sequence
+		analysis into a seamless whole. EMBOSS breaks the historical trend
+		towards commercial software packages.
+	</longdescription>
+  <upstream>
+    <remote-id type="sourceforge">emboss</remote-id>
+  </upstream>
+</pkgmetadata>