reinit the tree, so we can have metadata

4 files changed, 195 insertions, 0 deletions

diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
new file mode 100644
index 000000000000..d64545ddc9c6
--- /dev/null
+++ b/sci-biology/embassy-mse/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-mse-3.0.0.650_fix-build-system.patch 4274 SHA256 599b095e98864d4268b5959517c1002b3b591a45d865e42f409eb0059af5168b SHA512 bfb4663a4b38928f765813cc9b5e773ca712c2333c1650d9c78f457307aa450684f77a20c0a087d3795d5b51f059c6f8113e74da35aa78753c1cc666ba583f4b WHIRLPOOL 418dc60bb9cf2023d499eec13b132f1aaab7bd9538ba2bc12f3f19926a25f7e7f0fb3b9b99e80acddfb57a4762aba5c90e413ffe5c8aa05d593d1309ecc28db8
+DIST embassy-mse-3.0.0.660.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b
+EBUILD embassy-mse-3.0.0.660.ebuild 563 SHA256 95486ba509879ea87d6f2a7a97987b22857881181cb3fa0046299a45cc4bf20a SHA512 80cc7b8c36d5675f8f4caf9fb244ce1b2740bef6813c4f62e4084a07f31d173abc0fbc4b486e7fda12b701ffe9d99efb023e76fdceaf29c87c2b5182ea1609f9 WHIRLPOOL 422b7ce3a899e1260da66c78c5e763e986e438a9b9ae3ece5cd23cd5df516f395ebd0971563f505189d9a2a5d0cf03db03442c7ce8d05e1e083a0d197ab8a86a
+MISC ChangeLog 3557 SHA256 63d5d3e0ceb7785312a8ac18c6b3a6e7fd4569f0dbf7f9192d1684f403428e57 SHA512 ebad0d05b2493db898c50a6e1d268313da3d60705159dff3cef1f388d6a249bd7cb9e7c9e7a0639d99969316eb680a9d10be21935bc067bc70f758b6627d1671 WHIRLPOOL d4dd277affb7666a0380d0e3890c88a8f25725bb92fcc6bd81b0b866bc5234530cd6d3759732cf41014e6ea7a82fca160b7e4f2fd5190ac6aa60c8e924b2725e
+MISC ChangeLog-2015 6196 SHA256 33d5a20ceaea1924c0fc21af8053c9e4fd1385a6b352c4224c9ec6de563041ba SHA512 29895c8f1db31e3fb946dfbf95ba737530fd9eeecca7cab5713075f06cc0a4c3e647df72369cefc3023a8ef36f2aeaa2677158431e44239d8517fa7257403281 WHIRLPOOL c520584027ef2ffef27609a3388c995c90160a90c9039f5d88414e9a5c46c85c24fb3bd9f4af24e694de1320d05d065fd2d08108344be05aa2c8de965cc38471
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
new file mode 100644
index 000000000000..c22970155918
--- /dev/null
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+IUSE="ncurses"
+
+RDEPEND="ncurses? ( sys-libs/ncurses:0= )"
+
+S="${WORKDIR}/MSE-3.0.0.650"
+PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch )
+
+src_configure() {
+	emboss-r2_src_configure $(use_enable ncurses curses)
+}
+
+src_install() {
+	emboss-r2_src_install
+
+	insinto /usr/include/emboss/mse
+	doins h/*.h
+}
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..c1095b266d60
--- /dev/null
+++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
@@ -0,0 +1,149 @@
+ ckit/Makefile.am       |  2 +-
+ configure.ac           | 67 +++++++++++---------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++---
+ 4 files changed, 18 insertions(+), 59 deletions(-)
+
+diff --git a/ckit/Makefile.am b/ckit/Makefile.am
+index f87b131..a670d2b 100644
+--- a/ckit/Makefile.am
++++ b/ckit/Makefile.am
+@@ -2,7 +2,7 @@
+ 
+ lib_LTLIBRARIES = libckit.la
+ 
+-AM_CPPFLAGS = -I../h
++AM_CPPFLAGS = -I$(top_srcdir)/h
+ 
+ CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
+ seqspec.c ttyinterface.c nextseqentry.c \
+diff --git a/configure.ac b/configure.ac
+index a20d488..eb208bf 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
+@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"],
+ 
+ 
+ 
+-dnl emnu and mse only: uses curses
+-dnl Test if --with-curses is given
+-AC_ARG_WITH([curses],
+-   [AS_HELP_STRING([--with-curses],
+-                  [curses (or ncurses)])])
+-if test "${with_curses}" ; then
+-AC_MSG_CHECKING([for curses])
+-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-LDFLAGS="$LDFLAGS -L${with_curses}/lib"
+-fi
+-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses")
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
++
++AS_IF([test "x$enable_curses" = "xyes"], [
++  PKG_CHECK_MODULES([NCURSES], [ncurses])
++])
+ 
+ 
+ 
+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 b44632a..84e89b5 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../h -I${embprefix}/include \
+-	-I${embprefix}/include/eplplot -I${embprefix}/include/epcre \
+-	$(NLINCLUDES)
++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \
+ 	$(XLIB)
+ else
+ LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
+-	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++	-lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-mse/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>