reinit the tree, so we can have metadata

4 files changed, 178 insertions, 0 deletions

diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
new file mode 100644
index 000000000000..6bc01d894564
--- /dev/null
+++ b/sci-biology/embassy-emnu/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-emnu-1.05.650_fix-build-system.patch 4072 SHA256 fe36162b0925c6b2746d6663c91853cbdf964c42ab950fb5613506518d1cac15 SHA512 644c4f0930a157ae9121354b49ddeb756b25d823d25733405fcc500d2080067f013443ba43a1512c6940fc4fd19cfe38c336dd0c58237354bad580cf9ba68b2e WHIRLPOOL 36dd5eab9ad368e471fbf799443a4a0d8132b89e31f670b030735f768684d4afe21577962c3ae0476f949c116a514425a16345edfb8172548df156b61b0cd1ff
+DIST embassy-emnu-1.05.660.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a
+EBUILD embassy-emnu-1.05.660.ebuild 470 SHA256 b4d1cdbdb92f508690a3f20e6e9931022c9942460bf996f1fdeb4b07f9bf8103 SHA512 ec9df242ed5a421fdbc45b59c1a9a9a3cfe540bde2ea010a29ac56e758d26fa0f1a1c850de644e82486a574850b0702d7d87adebfd851cd40076e17596c88f05 WHIRLPOOL f040dee96571b9ebbb3d9c4c73873b9020acb657dba9e1c0492b90c7319f5aa3fe88db34bed269cecf6bfc3de07c3a9480b6c4487432e440eda3250ab3da483a
+MISC ChangeLog 3890 SHA256 b80d3323420fe549f7f0de661fcd6fbd323999f4f5904cf19d511123b321230f SHA512 dfdb5b23e58614ecc42d9cd39e66b3113816d53dfc820a7ec5422bfea9c433a9fb89102e996e066f57a465b0f7accb43288986671da403fb3700032cd408d2cb WHIRLPOOL e28af714bc0a187135230cc876001549b6c181d92ecc1ab133ed3e6618cc4d75df4bc422631ffe324624d9a797c55b8564520158b3403c6514f086e0c42a5d5e
+MISC ChangeLog-2015 5221 SHA256 c23b8feae038f5de8eb63d9f0f6c569b0acc03e25cebd2c9b5bfd4c7e45d0967 SHA512 34da4783348408202dbc240d9fdcbc370ac0385c1b41be4a73e9c565e25f84633b808525980edbdd47ec1a2f0f31cc03369d9208d340e4653de86cc8a90ab4c3 WHIRLPOOL 0047620191be27d41e3f7ed9d86b1e733b136379b8e263701b5fcc03f35fdd47bc511d26ca60b7e8b7b73aacd9b2bd0242875202cbc712a049189a87a9f8e8fb
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild
new file mode 100644
index 000000000000..fd6b02d8d235
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="Simple menu of EMBOSS applications"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+IUSE="ncurses"
+
+RDEPEND="ncurses? ( sys-libs/ncurses:0= )"
+
+S="${WORKDIR}/EMNU-1.05.650"
+PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch )
+
+src_configure() {
+	emboss-r2_src_configure $(use_enable ncurses curses)
+}
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
new file mode 100644
index 000000000000..4e14bac1704a
--- /dev/null
+++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
@@ -0,0 +1,139 @@
+ configure.ac           | 67 +++++++++++---------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  7 +++---
+ 3 files changed, 18 insertions(+), 58 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 7482ade..b815bdb 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+@@ -899,20 +864,16 @@ dnl fi
+ 
+ 
+ dnl emnu and mse only: uses curses
+-dnl Test if --with-curses is given
+-AC_ARG_WITH([curses],
+-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])])
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
+ 
+-AC_MSG_CHECKING([for curses])
+-
+-AS_IF([test "${with_curses}"],
+-[
+-  CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-  LDFLAGS="$LDFLAGS -L${with_curses}/lib"
++AS_IF([test "x$enable_curses" = "xyes"], [
++  PKG_CHECK_MODULES([NCURSES], [ncurses])
++  PKG_CHECK_MODULES([FORM], [form])
++  PKG_CHECK_MODULES([MENU], [menu])
+ ])
+ 
+-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"])
+-
+ 
+ 
+ 
+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 b295079..330c76f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,8 @@ 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) \
++	$(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	../../../plplot/libeplplot.la -lmenu -lform $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB)
++        -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-emnu/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>