reinit the tree, so we can have metadata

4 files changed, 142 insertions, 0 deletions

diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
new file mode 100644
index 000000000000..fa29a4858056
--- /dev/null
+++ b/sci-biology/embassy-iprscan/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 3167 SHA256 4ee85226fda51d4232bbce8c8f1f3d9b6deedb794864bb16c13eee514ad49b09 SHA512 b2b28377e60790db744f32eb5cd4de5b7e15129b603e21013eeeebaea5c06e6867937b6441f3d8e788effdbb58c57b8841880aa7d4b4eae2b0b83dc72242f4d8 WHIRLPOOL f7e9084619cc6b0b1e8425753e5f44ab41b22d309afe10e3a01eab67eb76258cebe3b6ecad340d247f6ca51bff0a1fac4f2125a8f8be5e30466b50fdee3ee494
+DIST embassy-iprscan-4.3.1.660.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8
+EBUILD embassy-iprscan-4.3.1.660.ebuild 363 SHA256 38f3fe16d5752340814d336e4c2152d3fb7e116ca2e1d889145af9754768726d SHA512 3b140b4b5f4e25d6935b4f159cf636d76dd5437c97fa3c4d0293287db5e1e52cda7db29eb4a0cd4b34aa9596da791725a51a653af27be52cdfbfb76c6ba1c1f6 WHIRLPOOL e80ec1b503269314457ea219e256061cace3775b3fc6293f33bb527932356d4bbc0445f9551b00f420b1c053a8bb99bd54d6d933c5f64a7219c1693f57fde9a1
+MISC ChangeLog 3703 SHA256 0e8e02ef4ddbf82293585913d79f0f614cccd638cd177b915f07ff93b3620d0b SHA512 a184d73c14b908ff8acfde1cf9592a8420682daec138c278fe3c7ead6fab9223028aa29a784471b40912414689f60e5b3d401d2cd6d8d2a5b55a82c77957ac40 WHIRLPOOL 8953578b043bc0f80b039529337eac4f0beb08bf915fcc7e92efa142fd20aa6e8972bff943435928a36939adbd1feef4cbdf419494ae998e9534676be388616f
+MISC ChangeLog-2015 1781 SHA256 015954d5dfc1ad4daa5ba6b0f4492b754cae024770b6a03fd1d4c55ae280a24a SHA512 2022d1f98a55d9f57600c6a9f7fef6bfc8a15678bce2b3d6b3531be7c532ae31f27e0b7626b180b39e5eca29cb581973eab307666c7819fead2b3f8047ba45ce WHIRLPOOL 42f145f36c3be160be823dc14c7ccd4ea831c569000064306a73b5cd87b367520545e16c1d0954ea0a379a32b9cc968625d33fc510e49a30ff49321a07e2dd1f
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild
new file mode 100644
index 000000000000..3279ed3bc8e8
--- /dev/null
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.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="InterProScan motif detection add-on package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}/IPRSCAN-4.3.1.650"
+PATCHES=( "${FILESDIR}"/${PN}-4.3.1.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..8c8a1060e30f
--- /dev/null
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 9052ca5..c12c268 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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/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 0afc96a..904b41a 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
+@@ -58,5 +56,5 @@ 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-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-iprscan/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>