reinit the tree, so we can have metadata

4 files changed, 142 insertions, 0 deletions

diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
new file mode 100644
index 000000000000..ed7c101c46c4
--- /dev/null
+++ b/sci-biology/embassy-esim4/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-esim4-1.0.0.650_fix-build-system.patch 3167 SHA256 25d191cabc62f3651e7f0cd999573b788827a2f3fb75e5c7be7716797c511577 SHA512 c8f4468998b1e91122e4ee5f355c5db451fa889892c05125edcc2f734051410251de85a9d7aaf5566dc802240d2925c709cfd448c8f96351aaa91c124eb1396f WHIRLPOOL 1558f5aca98ef8e6742c5990e7bb604d99ff80d6994147e01e2b1a3afc1c50e5efb56b9649d228da90bd955c83e3e12b65cfdc45c3bd50667de0c4236229be6b
+DIST embassy-esim4-1.0.0.660.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62
+EBUILD embassy-esim4-1.0.0.660.ebuild 345 SHA256 894db7ee83fc1895dc4a40318eba1e1e456d310afabbaa5f8a73b31f8061fbfc SHA512 baff9c211e98de225f8644a441b99b4693f16068c151b5ee5b59c481e6de564e5cce0f0617bdb52a3d96b642a3b22dd558eab3329098d3ac028527818dc16357 WHIRLPOOL 10d85eeb74a687704d2f542f11be349932f60bc3ae3d9a89896584a9961404ffce8e1ade74dc14d202b0122f764cd0b45af8f50adc458a066a08e07c6418c799
+MISC ChangeLog 3694 SHA256 cd070895ae878ac17a3e6e434ba823e1e4a5ed6930be5e89e7be98bc16caf30a SHA512 61189ae9edf9e4e3c6795f43909217448921e9a384aec01e90700b29c3453718ea689e130dc42d4082c2b0f9173f769393d94b63fc09e7f356d4cf8f482d4cb4 WHIRLPOOL f5d96dfb32b04b068131b8c20c53a851f106803d1ba0d427bd5f452f1e726343fc8e47982f45ff87ea24d10bc86a3bdc827ea577008d0599444ab9dd345d245f
+MISC ChangeLog-2015 5174 SHA256 97faf62dbc69f607804fe3204629293bd24a994c4ec0aa4fdcb437b5e427d180 SHA512 daa106d334327da2c13cbf74b4c4269e9fe2510ad1d1fcf67b7d9a90c51c972e608ad6434d531babe5af21cf18aa660d5cc779bcbcd6d9544b212e30846caae1 WHIRLPOOL 8a7780dfcf6a58321e586ba240eae5b0706d96244ba351e05be0a62ea87b2599758b68bd459264cb03e4d0502e555e93597ff0811e6b7420d52e8769be466e3c
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild
new file mode 100644
index 000000000000..16b6d29ebdaf
--- /dev/null
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.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="sim4 - Alignment of cDNA and genomic DNA"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/ESIM4-1.0.0.650"
+PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..ead54c91b5f3
--- /dev/null
+++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 924220a..2c45f46 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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 0620938..0304bb8 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
+@@ -63,5 +61,5 @@ 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-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-esim4/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>