reinit the tree, so we can have metadata

4 files changed, 133 insertions, 0 deletions

diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest
new file mode 100644
index 000000000000..330ea4156ac7
--- /dev/null
+++ b/sci-biology/embassy-domalign/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-domalign-0.1.650_fix-build-system.patch 2908 SHA256 3c4b3c8187942d52b5605f83cb2430cebb050fb7d6180e2784a041a4fe332d48 SHA512 5cd02b39812adc44d9b877cca8902b6a66e79c90975b50233a4f8f84392026ffad25d57665e68e5db533f28935f444b4dc75b7120bafd910e415b75737686ad2 WHIRLPOOL 0a7ddde136f33cb2618957ddfc5f7d7d62f1352e4902b700d1b22c636b0424bdbca28fb6946d97095d75ba5ce61b21b93647c10920ebe8e4539fba5751efca32
+DIST embassy-domalign-0.1.660.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37
+EBUILD embassy-domalign-0.1.660.ebuild 343 SHA256 af35754f603a88b67066c06f5d740c70558110c4a2d8e46eea840243c11880bf SHA512 bdc0f0bf6a006d2091f98c3a3258e402b522a743866db74324333c5ec9d14df181561b0beb75baa6aaec130636e1e866184e5c4ed414ceb4e8365e13801df84c WHIRLPOOL 99c14523285090460bb9a0f5a0cc5a2486ea34588ec8109844427a868fa66eaf755b6ba8debf619aca90af867115025573330bcf52fd6af79b3dc03956e8417e
+MISC ChangeLog 3713 SHA256 de038347386131ea00279d8e2ff4296cdc7584894e5314125f9836f396c11730 SHA512 9294affdf27cf379fa512089b072d3bd8ee3b26d96e7d2f8f53138a5f5a101bf7ab22f2f9cbb311bd8ff2163312f7c996f5612b04e86810a0e65b738dc569519 WHIRLPOOL 9a463e64b8885abef98b97691b8a9b1164d2e164676bf0611e310129de59f6c07ff8d9292fc925bc156e6a1de55548a6d9afd6f53b6669e50ce131abdf201fec
+MISC ChangeLog-2015 3920 SHA256 2c6a86ba92e5d72702153e3133653d4b169c16f3fcbe1bbc53407f2e47f94567 SHA512 d72ddff0bf2c5cd0076c6814bbbe724bcd86e373faec3b8484226049b29e4477b6fd2256aac247a9828c7f88633a16d9c40da799c80e3d306f7595353581a373 WHIRLPOOL 03a28fea0444fc3c68b3dc37f94c98465d4b96a34e6bd7712ee32bf6b3e9a309af5a69749fe1cc77578814c39f94877de01e50d7ca6a2c14fb6e069858c53285
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild
new file mode 100644
index 000000000000..a897dba4b060
--- /dev/null
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.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="Protein domain alignment add-on package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/DOMALIGN-0.1.650"
+PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..033ddf7b6535
--- /dev/null
+++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
@@ -0,0 +1,101 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  7 ++-----
+ 2 files changed, 9 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 693eb4d..dc0fda9 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 8785446..fe85f11 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${embprefix}/include \
+-	-I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	../../../plplot/libeplplot.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-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-domalign/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>