From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/embassy-clustalomega/Manifest | 6 ++ .../embassy-clustalomega-1.1.0.660.ebuild | 17 ++++ ...bassy-clustalomega-1.1.0_fix-build-system.patch | 100 +++++++++++++++++++++ sci-biology/embassy-clustalomega/metadata.xml | 11 +++ 4 files changed, 134 insertions(+) create mode 100644 sci-biology/embassy-clustalomega/Manifest create mode 100644 sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild create mode 100644 sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch create mode 100644 sci-biology/embassy-clustalomega/metadata.xml (limited to 'sci-biology/embassy-clustalomega') diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest new file mode 100644 index 000000000000..fd6bbeeca444 --- /dev/null +++ b/sci-biology/embassy-clustalomega/Manifest @@ -0,0 +1,6 @@ +AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2860 SHA256 21b6a87a19f37745f76fe9c45837d9a5bab6420dafcb9f50aa3899b88b3cd322 SHA512 6b1c8a2915c9c48ec203bc131461b9acecc3948da79f36941e2fd97a22bf044a35ee717e0be0b13f46d8a6f81148c29faa1e048ed4066cf768dbc705141a772d WHIRLPOOL 00b3a809502d22dfe01a3f5b12db5a62914753b81aaa4d4450c9506a1afcef65c9fa58706da6ca367de077395226aeb5ecb341cc5cb448aa0373a00569c9a778 +DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54 +EBUILD embassy-clustalomega-1.1.0.660.ebuild 384 SHA256 65cae24f4b0267a64896197967e01222c4f70fa67e8907ae566625e4759ae170 SHA512 8504bb9294da8a76c23114476fc16a011c45380b5f0f243bcf5a3bc68db6fd71fb7156f450ee14f78ec7825f8ecd46f4b0a7d0764c3dfd7ba1a2939026b123a4 WHIRLPOOL 7775f060bc5590ab9ac9cd99f734b445ca5cef7e9c2b4862ac50b59954884b91c3d8a6b5ba0a287dcad4c8f31fbc331b317e85b6ba876da46fdb87a27f22ba54 +MISC ChangeLog 3469 SHA256 4c77683d03e44a19a3a917d792b3fbf57524d874cc0e9c39f67e14c1db309dca SHA512 9b11c405c970db09f55c466ac67b7961062a05ef3d3e3b85aed5b865eb4bcc8834a782ba0d7b48a753da980ba21519e3c3d980915a379951fd2d53ce31bb8a09 WHIRLPOOL 8a6734e22cfc7aca3ff914962cbb001212e1bf1b9676831838d3793f332f4813d3446e0c889e95a6979186400a921e8862a26ea0925a959ee2feb9736a031bdc +MISC ChangeLog-2015 799 SHA256 b9f70f99fb963c9ccf78c43e36ac262753b16438a4b1fb7589d83c5796c010fc SHA512 2bbe112471e0e8042f170d73ac947b0d202cbbc86cefb596c97046bd1fd0319d15f24c17b99a6f69f8e1c346d44fa71ce039e0aee5e6829a8dc9b5c66e767ca4 WHIRLPOOL 99fe0031d3a5b19e5dfc757bb06764a705f063d0a71461cd735b04e95680b40ea9bc8a85f24b48fce2feb0228b96e3980a6119c3831ccf02c1f28a9942d17871 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild new file mode 100644 index 000000000000..2d2a2c62632c --- /dev/null +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND="sci-biology/clustal-omega" + +S="${WORKDIR}/CLUSTALOMEGA-1.1.0" +PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch ) diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch new file mode 100644 index 000000000000..5525d79b525f --- /dev/null +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f12ed19..b143922 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${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${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9135679..c201149 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ 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-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-clustalomega/metadata.xml @@ -0,0 +1,11 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + emboss + + -- cgit v1.2.3