diff options
Diffstat (limited to 'sci-biology/embassy-structure')
5 files changed, 136 insertions, 0 deletions
diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest new file mode 100644 index 000000000000..7cd125ec2b29 --- /dev/null +++ b/sci-biology/embassy-structure/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 +DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild new file mode 100644 index 000000000000..64b653083ff2 --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein structure add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild new file mode 100644 index 000000000000..b6fcd9770e3b --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein structure add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..bdd9e37714e4 --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_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 ee482ef..e4af4b1 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 81ade5d..2ed0d14 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 +@@ -66,5 +64,5 @@ 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-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-structure/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> |