diff options
11 files changed, 121 insertions, 21 deletions
diff --git a/eclass/emboss.eclass b/eclass/emboss.eclass index e06e43042..3ba65bbbe 100644 --- a/eclass/emboss.eclass +++ b/eclass/emboss.eclass @@ -1,20 +1,22 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/eclass/emboss.eclass,v 1.3 2012/09/27 16:35:41 axs Exp $ +# $Header: $ # @ECLASS: emboss.eclass # @MAINTAINER: # sci-biology@gentoo.org # jlec@gentoo.org +# ted.tanberry@gmail.com # @AUTHOR: # Original author: Author Olivier Fisette <ofisette@gmail.com> # Next gen author: Justin Lecher <jlec@gentoo.org> +# Next gen author: Ted Tanberry <ted.tanberry@gmail.com> # @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons). # @DESCRIPTION: -# The inheriting ebuild must set EAPI=4 and provide EBO_DESCRIPTION before the inherit line. +# The inheriting ebuild must set at least EAPI=4 and provide EBO_DESCRIPTION before the inherit line. # KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard # ebuild variables can be extended (FOO+=" bar"). -# Default installation of following DOCS="AUTHORS ChangeLog NEWS README" +# Default installation of following DOCS=() # # Example: # @@ -46,7 +48,6 @@ esac if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then AUTOTOOLS_AUTORECONF=1 - AUTOTOOLS_IN_SOURCE_BUILD=1 fi inherit autotools-utils eutils flag-o-matic @@ -85,14 +86,15 @@ if [[ ${PN} == embassy-* ]]; then fi DOCS=() -#DOCS="AUTHORS ChangeLog NEWS README" # @FUNCTION: emboss_src_prepare # @DESCRIPTION: -# Does following things +# Does the following things # -# 1. Patches with "${FILESDIR}"/${PF}.patch, if present -# 2. Runs eautoreconf, unless EBO_EAUTORECONF is set to no +# 1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present, +# and eventually runs eautoreconf in autotools-utils +# 2. Patches with "${WORKDIR}"/${P}-upstream-r1.patch, if ${EBO_PATCH} is set +# 3. Patches with "${FILESDIR}"/${PF}.patch, if present # emboss_src_prepare() { @@ -101,7 +103,7 @@ emboss_src_prepare() { epatch "${FILESDIR}"/${P}_fix-build-system.patch fi - [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch + [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream-r1.patch [[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch autotools-utils_src_prepare diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch index 811e41623..63c67a160 100644 --- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am ++++ CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch index a2e80ad6c..e73eb7b17 100644 --- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -118,3 +118,10 @@ - -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) + -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) endif +--- EMNU-1.05.650/emboss_acd/Makefile.am ++++ EMNU-1.05.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd 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 index 1e70061a7..827907180 100644 --- 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 @@ -88,4 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif - +--- ESIM4-1.0.0.650/emboss_acd/Makefile.am ++++ ESIM4-1.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd 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 index a3a7cb864..955005d51 100644 --- 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 @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am ++++ IPRSCAN-4.3.1.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch index f9dc2b9db..8b2f0574e 100644 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -102,7 +102,7 @@ -AM_CPPFLAGS = -I../h -I${embprefix}/include \ - -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ - $(NLINCLUDES) -+AM_CPPFLAGS = -I../h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) endif if ISSHARED @@ -113,3 +113,21 @@ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) endif +--- MSE-3.0.0.650/ckit/Makefile.am ++++ MSE-3.0.0.650/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +--- MSE-3.0.0.650/emboss_acd/Makefile.am ++++ MSE-3.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch index c4b2ffdb2..e0efb74bd 100644 --- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -78,7 +78,7 @@ - -I${embprefix}/include/eplplot \ - $(NLINCLUDES) \ - -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I../include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) endif if ISSHARED @@ -89,3 +89,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am ++++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch index 03da2af5a..7ddda05cb 100644 --- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- TOPO-2.0.650/emboss_acd/Makefile.am ++++ TOPO-2.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch index 71071882c..c9ece6912 100644 --- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -77,7 +77,7 @@ -AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ - $(NLINCLUDES) \ - -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I../H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) endif if ISSHARED diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index df13d6994..ad7f1e5e8 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,5 +1,4 @@ DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d SHA512 16f69feb693c36855733bf443e763c41de515324f87ac8c8bbad7d389b408ae0226bece39d7b6037fb279a6a140bb4137c0a7f553da0b3b8630a17bbe9e10e44 WHIRLPOOL 52eb01b1cd825ae978a1df3b7f4214c8c91f677639a67e0a5d0783daf63396a48edec206bcab0a0d21deb1acae56920f07329d67c0a0be6d4026859c2acdcb84 -DIST EMBOSS-6.5.7.tar.gz 99290173 SHA256 18b8d5d3eeb18fdee97f799f5b1fb4c10a4a5ed5b97d1f85f42110f64cfa556f SHA512 6a865e6a879a0449334fb8b400925e67a2b043165d561c56c8e5f7032263267cd2e1efa8fcc98851fac1e04f6c821672237cfa797e3a7fa42decae3e5ef9755d WHIRLPOOL df83bda991f9192572656922b2a552fb1556babaa465d09318f2113620737f3474dfbcc969978e6d1511729c4a3f91e86be9d8920d5e00df0ed37379f53dca42 DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe DIST emboss-6.3.1_p4-r2.patch.bz2 9429 SHA256 4ceb304032f9e0d1977afae43055975ff51c186f1707749476da8b0bfb8b3619 SHA512 91ba840adba573e3790d8291e0babc3f4b54f70eecbfbeaa888f12f8659cd6071773046226bbad6d18426207a9af16b3cce8c27a182028fccf642295786e234b WHIRLPOOL 1836ba8b4998beaa3e8f5afab3d7454eed072c4562fa3e1153df37ca8d9321f94bc3785ec535cd183bdc13dca25dd7dcfc7f5b2f173b88917fa879e6e9a61c1d DIST emboss-6.3.1_p4-upstream.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c SHA512 4653dc754df1ea8e7123b67749db4e25d5b0125f41ceee368c724dc46bc9f0fa32a16bce4c24b9264c04c7ce2a3b527b0c7f7179e962c7c2aff2d5c7256c9c7e WHIRLPOOL cea18119bcee441a0f1169b0fbc027a5d3657f4cb977d02700ef1caf78308272de4b08f7f0d496b75d1179e16077e3352c9b66ca032714e5b8b2bbd470440f86 diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch index 39e3cec8b..c831c3ba7 100644 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -1,12 +1,13 @@ --- EMBOSS-6.6.0/ajax/acd/Makefile.am +++ EMBOSS-6.6.0/ajax/acd/Makefile.am -@@ -3,16 +3,19 @@ +@@ -3,16 +3,20 @@ lib_LTLIBRARIES = libacd.la libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) +libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre @@ -24,7 +25,7 @@ libacd_la_LDFLAGS = -version-info 6:5:0 --- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am +++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am -@@ -3,14 +3,15 @@ +@@ -3,14 +3,16 @@ lib_LTLIBRARIES = libajaxdb.la libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) @@ -32,6 +33,7 @@ libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl -libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -94,7 +96,7 @@ +libensembl_la_LIBADD = ../core/libajax.la -libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libensembl_la_CPPFLAGS = ++libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -114,7 +116,7 @@ +libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) -libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajaxg_la_CPPFLAGS = ++libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -246,8 +248,11 @@ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL --- EMBOSS-6.6.0/emboss/Makefile.am +++ EMBOSS-6.6.0/emboss/Makefile.am -@@ -30,13 +30,15 @@ +@@ -28,15 +28,18 @@ + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre @@ -264,7 +269,7 @@ AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) AM_CPPFLAGS += $(JAVA_CPPFLAGS) -@@ -49,9 +51,11 @@ +@@ -49,9 +52,11 @@ if !ESYSTEMLIBS LDADD += ../ajax/zlib/libezlib.la LDADD += ../ajax/expat/libeexpat.la @@ -277,6 +282,41 @@ LDADD += $(XLIB) #if PURIFY +--- EMBOSS-6.6.0/jemboss/lib/Makefile.am ++++ EMBOSS-6.6.0/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ + jalviewApplet.jar \ + jemboss.jar + +-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java ++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java + if JAVA_BUILD + $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; + endif +--- EMBOSS-6.6.0/m4/idxdbs.m4 ++++ EMBOSS-6.6.0/m4/idxdbs.m4 +@@ -1,17 +1,8 @@ + AC_DEFUN([CHECK_IDXDBS], + [ +-AC_MSG_CHECKING(for EMBOSS pre-indexed databases) ++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) + +- +-if test -f ./emboss/index/edam.xac; then +-AC_MSG_RESULT(yes) +-else +-AC_MSG_RESULT(no) +-echo "" +-echo "Pre-indexed edam, taxon + drcat databases not found." +-echo "Please download them from within this directory using:" +-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." +-echo "and then repeat the configure step." +-exit 1 +-fi ++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], ++ [], ++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) + ]) --- EMBOSS-6.6.0/Makefile.am +++ EMBOSS-6.6.0/Makefile.am @@ -12,8 +12,11 @@ @@ -315,7 +355,7 @@ -libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot -libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libnucleus_la_CPPFLAGS = ++libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot +libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |