[96041] trunk/dports/science

[jmr at macports.org]

Revision: 96041
          https://trac.macports.org/changeset/96041
Author:   jmr at macports.org
Date:     2012-07-30 01:40:14 -0700 (Mon, 30 Jul 2012)
Log Message:
-----------
New port: exonerate (#33346)

Added Paths:
-----------
    trunk/dports/science/exonerate/
    trunk/dports/science/exonerate/Portfile
    trunk/dports/science/exonerate/files/
    trunk/dports/science/exonerate/files/patch-src-program-Makefile.am.diff
    trunk/dports/science/exonerate/files/patch-src-program-Makefile.in.diff

Added: trunk/dports/science/exonerate/Portfile
===================================================================
--- trunk/dports/science/exonerate/Portfile	                        (rev 0)
+++ trunk/dports/science/exonerate/Portfile	2012-07-30 08:40:14 UTC (rev 96041)
@@ -0,0 +1,36 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+
+name                exonerate
+version             2.2.0
+categories          science
+platforms           darwin
+maintainers         sanger.ac.uk:mg13
+license             GPL-3
+
+description         A generic tool for sequence alignment
+
+long_description    Exonerate is a generic tool for pairwise sequence \
+                    comparison. It allows you to align sequences using \
+                    many alignment models, using either exhaustive \
+                    dynamic programming, or a variety of heuristics.
+
+homepage            http://www.ebi.ac.uk/~guy/exonerate/
+master_sites        ${homepage}
+
+checksums           rmd160 3441a642c75af8b5676253b020f47650360ba320 \
+                    sha256 0ea2720b1388fa329f889522f43029b416ae311f57b229129a65e779616fe5ff
+
+patchfiles          patch-src-program-Makefile.am.diff \
+                    patch-src-program-Makefile.in.diff
+
+depends_lib         port:glib2
+depends_build       port:pkgconfig
+
+# sadly the code generation & compilation is unreliable unless...
+
+use_parallel_build  no
+
+# EOF


Property changes on: trunk/dports/science/exonerate/Portfile
___________________________________________________________________
Added: svn:keywords
   + Id
Added: svn:eol-style
   + native

Added: trunk/dports/science/exonerate/files/patch-src-program-Makefile.am.diff
===================================================================
--- trunk/dports/science/exonerate/files/patch-src-program-Makefile.am.diff	                        (rev 0)
+++ trunk/dports/science/exonerate/files/patch-src-program-Makefile.am.diff	2012-07-30 08:40:14 UTC (rev 96041)
@@ -0,0 +1,15 @@
+diff -ur ../exonerate-2.2.0.orig/src/program/Makefile.am ./src/program/Makefile.am
+--- ../exonerate-2.2.0.orig/src/program/Makefile.am	2008-02-08 17:35:36.000000000 +0000
++++ ./src/program/Makefile.am	2012-02-23 16:31:14.000000000 +0000
+@@ -67,9 +67,9 @@
+ BUILT_SOURCES = c4_model_archive.a
+ BOOTSTRAPPER = $(top_srcdir)/src/model/bootstrapper
+ c4_model_archive.h: $(BOOTSTRAPPER)
+-	$(BOOTSTRAPPER) --compiled no
++	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
+ c4_model_archive.a: $(BOOTSTRAPPER)
+-	$(BOOTSTRAPPER) --compiled no
++	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
+ 
+ # Special viterbi.o and scheduler.o for compiled model linking
+ viterbi.o: $(top_srcdir)/src/c4/viterbi.c

Added: trunk/dports/science/exonerate/files/patch-src-program-Makefile.in.diff
===================================================================
--- trunk/dports/science/exonerate/files/patch-src-program-Makefile.in.diff	                        (rev 0)
+++ trunk/dports/science/exonerate/files/patch-src-program-Makefile.in.diff	2012-07-30 08:40:14 UTC (rev 96041)
@@ -0,0 +1,14 @@
+--- ../exonerate-2.2.0.orig/src/program/Makefile.in	2008-10-17 11:04:45.000000000 +0100
++++ ./src/program/Makefile.in	2012-02-24 11:53:57.000000000 +0000
+@@ -361,9 +361,9 @@
+ mostlyclean distclean maintainer-clean
+ 
+ c4_model_archive.h: $(BOOTSTRAPPER)
+-	$(BOOTSTRAPPER) --compiled no
++	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
+ c4_model_archive.a: $(BOOTSTRAPPER)
+-	$(BOOTSTRAPPER) --compiled no
++	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
+ 
+ # Special viterbi.o and scheduler.o for compiled model linking
+ viterbi.o: $(top_srcdir)/src/c4/viterbi.c
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