[70161] trunk/dports/science
adfernandes at macports.org
adfernandes at macports.org
Fri Jul 30 18:11:18 PDT 2010
Revision: 70161
http://trac.macports.org/changeset/70161
Author: adfernandes at macports.org
Date: 2010-07-30 18:11:15 -0700 (Fri, 30 Jul 2010)
Log Message:
-----------
new port: bali-phy 2.1.0 - Bayesian Alignment and Phylogeny estimation
Added Paths:
-----------
trunk/dports/science/bali-phy/
trunk/dports/science/bali-phy/Portfile
trunk/dports/science/bali-phy/files/
trunk/dports/science/bali-phy/files/configure.patch
trunk/dports/science/bali-phy/files/scripts.patch
trunk/dports/science/bali-phy/files/src-tools-draw-tree.patch
Added: trunk/dports/science/bali-phy/Portfile
===================================================================
--- trunk/dports/science/bali-phy/Portfile (rev 0)
+++ trunk/dports/science/bali-phy/Portfile 2010-07-31 01:11:15 UTC (rev 70161)
@@ -0,0 +1,56 @@
+# $Id$
+
+PortSystem 1.0
+
+name bali-phy
+version 2.1.0
+description Bayesian Alignment and Phylogeny estimation
+long_description BAli-Phy can estimate phylogenetic trees from sequence data when the alignment \
+ is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy \
+ accounts for alignment uncertainty by integrating over all alignments. \
+ BAli-Phy does not rely on a guide tree because the alignment and the tree are \
+ co-estimated. Therefore it can construct phylogeny estimates of widely \
+ divergent sequences without bias toward a guide tree.
+categories science
+platforms darwin
+maintainers adfernandes
+homepage http://www.biomath.ucla.edu/msuchard/bali-phy/
+
+master_sites ${homepage}
+checksums sha1 0fd83d876d2ef1d0f2676c14ad10ff93621a8530
+
+patchfiles configure.patch scripts.patch src-tools-draw-tree.patch
+
+depends_lib port:gsl port:boost port:cairo
+
+configure.args --with-system-boost --enable-cairo
+
+variant no_cairo description {disable drawing routines} {
+ depends_lib-delete port:cairo
+ configure.args-delete --enable-cairo
+ patchfiles-delete src-tools-draw-tree.patch
+}
+
+variant openmpi description {enable OpenMPI parallelization} {
+ depends_lib-append port:openmpi
+ configure.args-append --with-mpi
+}
+
+variant gcc43 conflicts gcc44 gcc45 description {build using macports-gcc-4.3} {
+ depends_lib-append port:gcc43
+ configure.compiler macports-gcc-4.3
+}
+
+variant gcc44 conflicts gcc43 gcc45 description {build using macports-gcc-4.4} {
+ depends_lib-append port:gcc44
+ configure.compiler macports-gcc-4.4
+}
+
+variant gcc45 conflicts gcc43 gcc44 description {build using macports-gcc-4.5} {
+ depends_lib-append port:gcc45
+ configure.compiler macports-gcc-4.5
+}
+
+livecheck.type regex
+livecheck.url ${master_sites}
+livecheck.regex {BAli-Phy (\d+\.\d+\.\d+) released}
Property changes on: trunk/dports/science/bali-phy/Portfile
___________________________________________________________________
Added: svn:keywords
+ Id
Added: svn:eol-style
+ native
Added: trunk/dports/science/bali-phy/files/configure.patch
===================================================================
--- trunk/dports/science/bali-phy/files/configure.patch (rev 0)
+++ trunk/dports/science/bali-phy/files/configure.patch 2010-07-31 01:11:15 UTC (rev 70161)
@@ -0,0 +1,37 @@
+--- configure 2010-07-30 14:20:13.000000000 -0400
++++ configure 2010-07-30 14:20:22.000000000 -0400
+@@ -6299,7 +6299,7 @@
+ $as_echo_n "(cached) " >&6
+ else
+ ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lboost_filesystem${BOOST_SUFFIX} $LIBS"
++LIBS="-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX} $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h. */
+
+@@ -6330,13 +6330,13 @@
+ #define `$as_echo "HAVE_LIBboost_filesystem${BOOST_SUFFIX}" | $as_tr_cpp` 1
+ _ACEOF
+
+- LIBS="-lboost_filesystem${BOOST_SUFFIX} $LIBS"
++ LIBS="-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX} $LIBS"
+
+ else
+- echo "Error: I can't find the boost_filesystem library! (-lboost_filesystem${BOOST_SUFFIX})" ; exit 1
++ echo "Error: I can't find the boost_filesystem library! (-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX})" ; exit 1
+ fi
+
+-boost_libs="-lboost_program_options${BOOST_SUFFIX} -lboost_filesystem${BOOST_SUFFIX}";
++boost_libs="-lboost_program_options${BOOST_SUFFIX} -lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX}";
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking include/compile/link for the BOOST program_options library" >&5
+ $as_echo_n "checking include/compile/link for the BOOST program_options library... " >&6; }
+@@ -6397,7 +6397,7 @@
+ echo " * Not using system BOOST libraries: we'll build our own."
+
+ boost_includes="-isystem \$(top_srcdir)/boost/include"
+- boost_libs="\$(top_builddir)/boost/lib/filesystem/libboost_filesystem.a \$(top_builddir)/boost/lib/program_options/libboost_program_options.a"
++ boost_libs="\$(top_builddir)/boost/lib/filesystem/libboost_filesystem.a \$(top_builddir)/boost/lib/program_options/libboost_system.a \$(top_builddir)/boost/lib/program_options/libboost_program_options.a"
+
+ CXXFLAGS="$boost_includes $CXXFLAGS"
+ LIBS="$boost_libs $LIBS"
Added: trunk/dports/science/bali-phy/files/scripts.patch
===================================================================
--- trunk/dports/science/bali-phy/files/scripts.patch (rev 0)
+++ trunk/dports/science/bali-phy/files/scripts.patch 2010-07-31 01:11:15 UTC (rev 70161)
@@ -0,0 +1,40 @@
+--- scripts/bp-analyze.pl 2010-06-18 16:57:34.000000000 -0400
++++ scripts/bp-analyze.pl 2010-07-30 20:37:50.000000000 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl -w
+
+ # TODO
+
+--- scripts/compare-runs.R 2010-06-18 16:57:34.000000000 -0400
++++ scripts/compare-runs.R 2010-07-30 20:38:22.000000000 -0400
+@@ -1,3 +1,5 @@
++#!/usr/bin/env R CMD BATCH
++
+ # read filename from the command line
+ args = commandArgs(trailingOnly=T)
+ filename = args[1]
+--- scripts/fixedpt-alignment-distances 2010-06-18 16:57:34.000000000 -0400
++++ scripts/fixedpt-alignment-distances 2010-07-30 20:39:19.000000000 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+
+ #
+ # Program calculates the distance between a given (MAP) alignment and all alignments in
+--- scripts/pairwise-alignment-distances 2010-06-18 16:57:34.000000000 -0400
++++ scripts/pairwise-alignment-distances 2010-07-30 20:39:27.000000000 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+
+ #
+ # Program finds the posterior sample alignment that has the minimum average distance to all other samples.
+--- scripts/plot-path-graph.R 2010-06-18 16:57:34.000000000 -0400
++++ scripts/plot-path-graph.R 2010-07-30 20:38:41.000000000 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/R CMD BATCH
++#!/usr/bin/env R CMD BATCH
+
+ Rreverse = function(x) {
+ tmp =c(1:length(x))
Added: trunk/dports/science/bali-phy/files/src-tools-draw-tree.patch
===================================================================
--- trunk/dports/science/bali-phy/files/src-tools-draw-tree.patch (rev 0)
+++ trunk/dports/science/bali-phy/files/src-tools-draw-tree.patch 2010-07-31 01:11:15 UTC (rev 70161)
@@ -0,0 +1,22 @@
+--- src/tools/draw-tree.C 2010-07-30 16:51:37.000000000 -0400
++++ src/tools/draw-tree.C 2010-07-30 20:20:43.000000000 -0400
+@@ -2441,8 +2441,8 @@
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/topological_sort.hpp>
+-#include <boost/graph/kamada_kawai_spring_layout.hpp>
+-#include <boost/graph/fruchterman_reingold.hpp>
++#include "../../boost/include/boost/graph/kamada_kawai_spring_layout.hpp"
++#include "../../boost/include/boost/graph/fruchterman_reingold.hpp"
+
+ using namespace boost;
+
+@@ -2502,7 +2502,7 @@
+ };
+
+
+-#include <boost/graph/random_layout.hpp>
++#include "../../boost/include/boost/graph/random_layout.hpp"
+ #include <boost/random/linear_congruential.hpp>
+
+ graph_layout fruchterman_reingold_layout(graph_layout GL, double width, double height)
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