Update of /cvsroot/fink/experimental/dmacks/finkinfo
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv5530
Added Files:
tree-puzzle.info tree-puzzle.patch
Log Message:
Looks good except for test failures, which might be round-off
someone else pls verify...maybe need different -O level?
--- NEW FILE: tree-puzzle.patch ---
diff -Nurd -x'*~' tree-puzzle-5.2.orig/configure.ac tree-puzzle-5.2/configure.ac
--- tree-puzzle-5.2.orig/configure.ac 2006-06-26 20:05:01.000000000 -0400
+++ tree-puzzle-5.2/configure.ac 2006-06-26 20:23:08.000000000 -0400
@@ -74,23 +74,14 @@
fi
fi ])
-if test "$MPICC" != "" ; then
- AC_PATH_PROG(MPICC0, $MPICC)
+AC_ARG_ENABLE(mpi, [ --enable-mpi Enable parallel support (default=no)],
[enable_mpi=$enableval], [enable_mpi=no])
+if test "$enable_mpi" = "yes"; then
+ AC_PATH_PROG(MPICC0, mpicc)
+else
+ AC_PATH_PROG(MPICC0, cc)
fi
-AC_PATH_PROG(MPICC1, mpcc)
-AC_PATH_PROG(MPICC2, hcc)
-AC_PATH_PROG(MPICC3, mpicc)
-AC_PATH_PROG(MPICC4, mpicc_lam)
-AC_PATH_PROG(MPICC5, mpicc_mpich)
-AC_PATH_PROG(MPICC6, cc)
AC_TEST_MPICC($MPICC0)
-AC_TEST_MPICC($MPICC1)
-AC_TEST_MPICC($MPICC2)
-AC_TEST_MPICC($MPICC3)
-AC_TEST_MPICC($MPICC4)
-AC_TEST_MPICC($MPICC5)
-AC_TEST_MPICC($MPICC6)
ac_cv_prog_MPICC=$MPICC
--- NEW FILE: tree-puzzle.info ---
Info2: <<
Package: tree-puzzle%type_pkg[-mpi]
Version: 5.2
Revision: 1
Type: -mpi (boolean)
Source: http://www.tree-puzzle.de/%{ni}-%v.tar.gz
Source-MD5: 20fa9606434ddc789670e681d98fe68f
Patch: %{ni}.patch
BuildDepends: automake1.9, (%type_pkg[-mpi]) lammpi-dev, (%type_pkg[-mpi])
lammpi
Depends: (%type_pkg[-mpi]) lammpi-shlibs
ConfigureParams: (%type_pkg[-mpi]) --enable-mpi
CompileScript: <<
autoreconf -f -i
./configure %c
make
make check
<<
InstallScript: make install DESTDIR=%d
DocFiles: AUTHORS COPYING ChangeLog README doc/tree-puzzle.pdf
DescPackaging: <<
Overhauled configure script to make mpi support controlled by a flag.
<<
Description: Maximum likelihood analysis for sequences
DescDetail: <<
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
from molecular sequence data by maximum likelihood. It implements a
fast tree search algorithm, quartet puzzling, that allows analysis of
large data sets and automatically assigns estimations of support to
each internal branch. TREEPUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified
trees. Branch lengths can be calculated with and without the
molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood
mapping, a method to investigate the support of a hypothesized
internal branch without computing an overall tree and to visualize the
phylogenetic content of a sequence alignment. TREE-PUZZLE also
conducts a number of statistical tests on the data set (chi-square
test for homogeneity of base composition, likelihood ratio to test the
clock hypothesis, one and two-sided Kishino-Hasegawa test,
Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of
substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino
acids, and F81 for two-state data. Rate heterogeneity is modeled by a
discrete Gamma distribution and by allowing invariable sites. The
corresponding parameters (except for GTR) can be inferred from the
data set.
<<
License: LGPL
Maintainer: Daniel Macks <[EMAIL PROTECTED]>
Homepage: http://www.tree-puzzle.de/
<<
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