Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv23474
Added Files:
simcoal.info simcoal.patch
Log Message:
new pkg simcoal 1.0 from requests
https://sourceforge.net/p/fink/package-requests/1017/
--- NEW FILE: simcoal.patch ---
diff -ruN simcoal-orig/Makefile simcoal/Makefile
--- simcoal-orig/Makefile 2001-12-10 09:54:28.000000000 -0500
+++ simcoal/Makefile 2013-09-15 17:45:46.000000000 -0400
@@ -1,8 +1,8 @@
-CC=g++ -O
+CC=g++ -O3
SOURCES=$(shell ls *.cpp)
OBJECTS=$(shell for file in $(SOURCES);\
- do echo -n $$file | sed -e "s/\(.*\)\.cpp/\1\.o/"; echo -n "
";\
+ do echo $$file | sed -e "s/\(.*\)\.cpp/\1\.o/"; echo " ";\
done)
PRGNAME=simcoal
diff -ruN simcoal-orig/deme.cpp simcoal/deme.cpp
--- simcoal-orig/deme.cpp 2004-06-08 10:40:34.000000000 -0400
+++ simcoal/deme.cpp 2013-09-15 17:45:59.000000000 -0400
@@ -686,7 +686,7 @@
return 0;
}
}
- else MinCoalTimes->set_elems(MAXLONG);
+ else MinCoalTimes->set_elems(LONG_MAX);
//Compute total coalescent times within and among demes
root.compute_total_coal_times_among_demes(*this,*CoalTimes, *PairDiff,
*MinCoalTimes);
diff -ruN simcoal-orig/migrmat.h simcoal/migrmat.h
--- simcoal-orig/migrmat.h 1999-09-16 17:54:56.000000000 -0400
+++ simcoal/migrmat.h 2013-09-15 17:46:45.000000000 -0400
@@ -3,7 +3,11 @@
#include "cstring.h"
#include <fstream.h>
-#include <values.h>
+#if defined(WIN32) || (defined(__APPLE__) && defined(__MACH__))
+# include <float.h>
+#else
+# include <values.h>
+#endif
#include <iomanip.h>
#include <float.h>
#include <math.h>
--- NEW FILE: simcoal.info ---
Package: simcoal
Version: 1.0
Revision: 1
Description: Simulate coalescence of populations
License: Restrictive/Distributable
### Free to update, modify, and take over
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
BuildDepends: <<
dos2unix
<<
Source:
http://cmpg.unibe.ch/software/simcoal/Distributed%%20files/source/simcoal_linux.zip
NoSourceDirectory: true
Source-MD5: 16036158ae35d451c312612baf56678e
Source-Checksum: SHA1(c67af257321196c2fed3cca1ec25eb18c135b4da)
PatchFile: %n.patch
PatchFile-MD5: f3b1f9ffff549817c144fabb31fffbca
PatchScript: <<
dos2unix *.cpp *.h Makefile
mac2unix public*
%{default_script}
<<
UseMaxBuildJobs: false
GCC: 4.0
CompileScript: <<
make
head -n 10 coalmain.cpp > LICENSE
<<
InstallScript: <<
install -d -m 0755 %i/bin
install -m 0755 simcoal %i/bin
<<
DocFiles: LICENSE
Homepage: http://cmpg.unibe.ch/software/simcoal/
DescDetail: <<
SIMCOAL (ver 1.0) is a computer program for the simulation of molecular
genetic diversity in an arbitrary number of haploid populations examined
for a set of fully linked loci. It is based on the retrospective
coalescent approach initially described by Kingman (1982b; 1982a), and
clearly exposed in a series of other papers (Ewens 1990; Hudson 1990;
Donnelly and Tavare 1995). The coalescent backward approach does not
simulate the genetic history of the whole population, like in conventional
forward simulations, but rather reconstructs the gene genealogy
(coalescent history) of samples of genes drawn from different demes in a
population. For neutral genes, this coalescent process essentially depends
on the history and on the demography of the population, and is independent
from the mutational process. In our program, we simulate mutations
starting from the most recent common ancestor (MRCA) of all genes in the
sample, and add them independently on all branches of the genealogy
assuming a uniform and constant Poisson process. Using this two-step
(coalescent-mutation) approach, many replicates of haploid samples of DNA
sequences, RFLP, or microsatellite data can be simulated very quickly. The
analysis of a large number of simulated samples allows one to obtain the
empirical distribution of practically any statistic that can be derived
from genetic data, including statistics for which no analytical derivation
is available (Hudson 1993). Typical applications of our program include
the study of the effect of complex demographies on the pattern of genetic
diversity within and between populations, like in the case of bottlenecks,
complex cases of admixture, or metapopulation systems. While our program
generates haploid samples of genes or haplotypes, diploid data can be
generated under the hypothesis of Hardy-Weinberg equilibrium by taking
random pairs of haplotypes to form diploid genotypes.
Excoffier L, Novembre J and Schneider S (2000) SIMCOAL: a general
coalescent program for simulation of molecular data in interconnected
populations with arbitrary demography. J. Hered., 91, 506-509.
<<
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