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. << ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.cvs