User:Lindenb/Notebook/UMR915/20101124

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waiting for http://www.cell.com/immunity/home ...

Sysadmin

meeting with SC : we need space

Dindel

installing dindel from sources http://www.sanger.ac.uk/resources/software/dindel . Edit the Makefile and set the path to the samtools src then 'make'.

g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o DInDel.o DInDel.cpp
Library.hpp: In member function ‘void Library::calcProb(const std::vector<double, std::allocator<double> >&)’:
Library.hpp:89: warning: converting to ‘int’ from ‘const double’
g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o HapBlock.o HapBlock.cpp
g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o HaplotypeDistribution.o HaplotypeDistribution.cpp
g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o ObservationModelFB.o ObservationModelFB.cpp
Library.hpp: In member function ‘void Library::calcProb(const std::vector<double, std::allocator<double> >&)’:
Library.hpp:89: warning: converting to ‘int’ from ‘const double’
g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o GetCandidates.o GetCandidates.cpp
Library.hpp: In member function ‘void Library::calcProb(const std::vector<double, std::allocator<double> >&)’:
Library.hpp:89: warning: converting to ‘int’ from ‘const double’
g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o Faster.o Faster.cpp
Library.hpp: In member function ‘void Library::calcProb(const std::vector<double, std::allocator<double> >&)’:
Library.hpp:89: warning: converting to ‘int’ from ‘const double’
g++ -o dindel -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./  -Wno-deprecated  -O3   DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o   -L/usr/local/package/samtools-0.1.10  -lbam -lz -lboost_program_options -static  
/usr/local/package/samtools-0.1.10/libbam.a(knetfile.o): In function `socket_connect':
/home/lindenb/samtools-0.1.10/knetfile.c:99: warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking