User:Lindenb/Notebook/UMR915/20101124: Difference between revisions
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(New page: {{PLNB|20101123|20101125}} ==Cover== waiting for http://www.cell.com/immunity/home ... ==Sysadmin== meeting with SC : we need space ==Dindel== installing dindel from sources http://www.san...) |
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/usr/local/package/samtools-0.1.10/libbam.a(knetfile.o): In function `socket_connect': | /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</pre> | /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</pre> | ||
but<pre>[lindenb@srv-clc-02 HAJDU]$ /usr/local/package/dindel-1.01-src/dindel --analysis getCIGARindels --bamFile sampe.sorted.bam --outputFile dindel_output --ref mygene.fa | |||
Error parsing input options. Usage: (...)</pre> | |||
Revision as of 04:06, 24 November 2010
Cover
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
but
[lindenb@srv-clc-02 HAJDU]$ /usr/local/package/dindel-1.01-src/dindel --analysis getCIGARindels --bamFile sampe.sorted.bam --outputFile dindel_output --ref mygene.fa Error parsing input options. Usage: (...)
