help compiling genome assemblers

This is a discussion on help compiling genome assemblers within the C Programming forums, part of the General Programming Boards category; Hi all, I am at my wits end as to where i can get help for this. I'm doing a ...

  1. #1
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    help compiling genome assemblers

    Hi all,

    I am at my wits end as to where i can get help for this. I'm doing a project on genome assemblers, and i cant get any of them to compile or run. they are written in C code ( i believe) and also includes some perl scripts. I am using ubuntu hoary release, and have g++/gcc 3.3 installed, along with the defaults for perl etc. I also installed c shell. I am a newbie at this.

    Anyways if this is the wrong place to find help for this issue, then im sorry!!
    but there is the info:

    Arachne assembler (http://www.broad.mit.edu/wga/) - i cannot compile the .c files in Arachne_src. There is something wrong with Vec.c file. there errors are produced when i type in "make" in the src folder:
    g++ -W -Wall -Wno-unused -g3 -O3 -Wa,-oldas -DMAKE_DATE='"Sat Mar 25 01:27:49 PST 2006"' -DMAKE_OS_RELEASE='"2.6.10-5-386"' -DMAKE_RELEASE='"1.0"' -DNEW_MAKEFILE -ftemplate-depth-25 -I. -Ixerces_include -I/util/include -c Vec.cc
    In file included from /usr/include/c++/3.3/backward/strstream:51,
    from Vec.h:22,
    from Vec.cc:22:
    /usr/include/c++/3.3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <sstream> instead of the deprecated header <strstream.h>. To disable this warning use -Wno-deprecated.
    In file included from Vec.cc:22:
    Vec.h:41: warning: `vec<T>::const_iterator' is implicitly a typename
    Vec.h:41: warning: implicit typename is deprecated, please see the
    documentation for details
    Vec.h:41: warning: `vec<T>::const_iterator' is implicitly a typename
    Vec.h:41: warning: implicit typename is deprecated, please see the
    documentation for details
    Vec.cc: In function `void PrettyPrint(std:stream&, const vec<int>&, int,
    String)':
    Vec.cc:27: error: call of overloaded `log10(const int&)' is ambiguous
    /usr/include/bits/mathcalls.h:113: error: candidates are: double log10(double)
    /usr/include/c++/3.3/cmath:437: error: long double
    std::log10(long double)
    /usr/include/c++/3.3/cmath:429: error: float std::log10(float)
    Vec.cc:35: error: call of overloaded `log10(const int&)' is ambiguous
    /usr/include/bits/mathcalls.h:113: error: candidates are: double log10(double)
    /usr/include/c++/3.3/cmath:437: error: long double
    std::log10(long double)
    /usr/include/c++/3.3/cmath:429: error: float std::log10(float)
    Vec.cc: In function `void PrettyPrint(std:stream&, const vec<longlong>&, int,
    String)':
    Vec.cc:43: error: call of overloaded `log10(const long long int&)' is ambiguous
    /usr/include/bits/mathcalls.h:113: error: candidates are: double log10(double)
    /usr/include/c++/3.3/cmath:437: error: long double
    std::log10(long double)
    /usr/include/c++/3.3/cmath:429: error: float std::log10(float)
    Vec.cc:51: error: call of overloaded `log10(const long long int&)' is ambiguous
    /usr/include/bits/mathcalls.h:113: error: candidates are: double log10(double)
    /usr/include/c++/3.3/cmath:437: error: long double
    std::log10(long double)
    /usr/include/c++/3.3/cmath:429: error: float std::log10(float)
    make: *** [Vec.o] Error 1
    TIGR 2 (http://www.tigr.org/software/assembler/)
    -unable to make any of the source files as well. the errors are as follows:
    cc -O -c ./asmg.c -o ../obj/asmg.o
    In file included from asmg.c:12:
    matrices.h:163:8: warning: extra tokens at end of #endif directive
    In file included from asmg.c:13:
    asmg_global.h:1777:8: warning: extra tokens at end of #endif directive
    Assembler messages:
    FATAL: can't create ../obj/asmg.o: No such file or directory
    make: *** [../obj/asmg.o] Error 1
    Phusion (http://www.sanger.ac.uk/Software/production/phusion/ )
    I was able to compile everything. However I am not sure what they mean by this:
    Also, pm RP is used for a few codes, you need to make changes
    with this respect:

    unshift @INC,"/nfs/team71/psg/zn1/phusion_pipeline/Perl_scripts/";
    But when i run the the sample provided, this is the errors i get:
    sh.phusion: line 8: ../ssahaMates/ssahaMates: cannot execute binary file
    rm: cannot remove `pair.dat': No such file or directory
    sh.phusion: line 12: ../phusion/phusion: cannot execute binary file
    sh.phusion: line 16: ../fmate/fmate: cannot execute binary file
    cat: readname0*: No such file or directory
    sh.phusion: line 18: compress: command not found
    Im really sorry for posting. here.. but.. if u guys can help me figure out how to get it running.. i would really really appreciate it!

  2. #2
    Frequently Quite Prolix dwks's Avatar
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    sh.phusion: line 18: compress: command not found
    compress is a old compression program. You might need to get it before you can decompress this file. I don't know what formats compress used, but I have a suspicion that one of them was .ZOO.
    dwk

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