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Tophat install problem

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  • Tophat install problem

    Having a problem installing TopHat v.1.1.x onto a PC using cygwin. I have Bowtie 0.12.7 and Samtools 0.1.9 properly (as far as I can tell) installed and configured. Running ./configure for tophat I get :


    # ./configure --prefix=/path/to/install/directory/
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking build system type... i686-pc-cygwin
    checking host system type... i686-pc-cygwin
    checking for gcc... gcc
    checking for C compiler default output file name... a.exe
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables... .exe
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ANSI C... none needed
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking for g++... g++
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ accepts -g... yes
    checking dependency style of g++... gcc3
    checking for gawk... (cached) gawk
    checking for a BSD-compatible install... /usr/bin/install -c
    checking for ranlib... ranlib
    checking for ar... ar
    checking for perl... /usr/bin/perl
    checking for bash... /usr/bin/bash
    checking for a Python interpreter with version >= 2.4... python
    checking for python... /usr/bin/python
    checking for python version... 2.6
    checking for python platform... cygwin
    checking for python script directory... ${prefix}/lib/python2.6/site-packages
    checking for python extension module directory... ${exec_prefix}/lib/python2.6/s
    ite-packages
    checking for bamlib... yes
    checking how to run the C preprocessor... gcc -E
    checking for egrep... grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking if zlib is wanted... yes
    checking for inflateEnd in -lz... yes
    checking zlib.h usability... yes
    checking zlib.h presence... yes
    checking for zlib.h... yes
    checking for inflateEnd in -lz... (cached) yes
    checking zlib in /usr... ok
    checking how to run the C++ preprocessor... g++ -E
    checking for stdlib.h... (cached) yes
    checking for string.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for ANSI C header files... (cached) yes
    checking for stdlib.h... (cached) yes
    checking for string.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for stdbool.h that conforms to C99... yes
    checking for _Bool... no
    checking for an ANSI C-conforming const... yes
    checking for special C compiler options needed for large files... no
    checking for _FILE_OFFSET_BITS value needed for large files... no
    checking for _LARGE_FILES value needed for large files... no
    checking for gzread in -lz... yes
    checking for stdlib.h... (cached) yes
    checking for GNU libc compatible malloc... yes
    checking for memset... yes
    checking for strdup... yes
    checking for strrchr... yes
    checking for strtol... yes
    checking for strsep... yes
    checking if gcc accepts -m64... yes
    checking how to create a pax tar archive... gnutar
    checking dependency style of gcc... (cached) gcc3
    checking dependency style of g++... (cached) gcc3
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating src/Makefile
    config.status: creating config.h
    config.status: config.h is unchanged
    config.status: executing depfiles commands

    -- tophat 1.1.0 Configuration Results --
    C compiler: gcc -Wall -m64 -O3 -DNDEBUG
    C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
    GCC version: gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.1
    25)
    Host System type: i686-pc-cygwin
    Install prefix: /path/to/install/directory/
    Install eprefix: ${prefix}

    See config.h for further configuration information.
    Email <[email protected]> with questions and bug reports.

    Running make I get:

    # make
    make all-recursive
    make[1]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
    Making all in src
    make[2]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src
    '
    if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -Wall -m64 -O3 -DNDEBUG -I
    /usr/local/include -I./SeqAn-1.1 -Wall -m64 -O3 -DNDEBUG -I/usr/local/include -
    MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
    then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.T
    po"; exit 1; fi
    reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
    In file included from reads.cpp:20:
    bwt_map.h: In constructor `RefSequenceTable::RefSequenceTable(const std::string&
    , bool, bool)':
    bwt_map.h:332: warning: comparison between signed and unsigned integer expressio
    ns
    make[2]: *** [reads.o] Error 1
    make[2]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src'

    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
    make: *** [all] Error 2

    Any suggestions? I'm relatively new to all this computer stuff, so dumbed down answers would be appreciated. Thanks.

  • #2
    Code:
    checking if gcc accepts -m64... yes
    [...]
    -- tophat 1.1.0 Configuration Results --
    C compiler: gcc -Wall -m64 -O3 -DNDEBUG
    C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
    [...]
    reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
    You are suffering from the same problem that the person in this thread was: http://seqanswers.com/forums/showpos...99&postcount=4

    I thought that Cole had since fixed this configure bug, but apparently not. In tophat 1.1.4 (it looks like you're using 1.1.3 or so), you should change CFLAGS to CXXFLAGS on line 6670 of tophat-1.1.4/configure and rerun configure. This will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above, and you'll be able to proceed to build a 32-bit version.

    (If you were on a Mac, you would want to make the same change on lines 6632 and 6650 too.)

    Comment


    • #3
      Great. Thanks jmarshall. I had seen that previous thread, but the configure file I had was different and didn't know if there was a specific instance of CFLAGS that needed to be changed. It seems to have installed properly now.

      Next issue! When running the test data I get the following error:

      # tophat -r 20 test_ref reads_1.fq reads_2.fq

      [Wed Nov 17 14:09:55 2010] Beginning TopHat run (v1.1.4)
      -----------------------------------------------
      [Wed Nov 17 14:09:55 2010] Preparing output location ./tophat_out/
      [Wed Nov 17 14:09:55 2010] Checking for Bowtie index files
      [Wed Nov 17 14:09:55 2010] Checking for reference FASTA file
      [Wed Nov 17 14:09:55 2010] Checking for Bowtie
      Traceback (most recent call last):
      File "/path/to/install/directory/bin/tophat", line 2223, in <module>
      sys.exit(main())
      File "/path/to/install/directory/bin/tophat", line 2135, in main
      check_bowtie()
      File "/path/to/install/directory/bin/tophat", line 833, in check_bowtie
      bowtie_version = get_bowtie_version()
      File "/path/to/install/directory/bin/tophat", line 738, in get_bowtie_version
      if len(bowtie_version) == 3:
      TypeError: object of type 'NoneType' has no len()
      I already have $PATH pointed to the bowtie folder as some previous threads here suggest, and am at a loss as to what else to do.

      .....
      To anyone having these types of problems on a PC using Cygwin, and are novices like myself...try getting on a Mac. The installation and running of these programs goes a lot smoother!!!
      Last edited by jfofly; 12-07-2010, 01:02 PM. Reason: Problem Solved...Use a Mac!

      Comment


      • #4
        tophat 1.2.0 make error

        Hi,
        I'm having a similar but different issue. I'm getting a make error installing Tophat 1.2.0 on 32-bit linux (ubuntu 10.04).
        Configure is fine but the make returns:


        [email protected]:~/Downloads/tophat-1.2.0$ make
        make all-recursive
        make[1]: Entering directory `/home/sean/Downloads/tophat-1.2.0'
        Making all in src
        make[2]: Entering directory `/home/sean/Downloads/tophat-1.2.0/src'
        if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/local/include -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -I./SeqAn-1.1 -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -MT juncs_db.o -MD -MP -MF ".deps/juncs_db.Tpo" -c -o juncs_db.o juncs_db.cpp; \
        then mv -f ".deps/juncs_db.Tpo" ".deps/juncs_db.Po"; else rm -f ".deps/juncs_db.Tpo"; exit 1; fi
        In file included from juncs_db.cpp:32:
        bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
        bwt_map.h:680: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
        In file included from ./SeqAn-1.1/seqan/sequence.h:51,
        from juncs_db.cpp:26:
        ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::clear(seqan::String<TValue, TSpec>&) [with TValue = char, TSpec = seqan::CStyle]’:
        ./SeqAn-1.1/seqan/sequence/string_cstyle.h:492: instantiated from ‘static void seqan::_Assign_String_2_StringArray<TExpand, true>::assign_(seqan::String<char, seqan::CStyle>&, seqan::String<char, TSourceSpec>&) [with TSourceSpec = seqan::Alloc<void>, TExpand = const seqan::Tag<seqan::TagExact_>]’
        ./SeqAn-1.1/seqan/sequence/string_cstyle.h:522: instantiated from ‘void seqan::assign(seqan::String<TTargetValue, seqan::CStyle>&, seqan::String<TValue, TSpec>&, seqan::Tag<TTag>) [with TValue = char, TSourceSpec = seqan::Alloc<void>, TExpand = seqan::TagExact_]’
        ./SeqAn-1.1/seqan/sequence/string_base.h:737: instantiated from ‘void seqan::assign(seqan::String<TValue, TSpec>&, TSource&) [with TTargetValue = char, TTargetSpec = seqan::CStyle, TSource = seqan::String<char, seqan::Alloc<void> >]’
        ./SeqAn-1.1/seqan/sequence/string_cstyle.h:97: instantiated from ‘seqan::String<TTargetValue, seqan::CStyle>::String(TString&) [with TString = seqan::String<char, seqan::Alloc<void> >, TValue = char]’
        ./SeqAn-1.1/seqan/sequence/string_cstyle.h:798: instantiated from ‘typename seqan::Value<T, 0>::Type* seqan::toCString(T&) [with T = seqan::String<char, seqan::Alloc<void> >]’
        juncs_db.cpp:327: instantiated from here
        ./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String<char, seqan::CStyle>&, int)’
        make[2]: *** [juncs_db.o] Error 1
        make[2]: Leaving directory `/home/sean/Downloads/tophat-1.2.0/src'
        make[1]: *** [all-recursive] Error 1
        make[1]: Leaving directory `/home/sean/Downloads/tophat-1.2.0'
        make: *** [all] Error 2

        Comment


        • #5
          Originally posted by jmarshall View Post
          Code:
          checking if gcc accepts -m64... yes
          [...]
          -- tophat 1.1.0 Configuration Results --
          C compiler: gcc -Wall -m64 -O3 -DNDEBUG
          C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
          [...]
          reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
          You are suffering from the same problem that the person in this thread was: http://seqanswers.com/forums/showpos...99&postcount=4

          I thought that Cole had since fixed this configure bug, but apparently not. In tophat 1.1.4 (it looks like you're using 1.1.3 or so), you should change CFLAGS to CXXFLAGS on line 6670 of tophat-1.1.4/configure and rerun configure. This will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above, and you'll be able to proceed to build a 32-bit version.

          (If you were on a Mac, you would want to make the same change on lines 6632 and 6650 too.)
          Hi, I installed the newest tophat 2.0.9. And I have similar problem in configure.


          -- tophat 2.0.9 Configuration Results --
          C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/twotwo/software/boost_154/include -I/home/twotwo/software/samtools-0.1.19/samtools0119/include -I./SeqAn-1.3
          Linker flags:
          GCC version: gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
          Host System type: x86_64-unknown-linux-gnu
          Install prefix: /home/twotwo/software/tophat209
          Install eprefix: ${prefix}

          See config.h for further configuration information.
          Email <[email protected]> with questions and bug reports.


          when I ran make, I got the following error:
          thread.cpp.text+0x1c84): undefined reference to `clock_gettime'
          thread.cpp.text+0x1cfa): undefined reference to `clock_gettime'
          thread.cpp.text+0x1d65): undefined reference to `clock_gettime'
          thread.cpp.text+0x1dd0): undefined reference to `clock_gettime'
          thread.cpp.text+0x1e3b): undefined reference to `clock_gettime'
          /home/twotwo/software/boost_154/lib/libboost_thread.a(thread.o):thread.cpp.text+0x1ea6): more undefined references to `clock_gettime' follow
          collect2: ld returned 1 exit status
          make[2]: *** [segment_juncs] Error 1
          make[2]: Leaving directory `/home/twotwo/software/tophat-2.0.9/src'
          make[1]: *** [all-recursive] Error 1
          make[1]: Leaving directory `/home/twotwo/software/tophat-2.0.9'
          make: *** [all] Error 2

          Any comments?

          Comment


          • #6
            Originally posted by twotwo View Post
            Hi, I installed the newest tophat 2.0.9. And I have similar problem in configure.


            -- tophat 2.0.9 Configuration Results --
            C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/twotwo/software/boost_154/include -I/home/twotwo/software/samtools-0.1.19/samtools0119/include -I./SeqAn-1.3
            Linker flags:
            GCC version: gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
            Host System type: x86_64-unknown-linux-gnu
            Install prefix: /home/twotwo/software/tophat209
            Install eprefix: ${prefix}

            See config.h for further configuration information.
            Email <[email protected]> with questions and bug reports.


            when I ran make, I got the following error:
            thread.cpp.text+0x1c84): undefined reference to `clock_gettime'
            thread.cpp.text+0x1cfa): undefined reference to `clock_gettime'
            thread.cpp.text+0x1d65): undefined reference to `clock_gettime'
            thread.cpp.text+0x1dd0): undefined reference to `clock_gettime'
            thread.cpp.text+0x1e3b): undefined reference to `clock_gettime'
            /home/twotwo/software/boost_154/lib/libboost_thread.a(thread.o):thread.cpp.text+0x1ea6): more undefined references to `clock_gettime' follow
            collect2: ld returned 1 exit status
            make[2]: *** [segment_juncs] Error 1
            make[2]: Leaving directory `/home/twotwo/software/tophat-2.0.9/src'
            make[1]: *** [all-recursive] Error 1
            make[1]: Leaving directory `/home/twotwo/software/tophat-2.0.9'
            make: *** [all] Error 2

            Any comments?
            Try the suggestion in post #9: http://seqanswers.com/forums/showthread.php?t=28225

            Comment


            • #7
              Originally posted by GenoMax View Post
              great! Thanks!
              Here is my code. It really works.
              ./configure LIBS=-lrt --prefix=/home/twotwo/software/tophat209 --with-boost=/home/twotwo/software/boost_154 --with-bam=/home/twotwo/software/samtools-0.1.19/samtools0119

              Comment

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