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Re: SSAHA client/server binary compile probs

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  • jlim1197
    I m having problems compiling the code under various machines. Has anyone been able to compile successfully under x86 linux and Sun Solaris? Will there be
    Message 1 of 8 , Apr 16, 2003
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      I'm having problems compiling the code under various machines. Has
      anyone been able to compile successfully under x86 linux and Sun
      Solaris? Will there be client/server binaries released as well?

      I downloaded the source (both 3.0 and 3.1) and tried to build the
      client/server binary on my x86(Pentium 4) machine under Mandrake 9 and
      it failed to compile because my version of gcc/g++ is 3.2.

      I also tried to compile with g++ 2.95.2 on a Sun SPARC (Solaris 8) and
      still got errors:

      for "make ssaha":

      g++ -O3 -I/disk2/home/jlim/SSAHA -I/disk2/home/jlim/SSAHA/Global
      -I/disk2/home/jlim/SSAHA/SequenceReader
      -I/disk2/home/jlim/SSAHA/HashTable
      -I/disk2/home/jlim/SSAHA/QueryManager -D_REENTRANT -Wl,-S -o ssaha
      GlobalDefinitions.o HashTable.o HashTablePacked.o HashTableGeneric.o
      HashTableTranslated.o SequenceReader.o SequenceEncoder.o
      SequenceReaderMulti.o SequenceReaderFasta.o SequenceReaderFastq.o
      SequenceReaderFilter.o QueryManager.o MatchStoreUngapped.o
      MatchStoreGapped.o MatchStore.o MatchAligner.o SSAHAMain.o TimeStamp.o
      ld: fatal: dlopen() of support library (GlobalDefinitions.o) failed
      with error: ld.so.1: /usr/ccs/bin/ld: fatal: GlobalDefinitions.o: open
      failed: No such file or directory
      collect2: ld returned 1 exit status
      make: *** [ssaha] Error 1


      and for "make ssaha.a":

      g++ -c -O3 -I/disk2/home/jlim/SSAHA -I/disk2/home/jlim/SSAHA/Global
      -I/disk2/home/jlim/SSAHA/SequenceReader
      -I/disk2/home/jlim/SSAHA/HashTable
      -I/disk2/home/jlim/SSAHA/QueryManager -D_REENTRANT
      /disk2/home/jlim/SSAHA/HashTable/testHashTable.cpp
      g++ -O3 -I/disk2/home/jlim/SSAHA -I/disk2/home/jlim/SSAHA/Global
      -I/disk2/home/jlim/SSAHA/SequenceReader
      -I/disk2/home/jlim/SSAHA/HashTable
      -I/disk2/home/jlim/SSAHA/QueryManager -D_REENTRANT -o testHashTable
      HashTable.o HashTablePacked.o HashTableTranslated.o HashTableGeneric.o
      SequenceEncoder.o SequenceReader.o GlobalDefinitions.o TimeStamp.o
      testHashTable.o
      ld: fatal: file HashTable.o: wrong ELF machine type: EM_386
      ld: fatal: File processing errors. No output written to testHashTable
      collect2: ld returned 1 exit status
      make: *** [testHashTable] Error 1

      We also have an AIX IBM pServer box, but it's got g++ 3.2 installed.

      Help greatly appreciated!


      --- In ssahausers@yahoogroups.com, Will Spooner <whs@s...> wrote:
      > On Tue, 15 Apr 2003, jlim1197 wrote:
      >
      > > The only file I can find on the website is ssaha_v30_linux. Is this
      > > the file that I can run as a server process?
      >
      > No, this is the standalone ssaha executable.
      >
      > > If not, can someone
      > > provide the link? Thanks.
      >
      > You'll need to download the source code (ssaha_v30.tar.gz). There are
      > instructions on building the client/server binary in the 'EnsemblServer'
      > directory.
      >
      > Regards,
      >
      > Will
      >
      > >
      > >
      > > --- In ssahausers@yahoogroups.com, Will Spooner <whs@s...> wrote:
      > > >
      > > > Hi Jonathan,
      > > >
      > > > Unfortunatly there is currently no Perl API to SSAHA. However,
      if you're
      > > > building a web interface, you may like to look at the EnsemblServer
      > > > appliction from the SSAHA distribution. This is a TCP/IP
      client/server
      > > > implementation, which means that you can run a persistent SSAHA
      > > server on
      > > > a different machine to the web server. This is how we run the
      Ensembl
      > > > sshaview web application.
      > > >
      > > > Regards,
      > > >
      > > > Will
      > > >
      > > > ---
      > > > Dr William Spooner whs@s...
      > > > Ensembl Web Developer http://www.ensembl.org
      > > >
      > > > On Mon, 14 Apr 2003, jlim1197 wrote:
      > > >
      > > > > Hi there,
      > > > >
      > > > > I'd like to integrate a SSAHA search into a web-based gene
      annotation
      > > > > system (using Perl) that I'm developing. Just wondering if
      there's an
      > > > > API
      > > > > or Perl port of SSAHA that I can use to tie it in...or is the
      > > > > command-line tool all that's available?
      > > > >
      > > > > Thanks
      > > > >
      > > > >
      > > > >
      > > > >
      > > > >
      > > > > Jonathan Lim
      > > > > Bioinformatics Software Developer
      > > > > Centre for Molecular Medicine and Therapeutics
      > > > > University of British Columbia
      > > > >
      > > > >
      > > > >
      > > > > To unsubscribe from this group, send an email to:
      > > > > ssahausers-unsubscribe@yahoogroups.com
      > > > >
      > > > >
      > > > >
      > > > > Your use of Yahoo! Groups is subject to
      > > http://docs.yahoo.com/info/terms/
      > > > >
      > > > >
      > >
      > >
      > >
      > > To unsubscribe from this group, send an email to:
      > > ssahausers-unsubscribe@yahoogroups.com
      > >
      > >
      > >
      > > Your use of Yahoo! Groups is subject to
      http://docs.yahoo.com/info/terms/
      > >
      > >
    • Will Spooner
      ... Hmm, this is a bit tricky. The client/server builds fine using gcc on tru-64, but won t build cleanly under Linux. I ve fixed a few bits, but have hit my
      Message 2 of 8 , Apr 17, 2003
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        On Wed, 16 Apr 2003, jlim1197 wrote:

        > I'm having problems compiling the code under various machines. Has
        > anyone been able to compile successfully under x86 linux and Sun
        > Solaris? Will there be client/server binaries released as well?

        Hmm, this is a bit tricky. The client/server builds fine using gcc on
        tru-64, but won't build cleanly under Linux. I've fixed a few bits, but
        have hit my C/C++ knowledge limit (OK, I admit, I'm a Perl programmer). If
        anyone has a patch for this, or has the inclination to take a look,
        please shout!


        > I downloaded the source (both 3.0 and 3.1) and tried to build the
        > client/server binary on my x86(Pentium 4) machine under Mandrake 9 and
        > it failed to compile because my version of gcc/g++ is 3.2.

        Yup - you'll need to install gcc 2.95 in tandem with 3.2. This should
        be fine on Mandrake. I'd also be interested, however, in patching the code
        for gcc 3.2.


        > I also tried to compile with g++ 2.95.2 on a Sun SPARC (Solaris 8) and
        > still got errors:

        I've just got access to a sun box, so I'll see if I can build a binary for
        you (no promises though).


        The upshot; I would be delighted to hear from anyone inclined to
        contribute to the SSAHA code base. Whilst it works great here at Sanger,
        I'm well aware of the problems experienced on other (non
        tru-64) platforms. One possibility is setting up a ssaha
        project on sourceforge. Interested parties; please step forward!

        Regards,

        Will


        ---
        Dr William Spooner whs@...
        Ensembl Web Developer http://www.ensembl.org
      • jlim1197
        Interestingly, I came across a perl interface for the non-client/server binary. It s part of the Ensembl-Pipeline package
        Message 3 of 8 , Apr 17, 2003
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          Interestingly, I came across a perl interface for the
          non-client/server binary. It's part of the Ensembl-Pipeline package
          (http://www.ensembl.org/Docs/Pdoc/ensembl-pipeline/) - the module is
          Bio::EnsEMBL::Pipeline::Runnable::SSAHA. Strangely, there's also
          Bio::EnsEMBL::Pipeline::Runnable::Blat, which I've also been looking
          for. I've successfully done SSAHA and blat searches within my code
          using these modules and the command-line binaries. The SSAHA module
          worked with both v3.0 and 3.1 of SSAHA.


          --- In ssahausers@yahoogroups.com, Will Spooner <whs@s...> wrote:
          >
          > Hi Jonathan,
          >
          > Unfortunatly there is currently no Perl API to SSAHA. However, if you're
          > building a web interface, you may like to look at the EnsemblServer
          > appliction from the SSAHA distribution. This is a TCP/IP client/server
          > implementation, which means that you can run a persistent SSAHA
          server on
          > a different machine to the web server. This is how we run the Ensembl
          > sshaview web application.
          >
          > Regards,
          >
          > Will
          >
          > ---
          > Dr William Spooner whs@s...
          > Ensembl Web Developer http://www.ensembl.org
          >
          > On Mon, 14 Apr 2003, jlim1197 wrote:
          >
          > > Hi there,
          > >
          > > I'd like to integrate a SSAHA search into a web-based gene annotation
          > > system (using Perl) that I'm developing. Just wondering if there's an
          > > API
          > > or Perl port of SSAHA that I can use to tie it in...or is the
          > > command-line tool all that's available?
          > >
          > > Thanks
          > >
          > >
          > >
          > >
          > >
          > > Jonathan Lim
          > > Bioinformatics Software Developer
          > > Centre for Molecular Medicine and Therapeutics
          > > University of British Columbia
          > >
          > >
          > >
          > > To unsubscribe from this group, send an email to:
          > > ssahausers-unsubscribe@yahoogroups.com
          > >
          > >
          > >
          > > Your use of Yahoo! Groups is subject to
          http://docs.yahoo.com/info/terms/
          > >
          > >
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