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Re: [ssahausers] Re: SSAHA client/server binary compile probs

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  • 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 1 of 8 , Apr 17 2:28 AM
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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 2 of 8 , Apr 17 5:04 PM
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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
        > >
        > >
        > >
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