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Re: SSAHA API?

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  • jlim1197
    Thanks for the tip. I will give that a try. ... server on ... http://docs.yahoo.com/info/terms/
    Message 1 of 8 , Apr 15 11:21 AM
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      Thanks for the tip. I will give that a try.


      --- 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/
      > >
      > >
    • jlim1197
      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? If not, can someone provide the link? Thanks.
      Message 2 of 8 , Apr 15 11:46 AM
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        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? If not, can someone
        provide the link? Thanks.


        --- 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/
        > >
        > >
      • Will Spooner
        ... No, this is the standalone ssaha executable. ... You ll need to download the source code (ssaha_v30.tar.gz). There are instructions on building the
        Message 3 of 8 , Apr 16 12:49 AM
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          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/
          >
          >
        • 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 4 of 8 , Apr 16 1:49 PM
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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 5 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 6 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
                > >
                > >
                > >
                > > 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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