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SSAHA API?

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  • jlim1197
    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
    Message 1 of 8 , Apr 14 10:02 AM
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      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
    • Will Spooner
      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
      Message 2 of 8 , Apr 15 12:56 AM
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        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@...
        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
        Thanks for the tip. I will give that a try. ... server on ... http://docs.yahoo.com/info/terms/
        Message 3 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 4 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 5 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 6 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 7 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 8 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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