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36Re: SSAHA client/server binary compile probs

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  • jlim1197
    Apr 16, 2003
      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
      > > > >
      > > > >
      > > > >
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      > > > >
      > > > >
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