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ssaha2 v1.0.4

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  • Adam Spargo
    Hi, Sorry if I haven t replied to resent requests in person, all reported issues should be solved by this new release:
    Message 1 of 4 , May 4 8:21 AM
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      Hi,
      Sorry if I haven't replied to resent requests in person, all reported
      issues should be solved by this new release:

      http://www.sanger.ac.uk/Software/analysis/SSAHA2/

      Cheers,

      Adam.

      --
      Dr Adam Spargo
      High Performance Assembly Group email: aws@...
      Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
      Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
    • Charles Plessy
      ... Dear Adam, there is a major difference between SSAHA and SSAHA2: the first is free software, and unfortunately the second is not. I would be happy to
      Message 2 of 4 , May 5 2:04 AM
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        Le Fri, May 04, 2007 at 04:21:54PM +0100, Adam Spargo a écrit :
        >
        > Hi,
        > Sorry if I haven't replied to resent requests in person, all reported
        > issues should be solved by this new release:
        > [1]http://www.sanger.ac.uk/Software/analysis/SSAHA2/
        > Cheers,
        > Adam.
        > --

        Dear Adam,

        there is a major difference between SSAHA and SSAHA2: the first is free
        software, and unfortunately the second is not.

        I would be happy to pacakge SSAHA for the Debian GNU/Linux operating
        system, but I am not a C programmer, so I can not do anything without
        the patch for GCC 4.0 mentionnend on the homepage of SSAHA. But it seems
        to be lost... Do you have a copy somewhere ?

        Have a nice day,

        --
        Charles Plessy
        Debian-Med packaging team
        http://www.debian.org/devel/debian-med/
        Wako, Saitama, Japan
      • coxtonyj
        Dear Charles/Adam I have made the changes necessary to get original SSAHA to compile under gcc 4.1.2 and uploaded a new version of the package to this group
        Message 3 of 4 , May 18 3:32 AM
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          Dear Charles/Adam

          I have made the changes necessary to get 'original' SSAHA to compile
          under gcc 4.1.2 and uploaded a new version of the package to this
          group as a gzipped tar file. I suspect my changes replicate the
          patches Conrad Halling was kind enough to make, the link to which
          unfortunately no longer seems to work.

          I have taken the liberty of naming this 'version 3.3' of the SSAHA
          tarball and updating the release dates etc.

          I have verified that this new version compiles successfully with GCC
          4.1.2 under Cygwin and also with GCC 3.2.2 on RedHat 9. The test
          scripts and executables run to completion in both cases. Note that
          for the client/server version I only verified that the code compiled,
          however I did not change any of this code so there is no reason to
          suppose that it won't work.

          I hope this is useful, if there are any problems let me know and I
          will try to find the time to fix them.

          Best Wishes

          Tony Cox

          --
          Dr. Anthony J. Cox
          Principal Scientist
          UK Computational Biology Group
          Illumina Inc.
          Chesterford Research Park
          Little Chesterford, Essex CB10 1XL
          United Kingdom



          --- In ssahausers@yahoogroups.com, Charles Plessy <yahoo@...> wrote:
          >
          > Le Fri, May 04, 2007 at 04:21:54PM +0100, Adam Spargo a écrit :
          > >
          > > Hi,
          > > Sorry if I haven't replied to resent requests in person, all
          reported
          > > issues should be solved by this new release:
          > > [1]http://www.sanger.ac.uk/Software/analysis/SSAHA2/
          > > Cheers,
          > > Adam.
          > > --
          >
          > Dear Adam,
          >
          > there is a major difference between SSAHA and SSAHA2: the first is
          free
          > software, and unfortunately the second is not.
          >
          > I would be happy to pacakge SSAHA for the Debian GNU/Linux operating
          > system, but I am not a C programmer, so I can not do anything
          without
          > the patch for GCC 4.0 mentionnend on the homepage of SSAHA. But it
          seems
          > to be lost... Do you have a copy somewhere ?
          >
          > Have a nice day,
          >
          > --
          > Charles Plessy
          > Debian-Med packaging team
          > http://www.debian.org/devel/debian-med/
          > Wako, Saitama, Japan
          >
        • Charles Plessy
          ... Dear Tony, many thanks! I will announce on this mailing list when the Debian package will be ready. Have a nice day, -- Charles Plessy
          Message 4 of 4 , May 19 6:31 PM
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            Le Fri, May 18, 2007 at 10:32:22AM -0000, coxtonyj a écrit :
            >
            > Dear Charles/Adam
            > I have made the changes necessary to get 'original' SSAHA to compile
            > under gcc 4.1.2 and uploaded a new version of the package to this
            > group as a gzipped tar file. I suspect my changes replicate the
            > patches Conrad Halling was kind enough to make, the link to which
            > unfortunately no longer seems to work.
            > I have taken the liberty of naming this 'version 3.3' of the SSAHA
            > tarball and updating the release dates etc.

            Dear Tony,

            many thanks! I will announce on this mailing list when the Debian
            package will be ready.

            Have a nice day,

            --
            Charles Plessy
            http://charles.plessy.org
            Wako, Saitama, Japan
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