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Re: [ssahausers] ssaha2 v1.0.4

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  • 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 1 of 4 , May 5, 2007
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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 2 of 4 , May 18, 2007
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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 3 of 4 , May 19, 2007
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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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