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Steps for new installation with compatible blasr version?

PBJelly Tickets
Jesse Connell
2017-01-25
2017-01-26

  • Jesse Connell

    Jesse Connell - 2017-01-25

    I'm setting up a new install of PBSuite and running into compatability problems with my (recent) blasr version, just as the documentation warns about. (Specifically my mapping step fails as already described here.) But I can't see how to get the blasr version that PBSuite wants, since they don't have defined releases or tags or anything on the repository.

    So, what's the recommended installation method when starting with a clean slate? Should I aim to roll my blasr repo back to a particular commit and build that, or are there efforts underway to get PBSuite compatible with the more recent blasr code?

    Thanks for any suggestions.

     

  • Jesse Connell

    Jesse Connell - 2017-01-26

    After a cursory check this fork seems to make the example work once I've edited Protocol.xml to use the newer syntax. I think there are still things that don't quite match up, like the disappearance of the minPctIdentity option as Filip mentioned in his thread, so any input here is still very much welcome!

     

  • Jesse Connell

    Jesse Connell - 2017-01-26

    Oh, and my blasr reports version 5.3.241a522 and it looks like that git repository is based on the latest PBSuite release of 15.8.24 (just going by the changelog).

     

    • Adam English

      Adam English - 2017-01-26

      There are efforts to get the new blasr compatible, but I can't give a
      strong timeline for when it'll be released as this project is maintained in
      my spare time. If you'd like to try to use the development branch of
      PBSuite, you can check out the svn repo from here. Just last week I put in
      changes to accommodate the dash-dash blasr parameters. The dbrowneup fork
      you found seems to have made similar changes. Either way you go, we'll have
      to be careful trying to fix any problems you may run into since neither is
      a hardened release.

      On Thu, Jan 26, 2017 at 8:10 AM, Jesse Connell jesse08@users.sf.net wrote:

      Oh, and my blasr reports version 5.3.241a522 and it looks like that git
      repository is based on the latest PBSuite release of 15.8.24 (just going by
      the changelog).

      Steps for new installation with compatible blasr version?
      https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/051aa7fc/?limit=25#0591

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/

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      • Jesse Connell

        Jesse Connell - 2017-01-26

        Thanks, Adam. I tried svn checkout https://svn.code.sf.net/p/pb-jelly/code-0/trunk pb-jelly-code-0 as suggested by sourceforge but I don't think I'm seeing the latest commits; should I be getting the development version from somewhere else? In the web interface I just see content under trunk, but not branches. (Apologies for my SVN rustiness.)

         

        • Adam English

          Adam English - 2017-01-26

          That's actually on me. I never committed the blasr changes. r108 has them
          now and you can try svn up to grab it.

          On Thu, Jan 26, 2017 at 12:11 PM, Jesse Connell jesse08@users.sf.net
          wrote:

          Thanks, Adam. I tried svn checkout https://svn.code.sf.net/p/pb-
          jelly/code-0/trunk pb-jelly-code-0 as suggested by sourceforge but I
          don't think I'm seeing the latest commits; should I be getting the
          development version from somewhere else? In the web interface I just see
          content under trunk, but not branches. (Apologies for my SVN rustiness.)

          Steps for new installation with compatible blasr version?
          https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/051aa7fc/?limit=25#0591/5694/93fc

          Sent from sourceforge.net because you indicated interest in
          https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/

          To unsubscribe from further messages, please visit
          https://sourceforge.net/auth/subscriptions/

           
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          • Jesse Connell

            Jesse Connell - 2017-01-26

            Got it, I can see the changes now. Looks like we're all set on my end! Thanks!

             

  • Abhinay Ramaprasad

    Abhinay Ramaprasad - 2017-02-14

    Hi Adam
    I was also facing the same problem, and I followed your instructions here and downloaded the r108 version. But still Jelly.py mapping Protocol.xml throws up this error- -sa is not a valid option. in the mapping_chunk0.out. Did this work for Jesse?
    Alternatively, could you give access to the earlier blasr version that you have and is compatible with Pbsuite. I am unable to get it from blasr website as they do not keep versions (weird!).
    Thanks!

     

  • Brad Langhorst

    Brad Langhorst - 2017-03-01

    I also tried checking out the trunk... I see a commit from a while ago that's looks like some partial conversion to python 3. I think that's causing my trouble with python 2.7.11

    Traceback (most recent call last):
  File "bin/Jelly.py", line 19, in <module>
    from pbsuite.jelly import Stages
  File "/mnt/home/langhorst/src/PBSuite-trunk/pbsuite/jelly/Stages.py", line 7, in <module>
    from pbsuite.utils.FileHandlers import GapInfoFile
  File "/mnt/home/langhorst/src/PBSuite-trunk/pbsuite/utils/FileHandlers.py", line 583, in <module>
    revComp = str.maketrans("ATCGNatcgn","TAGCNtagcn")
AttributeError: type object 'str' has no attribute 'maketrans'

    I tried cloning
    https://github.com/dbrowneup/PBSuite
    and Jelly.py from there does produce output

    Adam - what do you think about moving this to github, maybe others could more easitly share the maintenance load there?

     

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