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  • help with topcons membrane prediction

    Hi,

    I have been trying to use topcons membrane prediction.
    I am trying to run the consensus one, but I am stuck with

    Code:
    run_blast.sh
    of octopus.
    I am stuck at this.
    Running topcons is a 3 step process:
    1) get file from run_blast.sh
    2) process that output for modhmm profile
    3) create .mtx file

    The read_me file doesn't say clearly.
    It has instructions based on OLDER version of Blast.

    Can someone please help me with this?

    There is an other way round this:
    1) run_topcons_single.sh
    2) run_topcons.sh

    I fail to understand which one to use and how.

    I have the dependencies for TOPCONS.sh in my PATH.

    I need this prediction on standalone tools.
    I have a protein file with 35 protein sequences and I have 20 such files.

    Any help shall be greatly appreciated.
    Thank you.
    Bioinformaticscally calm

  • #2
    You get an error message? Please add more details about you problem.

    Comment


    • #3
      I get error as:

      Directory /home/robber/bin/../var/www/topcons.cbr.su.se/docroot/topcons/ does not exist

      However, the aboce directory exists in the location.
      I have added that location in my PATH as well.

      Originally posted by TiborNagy View Post
      You get an error message? Please add more details about you problem.
      Last edited by bio_informatics; 01-27-2014, 06:48 PM. Reason: Error more clear
      Bioinformaticscally calm

      Comment

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