#20 minimus2-blat with hardcoded path to blat

open
nobody
None
5
2014-08-15
2011-08-02
No

When I tried to install amos in a non-standard location, minimus2-blat was looking for the blat executable in /usr/bin/blat despite my setting the BLAT environmental variable. It appears as if this behavior was hardcoded in the file src/Pipeline/minimus2-blat.acf.
Perhaps this could be changed ?

Discussion

  • Sébastien Moretti

    I noticed the same thing for other variables, set at the configure step, not passed through all programs.
    It happens for some $BASEDIR, BINDIR, NUCMER, BLAT, DELTAFILTER, SHOWCOORDS, show-tiling variables.

    Also some programs have typos, or no more extension, when called from another program of the package. E.g. preTA.pl instead of preTA, ca2ta, ...

    Some other calls are to package not mentioned at all in the documentation like Tigr Assembler, ...

    Is there a new amos release planned soon?

     
  • jw bargsten

    jw bargsten - 2014-08-15

    here is a patch for the DELTAFILTER and SHOWCOORDS variables. It seems that the variables are (1) either not substituted or (2) a required TAB character was replaced by a space in the configuration

     
    • Jeff

      Jeff - 2015-04-23

      Thanks for the patch, it updated the path vars in minimus2!

      If anyone could benefit from the steps so far:
      first installed all dependencies, as needed

      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      cd ~/git
      git clone https://github.com/nathanhaigh/amos.git
      cd amos

      PATCH is needed (minimus2 will fail downstream, because of hardcoded paths)

      from thread https://sourceforge.net/p/amos/bugs/20/

      cd ~/git/amos
      wget https://sourceforge.net/p/amos/bugs/_discuss/thread/a6a7b6be/9445/attachment/0001-bugfix-MUMmer-integration.patch
      git apply 0001-bugfix-MUMmer-integration.patch

      ./bootstrap #creates a configure file
      ./configure --with-Boost-dir=/home/jcx9dy/bin/boost_1_58_0
      make
      make install
      add ~/git/amos/bin to path in .bashrc

      afterwards, check these files to make sure paths are proper:

      patch succesfully fixed

      /home/jcx9dy/git/amos/bin/minimus
      /home/jcx9dy/git/amos/bin/minimus2
      /home/jcx9dy/git/amos/bin/minimus2-blat

      patch did not correct (not needed?)

      /home/jcx9dy/git/amos/src/Pipeline/minimus.acf
      /home/jcx9dy/git/amos/src/Pipeline/minimus2.acf
      /home/jcx9dy/git/amos/src/Pipeline/minimus2-blat.acf

      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      edit: minimus2 can detect paths correctly now; make sure to check bottom of run logs (where new log info is appended) if rerunning on same fasta file!

       
      Last edit: Jeff 2015-04-23

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