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  • gfmgfm
    Member
    • Jun 2010
    • 64

    galaxy error: No module named galaxy_utils.sequence.fastq

    Hello all,

    We installed local galaxy and wanted to use a command, such as:

    python /usr/local/src/galaxy-central.orig/tools/fastq/fastq_groomer.py

    but it gives the following message:

    File "/usr/local/src/galaxy-central.orig/tools/fastq/fastq_groomer.py", line 3, in <module>
    from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter
    ImportError: No module named galaxy_utils.sequence.fastq

    Does anyone knows what could possibly be the problem?
  • Dannon
    Junior Member
    • Dec 2010
    • 5

    #2
    Galaxy's command line tools can be run outside of Galaxy itself, but you will need to make sure the lib directory is on your PYTHONPATH. In your case, "/usr/local/src/galaxy-central.orig/lib/"

    Comment

    • gfmgfm
      Member
      • Jun 2010
      • 64

      #3
      thanks a lot!

      Comment

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