Hi Dan,

Thanks for the solution! It did help me to identify a missing index
file. I think the indexing run of that particular config maf file
failed for some reason. Since I don't expect much interesting thing on
that, I just remove that for now.

hmei@ubuntu:/mnt/galaxyTools/galaxy-central/scripts/tools/maf$ python
check_loc_file.py ../../../tool-data/maf_index.loc
UserWarning: /home/hmei/.python-eggs is writable by group/others and
vulnerable to attack when used with get_resource_filename. Consider a
more secure location (set with .set_extraction_path or the
PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)
Line 6 is invalid: [Errno 2] No such file or directory:

So now I have my MAF functions working. Thanks again!


On Wed, Sep 11, 2013 at 9:18 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Leon,
> Can you see if there is any info reported reported by running the MAF 
> consistency checking script at scripts/tools/maf/check_loc_file.py 
> path/to/maf_index.loc?
> You'll need to make sure that required dependencies (e.g. galaxy_root/lib and 
> galaxy_root/eggs) are included in your PYTHONPATH.
> As far as cutting down a MAF to only contain the set of desired species and 
> depending upon your needs, you can use the tools included with Galaxy, or 
> alternatively the maf_thread_for_species.py script in bx-python.
> Thanks for using Galaxy,
> Dan

Hailiang (Leon) Mei
Netherlands Bioinformatics Center
BioAssist NGS Taskforce
 - http://ngs.nbic.nl
Skype: leon_mei    Mobile: +31 6 41709231
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