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 /usr/local/lib/python2.7/dist-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py:1025: 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: '/mnt/galaxyIndices/alignments/maf/chr11_gl000202_random.maf.index' hmei@ubuntu:/mnt/galaxyTools/galaxy-central/scripts/tools/maf$ == So now I have my MAF functions working. Thanks again! Leon On Wed, Sep 11, 2013 at 9:18 PM, Daniel Blankenberg <dan@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