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 <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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
