Python is not my speciality. Where do I call maf_build_index.py so that the required packages are loaded? Do I need to modify the script in any way for local installation? So I need to set any environment variables first?
David
On Nov 8, 2010, at 9:47 AM, Daniel Blankenberg wrote:
Hi David,
The sample is correct. The wiki has been updated to reflect this.
Thanks,
Dan
On Nov 8, 2010, at 9:43 AM, David Hoover wrote:
The first problem I see is that the maf_index.loc file has 5 fields, instead of 4. Which is correct, the wiki or the sample .loc file?
David
On Nov 8, 2010, at 9:38 AM, Daniel Blankenberg wrote:
Hi David,
There are a couple of reasons that you could get this error, one of them being that the precached MAFs have not been indexed. This wiki page has more information about what is needed to set up the precached MAFs: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ToolData/AddMAFs
Please do let us know if this is not able to fix the problem that you are experiencing.
Thanks for using Galaxy,
Dan
On Nov 8, 2010, at 8:42 AM, David Hoover wrote:
We have a local copy of MAF files for hg18, and I modified the ~/tool-data/maf_index.loc file to list the full paths to the .maf files. After restarting Galaxy, the MAF Source and Type are listed in the MAF Coverage Stats tool, as expected. However, after trying to run with an interval file, it gives an error "The MAF source specified (17_WAY_MULTIZ_hg18) appears to be invalid".
Is there somewhere else I need to edit to get to the locally cached MAF files?
David Hoover Helix Systems Staff http://helix.nih.gov
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev