Sorry for any trouble you may have had. We'll work to enhance the wiki to make the
necessary steps more clear. Please let us know if we can be of further assistance.
Thanks for using Galaxy,
On Nov 8, 2010, at 10:29 AM, David Hoover wrote:
Wait a second. We are using RedHat Linux Enterprise 3 instead of
Ubuntu, so I couldn't quite understand the wiki.
After getting 'easy_install'
) in place, I installed bx-python
quite easily into our local python instance:
$ easy_install bx-python
Then, it was very straightforward:
The wiki is not as verbose as I would like, but I guess I'm trying to do something no
one else needs.
On Nov 8, 2010, at 9:54 AM, David Hoover wrote:
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?
On Nov 8, 2010, at 9:47 AM, Daniel Blankenberg wrote:
The sample is correct. The wiki has been updated to reflect this.
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?
> 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:
> Please do let us know if this is not able to fix the problem that you are
> Thanks for using Galaxy,
> 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
>> galaxy-dev mailing list
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