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

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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

Hi David,

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,

Dan

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' (http://packages.python.org/distribute/easy_install.html) in place, I installed bx-python quite easily into our local python instance:

$ easy_install bx-python

Then, it was very straightforward:

$ python ../lib/python2.6/site-packages/bx_python-0.6.0-py2.6-linux-x86_64.egg/EGG-INFO/scripts/maf_build_index.py chr22_random.maf

The wiki is not as verbose as I would like, but I guess I'm trying to do something no one else needs.

David

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?

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

---

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