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Question: alignseq_seq.loc file missing
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gravatar for lachlan.simpson
11 weeks ago by
lachlan.simpson • 20
lachlan.simpson • 20 wrote:

Hi,

I've got an error in my data tables page saying alignseq_seq.loc is missing.

alignseq.loc and alignseq.loc.sample exist.

Am I missing something or has there been an error in the naming of the file/calling of the file?

I've seen this in both 17.09 and 18.05
twobit data tables • 84 views
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modified 11 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 11 weeks ago by lachlan.simpson • 20
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gravatar for Jennifer Hillman Jackson
11 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When creating .2bit indexes, the DM created table's file path is nested and will be a path like this one:

 ../galaxy/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/df883cc67fbd/alignseq.loc

It is possible to configure the data tables/paths to point to multiple location (".loc") files for a particular index type. The configuration files involved are covered in the Galaxy Admin docs here: https://docs.galaxyproject.org/en/master/admin/config.html?highlight=data%20managers with training available here: https://github.com/galaxyproject/dagobah-training/tree/master.

Mixed data sources require a more complex configuration. Galaxy Main (https://usegalaxy.org) has a mix of DM and legacy data. How we configure is public and described here as an example: https://github.com/galaxyproject/usegalaxy-playbook/wiki/Publishing-Indexes-to-Main

That said, if you think there is a bug somewhere, please vet it with the Galaxy development community at Gitter https://gitter.im/galaxyproject/Lobby. They'll want more details about your configuration and methods (are you using Data Managers? Ephemeris? CVMFS? Your own legacy data? A mix of sources?).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 weeks ago by Jennifer Hillman Jackson ♦ 25k
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