Hi Daniel,

Thank you for your response! I tried this again and this time it worked
just fine.
It appears the weird file is garbage collected after a while or when the
galaxy server is restarted.

Thanks again!
Jeremy Liu
jeremy....@yale.edu

On Tue, Jan 13, 2015 at 2:35 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Jeremy,
>
> I just installed and tried the data manager and it looks to be working.
> Have you changed any of these settings in your galaxy.ini file:
> # Data manager configuration options
> # Allow non-admin users to view available Data Manager options
> #enable_data_manager_user_view = False
> # File where Data Managers are configured
> #data_manager_config_file = data_manager_conf.xml
> # File where Tool Shed based Data Managers are configured
> #shed_data_manager_config_file = shed_data_manager_conf.xml
> # Directory to store Data Manager based tool-data; defaults to
> tool_data_path
> #galaxy_data_manager_data_path = tool-data
>
>
> Otherwise, the entry should be appearing under something like:
> tool-data/testtoolshed.g2.
> bx.psu.edu/repos/jeremyjliu/region_motif_data_manager/8bf194e522bf/motif_databases.loc
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bx.psu.edu_repos_jeremyjliu_region-5Fmotif-5Fdata-5Fmanager_8bf194e522bf_motif-5Fdatabases.loc&d=AwMF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=QF8ofPosM7nnznQDQjyk5MJ_KjS1kOz-4Oa6IWHcy-k&m=E8DHeUXLLSEyAcy05Rq6rcwKbpQAcsdLAUvIKzOKM5M&s=YRAzVVO_XnX4DNV06XjV1v4Fd3BBZcSPxlC_lkt1Cco&e=>
> Can you check if that file is being created and used correctly?
>
> The data manager maintains its own .loc file to keep it separate from the
> one that you would ordinary modify by hand. Galaxy will keep track of these
> separate files and merge the various .loc file entries into a single
> in-memory data table.
>
>
> The tool_data_table_conf.xml.sample include provides the description for
> the data tables included in the toolshed bundle, the contents of these
> files will get automatically merged by Galaxy, although Galaxy will store
> the data tables installed from a toolshed in a different file than those
> installed by hand, this is transparent within the application. This merging
> process does rely on the column assignments to be the same, so it is a good
> idea to pick descriptive names for the data table to avoid potential
> clashes with other possible tools (a name of just ‘indexes’ would be a poor
> choice).
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Jan 12, 2015, at 11:48 PM, Jeremy Liu <jeremy....@yale.edu> wrote:
>
> Galaxy Devs,
>
> I have a (semi) working data manager and I'm stuck on what exactly is
> going wrong. Most of it appears to be working properly, the intended
> file (pouya_test_motifs.bed.bgz) is being downloaded to the right
> directory (/galaxy-dist/tool-data/motifs). However, the .loc file that
> describes the data table isn't being set to the right place. It should
> be going to (/galaxy-dist/tool-data/motif_databases.loc) but it ends
> up in (./database/tmp/tmp-toolshed-gmfcrTJ8T4R/motif_databases.loc). I
> think it's because /galaxy-dist/tool_data_conf.xml isn't being
> updated.
>
> In addition, I have been working off of the example data manager
> data_manager_fetch_genome_all_fasta. What is the usage of
> tool_data_table_conf.xml.sample? Does it get automatically merged with
> tool_data_table_conf.xml in the galaxy root directory?
>
> For reference, the tools is "region_motif_data_manager" in the
> testtoolshed. Has anyone else run into this problem? Thanks!
>
> Jeremy Liu
> jeremy....@yale.edu
> PO Box 207077
> New Haven, CT 06520-7077
> 352.871.1258
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