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

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.liu@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.liu@yale.edu
PO Box 207077
New Haven, CT 06520-7077
352.871.1258

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