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.liu@yale.edu

On Tue, Jan 13, 2015 at 2:35 PM, Daniel Blankenberg dan@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.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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

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