Hello,

Xianjun Dong wrote:

2. How to set the data(databases) it needed?
For example, in the "Get ENCODE Data" menu, when I click the sub-menu, it's empty, with no ENCODE data list as your Galaxy site listed. How/Where can I get it and set it in my local server?
Also, the tool like liftover is empty, "The To list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset.", how can I set this?


The Galaxy distribution includes a ~/tool-data subdirectory which consists of <data>.loc.sample files.  These sample files each include information that enables you to create your own version of the file that will point to the location of your data on disk.  The "Get ENCODE Data" tool uses the "encode_datasets.loc" ( see the tool's config file in ~/tools/data_source/encode_import_gencode.xml.  The encode_datasets.loc.sample file includes the following information to enable you to create your own encode_datasets.loc file:

#This is a sample file distributed with Galaxy that enables tools
#to use ENCODE data.  The encode_datasets.loc file has this format
#(white space characters are TAB characters):
#
#<EncodeGroup>    <build>    <DisplayName>    <UniqueID>    <FullPathToFile>    <Format>
#             Encode Groups: ShortHandCode = Group
#                                       CC = chromatin and chromosomes
#                                       GT = genes and transcripts
#                                      MSA = multi-species sequence analysis
#                                       TR = transcription regulation
#                                      ALD = All Latest Datasets

Similarly, the liftOver tool uses the liftOver.loc file and the liftOver.loc.sample file includes details letting you know what your local version of the file should look like.

See the tool config ( XML ) files for the tools that use locally cached data like this to help you determine which ".loc" file the tool uses.

Let me know if you have any issues getting these set up.

Thanks very much,

Greg Von Kuster
Galaxy Development Team