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