[galaxy-dev] learning pulsar for galaxy

2018-10-02 Thread Wong, Kai Leung
Hello, We are working on a project in providing a Cloud based research platform for Health Informatics and Bioinformatics. Long story short, one of the components to be provided by the project is a Galaxy Server for our genomics researchers; and on the other hand, GWU also has a HPC system for hig

Re: [galaxy-dev] tool data confusion

2018-10-02 Thread Peter Cock
Hi Matthias, I'm getting out of my depth here - but if tool-data/xxx.loc is being ignored, you may need to enable this by adding the XML data table entries from the relevant tool_data_table_conf.xml.sample file for tool xxx to $GALAXY/config/tool_data_table_conf.xml. At least, that's what I had t

Re: [galaxy-dev] tool data confusion

2018-10-02 Thread Matthias Bernt
Hi Peter, then the I need to update all the paths in: `config/shed_tool_data_table_conf.xml`? Because currently the $GALAXY/tool-data/*.loc files are ignored in my instance. For me it looks like a bug (caused by a misconfiguration?) that there are all xml files refer to the same loc file.

Re: [galaxy-dev] tool data confusion

2018-10-02 Thread Peter Cock
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did. If you use a data manager, I don't know which