[galaxy-dev] how to access galaxy model in the tool wrapper

2013-06-08 Thread BingXin Lu
Hi all, Do you know any way to access galaxy model (like 'HistoryDatasetAssociation') in the tool wrapper python file for a newly added tool, without overriding 'exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr)'? Thank you very much. Best Regards, -Bingxin

[galaxy-dev] about the permission of stdout and stderr

2013-04-18 Thread BingXin Lu
Hi all, I updated my galaxy yesterday, after that every time I clicked stdout and stderr in the history panel, it shows the following message: 'Invalid dataset ID or you are not allowed to access this dataset'. I have tried to change the permission for the history, but it does not work. Have you

Re: [galaxy-dev] How to show alert message to user when running a tool in galaxy

2013-04-08 Thread BingXin Lu
I will try this method. Thank you very much! 2013/4/8 Nate Coraor n...@bx.psu.edu On Apr 4, 2013, at 9:41 AM, BingXin Lu wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure

[galaxy-dev] How to show alert message to user when running a tool in galaxy

2013-04-04 Thread BingXin Lu
Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I

[galaxy-dev] How to show alert message to user when running a tool in galaxy

2013-04-04 Thread BingXin Lu
Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I