[galaxy-dev] Get workflow info API problem

2013-01-06 Thread Hagai Cohen
Hi, I'm trying to use the API for showing workflow info which should be something like: /api/workflow/ But I'm getting the following error: .../galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 80, in show label_name = step.tool_inputs['name'] TypeError: 'NoneType' object has no at

[galaxy-dev] text manipulation Compute tool error

2013-01-06 Thread mark.rose
Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get

[galaxy-dev] Stumped by GridOperation

2013-01-06 Thread Ted Goldstein
Hi, Based on a suggestion by James Taylor, I am working on extending the security model so that pages can use the same RBAC permission system used in libraries. In fact, many of my pages have assets (images, etc) which are stored in a library. So this is a natural model. Therefore I want to make

Re: [galaxy-dev] Stumped by GridOperation

2013-01-06 Thread Greg Von Kuster
Hi Ted, If I understand what your trying to do, I believe I've implemented grid operations similar to what your attempting in several places in the Galaxy tool shed, so checking the various grid classes and associated methods in /lib/galaxy/webapps/community/controllers will give you some examp

Re: [galaxy-dev] Galaxy cloud: Tool execution generated the following error message

2013-01-06 Thread Brad Chapman
Alicia; Thanks for the useful feedback. I'm agreed that Cloud Galaxy usage requires more IT knowledge compared to running directly on a hosted Galaxy instance. Dannon, Enis and everyone are working hard to make it easier, but at this point it does require understanding Amazon EC2. For your termin

Re: [galaxy-dev] Stumped by GridOperation

2013-01-06 Thread Ted Goldstein
HI Greg, I thought of this. But there is potential bug in it which has security implications. Though it is a low probability event, I have seen this sort of leakage happen in other environments where user data was stuck into globally shared objects. The grid object is shared by all requests.