[galaxy-dev] Plugin for debug / replay and display parameters

2014-11-14 Thread Rémy Dernat
Hi, We created a plugin to display all history parameters in a single page and generate a shell script from an history. It adds two inputs to the main menu: "parameters" (for all users) and "debug" (for admins). An admin can easily switch from an history to another without having to impersonate

Re: [galaxy-dev] SMALT Docker integration run unsteadily

2014-11-14 Thread John Chilton
I believe this is the result of a Docker bug https://github.com/docker/docker/issues/7792 - (tl;dr a change in go resulted in the volume map being randomized). This bug and supporting Docker volume handling pre, during, and post bug is going to be complicated and I need to work out if that is even

Re: [galaxy-dev] Jobs stuck in "new" state - Data Library datasets to blame?

2014-11-14 Thread Lance Parsons
Thanks for looking into this John. I'm pretty sure there are multiple reasons for stuck jobs. (In fact I'm running into another I'll discuss separately, likely in a Trello ticket). But it turns out in my most recent run-in with this issue, the problem turned out to be caused by datasets that w

Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap

2014-11-14 Thread Bruno Grande
Daniel's instructions did the trick! I tried different combinations, and it seems that I needed to specify the TOOL_SHED_CONFIG_FILE environment variable in addition to including the protocol in the source Tool Shed URL ( *i.e.* https://). Otherwise, I also had to change my password to one without