Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.

2015-01-26 Thread John Chilton
I have created a Trello card to track this request here https://trello.com/c/qCtBBB8n. Any chance you can share the tool with me? I understand that this instinct is too simplistic - but it seems to me like the option to repeatedly run a tool over many datasets should not be the concern of the

Re: [galaxy-dev] data collections - workflow - bug?

2015-01-26 Thread John Chilton
Hey, Really intensive database operations including datasest collections but other things too like multi-running tools or workflows over many individual datasets for instance - can very easily overwhelm the default sqlite database. This is frustrating and shouldn't happen - but it does

Re: [galaxy-dev] concatenate_datasets docker image can't create output

2015-01-26 Thread John Chilton
Can you send me a screenshot of the Tool form right before you hit submit. It is odd that two commands are executed barely differing at all. There were some recent UI changes and I want to make sure that you are passing two inputs once and not submitting one input twice in the newly named batch

Re: [galaxy-dev] concatenate_datasets docker image can't create output

2015-01-26 Thread Jeltje van Baren
See attached for screenshot! Thanks for the links. On Mon, Jan 26, 2015 at 11:37 AM, John Chilton jmchil...@gmail.com wrote: Can you send me a screenshot of the Tool form right before you hit submit. It is odd that two commands are executed barely differing at all. There were some recent

[galaxy-dev] Galaxy XML from python's argparse

2015-01-26 Thread Eric Rasche
Howdy devs, I put together a library recently, and since it seems to be functional I thought I'd share with the rest of -dev in case it's of interest to anyone. If anyone has feedback, bugs/issues, or PRs, I'd be happy to receive them! https://github.com/erasche/gxargparse So, what is it?

Re: [galaxy-dev] CloudMan + Ansible + AWS

2015-01-26 Thread Dannon Baker
Thanks for the pointer, this is great stuff and I had not seen it before. I’ve wanted to do something similar for a while now, and it’s becoming even more important as we loop in GCE.  I’ll definitely read through and play with this and see what we might be able to use, contribute back to,

Re: [galaxy-dev] CloudMan + Ansible + AWS

2015-01-26 Thread Brad Chapman
Enis, John and all; I spotted ansible-cloudman on GitHub today which reminded me I've been meaning to write about the approach we setup late last year to run bcbio on AWS. It uses elasticluster (https://github.com/gc3-uzh-ch/elasticluster) which has the advantage of being all Ansible scripts and