[galaxy-dev] Galaxy in Amazon

2015-08-19 Thread Ryan G
Hi all - We are running a local instance of Galaxy on our internal infrastructure. It seems to be going well. We've gotten to the point where we are ready to migrate our NGS data to Amazon for storage in S3. We are also looking at how Galaxy can be used in Amazon. Specifically, we are

Re: [galaxy-dev] Galaxy in Amazon

2015-08-19 Thread Enis Afgan
Hi Ryan, What you're suggesting to do is still somewhat experimental but we're continuing to work on it to make it more integrated into the Galaxy ecosystem and more robust. There are really three general approaches: 1. Run Galaxy via CloudMan 100% on AWS. This option is most robust and basically

Re: [galaxy-dev] Unable to run simple Docker tool

2015-08-19 Thread Mikel EgaƱa Aranguren
2015-08-19 15:50 GMT+02:00 John Chilton jmchil...@gmail.com: I don't know to be honest - a couple of things to verify. I wrote a bunch of debug stuff right away at the end of the e-mail and you can try if I am wrong, but after I wrote I realized the problem. You are not using sudo for

[galaxy-dev] Get dataset/API ids for a dataset

2015-08-19 Thread Asma Riyaz
Hello Galaxy-dev, I thank you so much for all the help you have given me. I have a question about data set ids in galaxy. As a background, I am running my own galaxy instance on a server. A pipeline implemented in the lab produces the following files in the history: 1) 2 BAM files 2) A JSON

Re: [galaxy-dev] Dataset Collections status

2015-08-19 Thread John Chilton
On Fri, Aug 7, 2015 at 8:01 PM, Keith Suderman suder...@cs.vassar.edu wrote: Greetings, I started pulling Galaxy code from the dev branch a few months ago to take advantage of the (then just emerging) dataset collections feature. However, it is not clear to me from the latest release notes

Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

2015-08-19 Thread Dave Clements
Hi All, Just a reminder that the next GalaxyAdmins online meetup is tomorrow, Thursday, August 20 https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_08_20 at your local time

Re: [galaxy-dev] Dataset Collections status

2015-08-19 Thread Suderman Keith
Hi John, I will try what we have against master. I just went through my old emails and it looks like the developer branch was recommended in response to a UI issue I experienced with large dataset collections and not the collections themselves. For reference, the UI issue occurred when I

Re: [galaxy-dev] new visualization tool for composite datatype?

2015-08-19 Thread Carl Eberhard
Yes, you can still use the framework to create interactive python-only visualizations. The simplest way to do this is form-based interaction. 1. The visualization mako page renders a form that contains the options the user can choose from 2. The user chooses and submits the form 3. Galaxy will