[galaxy-dev] docker-galaxy image with custom tools as new container?

2015-09-04 Thread Piotr Grabowski
Dear Galaxy-Devs, I am currently developing a tool/workflow based on KNIME platform for data analysis. The plan is for my group to publish this tool at some point and we decided that Galaxy might be a very good platform to base it on. Galaxy could simply run KNIME on a server (along with R script

[galaxy-dev] custom tool - accessing user's data in bash script

2015-09-11 Thread Piotr Grabowski
Hello Galaxy Devs and Deployers! I have a rather basic question about how to handle custom tools in Galaxy (I'm fresh to this framework). I am trying to link my local Galaxy with KNIME workflow that we developed in our group. I am trying to link it via a bash script that is running headless KNIME

[galaxy-dev] simplifying Galaxy interface to the max (zen-like)

2015-09-14 Thread Piotr Grabowski
Dear Galaxy-Devs, I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a list of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute. Ev

Re: [galaxy-dev] simplifying Galaxy interface to the max (zen-like)

2015-09-15 Thread Piotr Grabowski
xy to emphasize certain > workflows would be RNA Rocket (http://rnaseq.pathogenportal.org/). > Checkout out their paper here - > > http://bioinformatics.oxfordjournals.org/content/early/2015/02/02/bioinformatics.btv002.long > . > > -John > > > On Mon, Sep 14, 2015 a