[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

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

2015-09-11 Thread Bjoern Gruening
Hi Piotr, I guess you need to work a lot with symlinks. link all your Galaxy inputs to a temp folder, provide the path to the temp folder to KNIME + a path to a second tempfolder with the results and tell Galaxy to collect all files int the result folder. Cheers, Bjoern On 11.09.2015