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Published 20 hours ago • verified publisher icon bgruening

R Missing from latest Galaxy Docker container?

Open mryaninsilico opened this issue 7 years ago • 3 comments

Our tools use R and have always run when installed on the stable galaxy docker container. With the latest version, R seems to be missing. Was this changed?

mryaninsilico avatar Jan 24 '18 14:01 mryaninsilico

Hi @mryaninsilico, R was never installed in this image, instead Galaxy is able to pull down the dependencies during tool-installation or tool-run time. Which Galaxy flavor are you using or which tool does not work?

bgruening avatar Jan 24 '18 15:01 bgruening

@bgruening Thanks for the quick reply. We build an image starting with docker-galaxy-stable and then add our NG-CHM heatmap tools to create a docker galaxy image with our tools already installed. The tool runs a shell script that calls R and some other things. On previous images it worked fine but now fails because R is not installed. I will just add an apt-get install R-base to our docker make file.

mryaninsilico avatar Jan 24 '18 16:01 mryaninsilico

We really did not changed anything in regards to R. Does your tool contains a <requirement type="package" version="3.4.1">r-base</requirement> field? If so this should be installed automatically.

Are you installing from the Tool Shed?

bgruening avatar Jan 24 '18 16:01 bgruening