Hi, trying to get my tools going, part 29. I have a Docker image with the latest Galaxy release, patched to fix the Conda install bug I found earlier, my tools are installed ok and I’ve added a few from the toolshed for good measure.
One of my tools requires R 3.0.2 which is installed ok. I also installed scatterplot from the toolshed which requires R 2.11; that is also installed ok by conda. However, I get this message when trying to run scatterplot:
Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.pyhttp://toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py", line 5, in <module> from rpy import * File "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py", line 134, in <module> """ % RVERSION) RuntimeError: No module named _rpy3002
RPy module can not be imported. Please check if your rpy installation supports R 3.0.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example:
>>> from rpy_options import set_options >>> set_options(RHOME='c:/progra~1/r/rw2011/') >>> from rpy import *
So it seems that rpy is installed and is aware of one version of R but not the other, and the other is being found (perhaps because it’s the default install in the Docker image?)
FYI my docker image recipe is here:
https://github.com/Alveo/docker-galaxy-alveo
and the image itself is here:
https://hub.docker.com/r/stevecassidy/alveo-galaxy/
Any pointers to the way forward appreciated.
Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy