Hi,
I have a local instance of galaxy )version 17.01) from github. I installed miniconda3 in my home directory. I want galaxy to use the conda executable from miniconda3 in my home directory. Accordingly, I set the galaxy.sample.ini configuration as :
conda_prefix is the location on the filesystem where Conda packages and environments are installed
IMPORTANT: Due to a current limitation in conda, the total length of the
conda_prefix and the job_working_directory path should be less than 50 characters!
conda_prefix = /home/amit/miniconda3
Override the Conda executable to use, it will default to the one on the
PATH (if available) and then to <conda_prefix>/bin/conda
conda_exec =home/amit/miniconda3/bin/conda
Pass debug flag to conda commands.
conda_debug = False
conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html)
the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8)
conda_ensure_channels = iuc,bioconda,r,defaults,conda-forge
Yet when I run galaxy it skips :
galaxy.tools.deps.conda_util WARNING 2017-06-22 16:04:17,838 Skipping installation of Conda into conda_prefix '/home/amit/miniconda3', since conda_exec 'home/amit/miniconda3/bin/conda' is set to a path outside of conda_prefix. galaxy.tools.deps.conda_util WARNING 2017-06-22 16:04:17,838 Skipping installation of Conda into conda_prefix '/home/amit/miniconda3', since conda_exec 'home/amit/miniconda3/bin/conda' is set to a path outside of conda_prefix.
Can someone help. Thanks