Question: conda prefix galaxy local instance
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gravatar for amitpande74
7 months ago by
amitpande7410
amitpande7410 wrote:

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

conda galaxy • 229 views
ADD COMMENTlink written 7 months ago by amitpande7410
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