Question: Using Conda to resolve dependencies
gravatar for gkuffel22
7 months ago by
United States
gkuffel22170 wrote:


Do I need to change the galaxy.yml file to enable Conda? As I understood it the newer versions of Galaxy would be preconfigured to use Conda. I have read all of the documentation at but maybe I am confused with replacing the default with my own path? I see a directory <tool_dependency_dir>, but I cannot change into this directory. Do I need to modify the following line of code and enter my own path to Conda?

conda_prefix: <tool_dependency_dir>/_conda
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by gkuffel22170
gravatar for Bjoern Gruening
7 months ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

With a recent Galaxy version you don't need to configure anything to enable Conda. Galaxy will install miniconda3 for you in <tool_dependency_dir>/_conda. Can you check you see something in this path, after have run ./ at least once.

ADD COMMENTlink written 7 months ago by Bjoern Gruening5.1k

I guess that is my big problem. I don't know how to change directories into <tool_dependency_dir>/_conda. I do see conda installed at this path: /home/galaxy/galaxy/database/dependencies

ADD REPLYlink written 7 months ago by gkuffel22170

Ah, now I got it. tool_dependency_dir is another variable in your galaxy.yml file, that points you probably to /home/galaxy/galaxy/database/dependencies

ADD REPLYlink written 7 months ago by Bjoern Gruening5.1k

Ah, that makes much more sense. I am used to seeing variables like this $tool_dependency_dir instead of encapsulated in < >.

So my next question would be, do I have to modify the galaxy.yml file to define this variable as I have done below or does this come preconfigured?

# Path to the directory in which tool dependencies are placed.  This
  # is used by the Tool Shed to install dependencies and can also be
  # used by administrators to manually install or link to dependencies.
  # For details, see:
  # dependencies Set the string to None to explicitly disable tool
  # dependency handling. If this option is set to none or an invalid
  # path, installing tools with dependencies from the Tool Shed will
  # fail.
  tool_dependency_dir: /home/galaxy/galaxy/database/dependencies
ADD REPLYlink modified 7 months ago • written 7 months ago by gkuffel22170

Everything that is commented out, comes preconfigured with the variable in the commented out section.

ADD REPLYlink written 7 months ago by Bjoern Gruening5.1k
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