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Question: Reserved variable for conda env in XML?
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gravatar for asmariyaz23
4 months ago by
asmariyaz23 • 10
United States
asmariyaz23 • 10 wrote:

Hello,

Is there a reserved variable name like $__tool_directory__ for conda_prefix that can be accessed in the command section in an xml? A tool_script.sh is written when tool is executed which assigns the conda environment to a variable named $CONDA_DEFAULT_ENV. I would like to use that in the xml. How do I do this?

Thank you, Asma
reserved_variable conda xml • 206 views
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modified 4 months ago by Bjoern Gruening ♦ 5.1k • written 4 months ago by asmariyaz23 • 10
1
gravatar for Bjoern Gruening
4 months ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Asma,

we do not have such a variable. Please keep in mind that Conda is just one of many dependency resolvers, and a tool should be written in a way that it is independent of Conda. For example you could run your tool in Docker or Singularity without Conda.

What is your concrete use-case? You could use something like this instead:

export SAMTOOLS_PATH=`which samtools`
ADD COMMENT • link written 4 months ago by Bjoern Gruening ♦ 5.1k
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