NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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Use option -a2t for malt-build for version compatibility #33

Closed percyfal closed 2 years ago

percyfal commented 2 years ago

That was the first attempt but it will fail for conda environments due to the simple fact that the environment is not activated when the function is called. Putting it in a wrapper ensures the environment is active.

Another alternative I thought of yesterday would be to use the script directive. Then, the conda environment will be active, and the entire build command wrapped in a script (e.g. scripts/malt-build.py) with the following modification to the rule:

script: "scripts/malt-build.py"