Execute a Snakemake workflow via Tibanna on AWS

Question

I am trying to execute the workflow of the Snakemake's official tutorial via Tibanna on AWS.

As instructed here,

1. I have installed Tibanna and set up environment variables.
2. Then I deployed Tibanna Unicorn to a folder snakemake-tutorial in a specific S3 bucket specific-bucket.
3. I set up the default unicorn.
4. As a last step, I run the following command:

$ snakemake --tibanna --default-remote-prefix=specific-bucket/snakemake-tutorial

However, I get an error at bwa_map rule. And the log says that:

/bin/bash: bwa: command not found
/bin/bash: samtools: command not found

For some reason, I am not able to use conda and/or packages.

Answer 1

I was able to solve this problem with the --precommand flag.

snakemake --tibanna --default-remote-prefix=sm-tut-test/sm --precommand="conda install -c bioconda bwa"

I am still investigating for an elegant solution though.

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Added later: I found a better solution using Integrated package management feature.