Benjamin Cohen

Thank you @aquaskyline and @JasonCLEI . I'm running on docker using the following command: ```docker run -i -v {INPUT}:{INPUT} -v {OUTPUT}:{OUTPUT} hkubal/clairs-to:latest /opt/bin/run_clairs_to --tumor_bam_fn {INPUT_BAM} --ref_fn {GENOME_REF} --thread 8 --platform...

That's true, but it's called in [report_binaries()](https://github.com/nanoporetech/medaka/blob/master/medaka/__init__.py#L89), which will throw an error if anything is missing, preventing the script from running.

Update: By installing all of the tools using `apt` (as opposed to manually installing them), they are now all detected except for `samtools`. I have uninstalled and reinstalled `samtools`, but...