geofetch container lacks samtools

[nsheff]

geofetch executes some other commands (prefetch, samtools). This means these must exist in the container.

geofetch -i accessions.txt -n paqc --m paqc_geo_metadata
WARNING: Bind mount '/home/ns5bc => /home/ns5bc' overlaps container CWD /home/ns5bc/code/paqc, may not be available
WARNING: Skipping mount /etc/localtime [binds]: /etc/localtime doesn't exist in container
Given metadata folder: paqc_geo_metadata (paqc_geo_metadata)
Initial raw metadata folder: /home/ns5bc/code/paqc/paqc_geo_metadata (/home/ns5bc/code/paqc/paqc_geo_metadata)
Final raw metadata folder: /home/ns5bc/code/paqc/paqc_geo_metadata/paqc (/home/ns5bc/code/paqc/paqc_geo_metadata/paqc)
For SAM/BAM processing, samtools should be on PATH.

solution 1: add all required tools into this container
solution 2: don't run this in a container; it's like a pipeline, and its commands run in a container, but it itself doesn't
solution 3: make this container link to the host docker

solution 3 is cool but is impossible with singularity from what I've read.

this same issue comes up, but with more pronounced, for pipeline software like pypiper -- it can run anything, so solution 1 isn't possible. thus, solution 2 is the only real possibility (or 3, but probably only with docker)