Running the container as Singularity image

[moldach]

We've migrated to an air-gap system with no outgoing internet connection and I can no longer get MToolBox to work.

I filed an issue a month ago but haven't heard anything back (mitoNGS/MToolBox#96) so I'm trying to get a container solution working.

However, I need some help getting this to run: https://hub.docker.com/r/mitongs/mtoolbox

It's not clear to me how I can edit/provide-symlinks for analysis.tab, datasets.tab, reference_genomes.tab and provide the datasets to the container.

Question 1:

Can you please help show me how the syntax would look like for that?

Question 2:

I'm able to activate the mtoolbox conda environment from the Docker container:

$ sudo docker run -it mitongs/mtoolbox:latest
 :: MToolBox ::  / >>> source activate mtoolbox
(mtoolbox)  :: MToolBox ::  / >>> 

However, I'm not able to do so from the Singularity container?
Can you spot what I'm doing wrong?

$ sudo singularity build --sandbox mtoolbox.sif docker://mitongs/mtoolbox:latest
$ singularity run mtoolbox.sif 
Singularity> source activate mtoolbox
Could not find conda environment: mtoolbox
You can list all discoverable environments with `conda info --envs`.