# Getting into sRNAtoolbox with singularity

## Getting and entering the container

> This starts off just on the regular log-in node, which is fine for getting the container at first, and jumping into it to look for things. But if trying to do any heavy processing, we'll want to be sure we are on a compute node – example in next section for doing that.

With singularity installed already (which is the case on our system):

# pulling the image and building container (only needs to be done once)
# this will put it in the current working directory
singularity pull docker://ugrbioinfo/srnatoolbox:latest

# entering the container (this is if it's in our current working directory, otherwise we'd need to provide a longer path to its location)
singularity shell srnatoolbox_latest.sif

Running that will change our prompt to signify we are inside, and we still have access to our files/directories.

There we'd want to test that their commands are present, but i don't know any of them yet. We can see we are in a different environment though:

# we can check our PATH (which in here will have much fewer directories)
echo $PATH | tr ":" "\n"

# and our python version in the container
python --version
which python

# then exit and check outside the container
exit
python --version
which python

As done above, typing `exit` gets us out of the container back to our normal environment.

## Switching to a compute node

Ideally we'll want to be on a compute node when doing things. We'd want to do this while *not* in the container yet. One way to switch to node via slurm is:

# check where we are first
hostname

# hop into one
srun --nodes=1 --pty bash

# check we are on a compute node
hostname

But sometimes if things are jammed up, that won't let us in. Saying something like queued and waiting for resources.

Once on the node, you'd need to still run the command to enter into the container like shown above.

## Finding things in the container

This [github issue](https://github.com/bioinfoUGR/sRNAtoolbox/issues/26) might be helpful for us finding things in the container.

The main sRNAbench jar seems to be here: `/srv/java/sRNAbench`.