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Using BioShell Connecting to BioShell

BioShell uses SSH key authentication. Before your environment can be set up, you need to generate an SSH key pair and email the public key to the BioShell team. If you have not done this yet, follow the SSH key generation tutorial first.

Once your environment is provisioned, the BioShell team will email you your connection details.

Connect via SSH

You connect to BioShell over SSH (Secure Shell), so you will need an SSH client on your local machine. Most operating systems now ship with one built in, and a few graphical clients are also popular on Windows. Choose whichever suits your platform:

Platform SSH client
macOS The built-in Terminal app (Terminal.app) includes the ssh command.
Linux Your terminal emulator with the built-in OpenSSH ssh command.
Windows The built-in ssh command in Windows Terminal or PowerShell, or a graphical client such as MobaXterm, PuTTY, or an X server client.
Any platform Visual Studio Code with the Remote - SSH extension, which connects and lets you edit files and run terminals inside your BioShell environment.

Add an entry to ~/.ssh/config so SSH automatically uses your BioShell key without needing to specify it each time:

Host bioshell
    HostName <your-bioshell-ip>
    User <username>
    IdentityFile ~/.ssh/bioshell_key

Then connect with:

ssh bioshell

Or connect directly without the config entry:

ssh -i ~/.ssh/bioshell_key <username>@<your-bioshell-ip>

First login

When you connect for the first time you are greeted by the BioShell welcome message and land in your home directory:

Confirm where you are with pwd:

pwd

You should see your home directory path:

/home/<username>

Once you are logged in, verify the two things you will rely on most: the software file system (CVMFS) and your storage volumes.

Software and data access

BioShell delivers its bioinformatics tools and reference data through a read-only network file system mounted at /cvmfs/. Confirm the repositories are connected by running the probe command:

cvmfs_config probe

You should see OK for each repository:

Probing /cvmfs/data.galaxyproject.org... OK
Probing /cvmfs/singularity.galaxyproject.org... OK

You can also list the mounted repositories directly:

ls /cvmfs/

data.galaxyproject.org  singularity.galaxyproject.org
Repository Contents
singularity.galaxyproject.org Containerised bioinformatics tools from BioContainers
data.galaxyproject.org Reference genome builds and pre-built indexes

For how to find, install, and load tools from these repositories, see the Tools and reference data page.

Storage volumes

BioShell provides two storage locations:

Location Volume Purpose
/home/<username> Root volume (/dev/vda2) Your home directory: configuration, scripts, and installed modules.
/mnt/data Data volume (/dev/vdb) Your working data: analysis inputs and outputs.

Use lsblk to see how the volumes are laid out:

lsblk

NAME   MAJ:MIN RM SIZE RO TYPE MOUNTPOINTS
vda    253:0    0  30G  0 disk
├─vda1 253:1    0   1M  0 part
└─vda2 253:2    0  30G  0 part /
vdb    253:16   0 100G  0 disk /mnt/data

This shows your home directory on the root volume (vda) and your data volume (vdb) as a separate disk. Check the size and available space of your home directory with df:

df -hT /home/<username>/

Filesystem     Type  Size  Used Avail Use% Mounted on
/dev/vda2      ext4   30G   14G   15G  49% /

And your data volume:

df -hT /mnt/data

Filesystem     Type  Size  Used Avail Use% Mounted on
/dev/vdb       ext4  100G   28K   99G   1% /mnt/data

Interactive environments

Once connected, you can also open browser-based environments directly:

Environment URL
JupyterLab http://<your-bioshell-ip>:8888
RStudio http://<your-bioshell-ip>:8787

See the Interactive environments page for full setup instructions.