1.1 SAW Installation via Singularity
! Please replace the red highlighted inputs with your own data path.
Step 1: Pull the SAW docker image (2 options)
$ singularity build SAW_v7.0.sif docker://stomics/saw:06.1.0 ## option 1
$ singularity build --sandbox SAW_v7.0/ docker://stomics/saw:06.1.0 ## option 2
For non-root users, especially who don’t have enough space in the /home/ directory, please try:
$ export SINGULARITY_CACHEDIR=/path/to/build$ singularity build --sandbox SAW_v7.0/ docker://stomics/saw:06.1.0
Step 2: Run pipelines (3 options)
Please Note! All the requested paths need to be mounted before input. For example, it is necessary to bind directories that store input files (/path/to/data), reference genome (/path/to/genomeDir), and outputs (/path/to/output).
$ export SINGULARITY_BIND="/path/to/data,/path/to/genomeDir,/path/to/output"
Option 1: Run pipelines within the container from the host system.
$ /path/to/SAW_v7.0.sif <application> ## option 1.1
$ singularity exec /path/to/SAW_v7.0.sif <application> ## option 1.2
Option 2: Shell into the SAW container and interactively run bash commands. Run exit to exit the environment.
$ /path/to/SAW_v7.0.sif /bin/bash ## option 2.1
Singularity>
Singularity> <shell-command>
Singularity> exit
$
$ singularity shell /path/to/SAW_v7.0.sif ## option 2.2
Singularity>
Singularity> <shell-command>
Singularity> exit
$
$ singularity shell SAW_v7.0 ## option 2.3 for sandbox
Singularity>
Singularity> <shell-command>
Singularity> exit
$
Option 3: Use “-B directory on the host-machine:directory in the container” to mount a host directory into the container and execute the command in the container.
$ singularity shell -B /path/to/directory/on/the/host-machine:/path/to/directory/mounted/in/the/container /path/to/SAW_v6.0.sifSingularity>
Singularity> <shell-command>
Singularity> exit
$
