1. SAW Docker Image Installation
SAW is delivered as a docker image that bundles all of its required software dependencies. You can pull the SAW docker image from Docker Hub to your local system and run analyses offline.
Please download the latest version of the software and use it with the corresponding Stereo-seq Analysis Workflow Software Suite User Manual version.
We support using Singularity and Docker to install and run the SAW. Here we take SAW version 5.5.3 as an example.
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_v5.5.3.sif docker://stomics/saw:05.5.3 ## option 1
$ singularity build --sandbox SAW_v5.5.3/ docker://stomics/saw:05.5.3 ## 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_v5.5.3/ docker://stomics/saw:05.5.3
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_v5.5.3.sif <application> ## option 1.1
$ singularity exec /path/to/SAW_v5.5.3.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_v5.5.3.sif /bin/bash ## option 2.1
Singularity>
Singularity> <shell-command>
Singularity> exit
$
$ singularity shell /path/to/SAW_v5.5.3.sif ## option 2.2
Singularity>
Singularity> <shell-command>
Singularity> exit
$
$ singularity shell SAW_v5.5.3 ## 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_v5.4.0.sifSingularity>
Singularity> <shell-command>
Singularity> exit
$
1.2 SAW Installation via Docker
Step 1: Pull the SAW docker image
$ docker pull stomics/saw:05.5.3
Step 2: Run pipelines
$ docker run -d -v /path/to/data:stomics/saw:05.5.3 /bin/sh -c "<shell-command>"
2. SAW GitHub
Please visit GitHub for instruction regarding the installation of singularity and indexing reference genome. The page also provides SAW shell script examples for users.
Please Note! Please build your reference before running SAW analysis.
3. SAW Test Data
SAW test data can be downloaded from SAW GitHub page. Key outputs are shown in Chapter 3 Test Data Demonstration. The reference genome version for SAW testing is:
- genome-build: GRCm38.p6
- genome-version: GRCm38
- genome-date: 2012-01
- genome-build-accession: NCBI:GCA_000001635.8
4. SAW Output File Format
Please check Stereo-seq File Format Manual to get more information on SAW output file format.
