This repository consists of a suite of R and Perl scripts performing the evolutionary SAAR analysis. The workflow is automatized and maintained by Snakemake software.
For the convenience of the portability and ease of use it is also distributed as a Docker container, which can be accessed at DockerHub repository.
1. Install the Docker software
The Docker installation guide can be found here
2. Downolad the container with the pipeline setup and all dependencies installed
(sudo) docker pull mstolarczyk/saarpipeline
3. Make sure the image is available
(sudo) docker images
The line above should output similar to the one presented below
REPOSITORY TAG IMAGE ID CREATED SIZE
mstolarczyk/saarpipeline latest 1142d796e7ad 3 minutes ago 6.27GB
4. Run the image
(sudo) docker run -it mstolarczyk/saarpipeline
5. Perform the analysis
The commands that will run the analysis are Snakemake commands:
snakemake <target file>
To test the part of workflow to be executed run
snakemake -np <target file>
The line above will show the execution plan instead of actually perform the steps. The -p flag instructs Snakemake to also print the resulting shell command for illustration
More details regarding the usage will be provided soon
After completion of the analysis exit the container
exit
6. Save the docker container state and copy the results
In order to pick up when you have left save the state of the container
(sudo) docker commit <container ID> <tag>
e.g. sudo docker commit 1bf3b5f36b94 mstolarczyk/saarpipeline_changed
(sudo)
To copy the results of the analysis use the Docker docker cp command, for more details see the website
docker cp [OPTIONS] CONTAINER:SRC_PATH DEST_PATH|-
docker cp [OPTIONS] SRC_PATH|- CONTAINER:DEST_PATH