rna-seek cache¶

1. About¶

The rna-seek executable is composed of several inter-related sub commands. Please see rna-seek -h for all available options.

This part of the documentation describes options and concepts for rna-seek cache sub command in more detail. With minimal configuration, the cache sub command enables you to cache remote resources for the RNA-seek pipeline. Caching remote resources allows the pipeline to run in an offline mode.

The cache sub command creates local cache on the filesysytem for resources hosted on DockerHub or AWS S3. These resources are normally pulled onto the filesystem when the pipeline runs; however, due to network issues or DockerHub pull rate limits, it may make sense to pull the resources once so a shared cache can be created and re-used. It is worth noting that a singularity cache cannot normally be shared across users. Singularity strictly enforces that its cache is owned by the user. To get around this issue, the cache subcommand can be used to create local SIFs on the filesystem from images on DockerHub.

Caching remote resources for the RNA-seek pipeline is fast and easy! In its most basic form, rna-seek cache only has one required input.

2. Synopsis¶

$ ./rna-seek cache [-h] --sif-cache SIF_CACHE \
                        [--dry-run] 

The synopsis for each command shows its parameters and their usage. Optional parameters are shown in square brackets.

A user must provide a directory to cache remote Docker images via the --sif-cache argument. Once the cache has pipeline completed, the local sif cache can be passed to the --sif-cache option of the rna-seek build and rna-seek run subcomand. This enables the build and run pipeline to run in an offline mode.

Use you can always use the -h option for information on a specific command.

2.1 Required Arguments¶

--sif-cache SIF_CACHE

Path where a local cache of SIFs will be stored.
type: path

Any images defined in config/containers/images.json will be pulled into the local filesystem. The path provided to this option can be passed to the --sif-cache option of the rna-seek build and rna-seek run subcomand. This allows for running the build and run pipelines in an offline mode where no requests are made to external sources. This is useful for avoiding network issues or DockerHub pull rate limits. Please see rna-seek build and run for more information.

Example: --sif-cache /data/$USER/cache

2.2 Options¶

Each of the following arguments are optional and do not need to be provided.

-h, --help

Display Help.
type: boolean

Shows command's synopsis, help message, and an example command

Example: --help

--dry-run

Dry run the pipeline.
type: boolean

Displays what steps in the pipeline remain or will be run. Does not execute anything!

Example: --dry-run

3. Example¶

# Step 0.) Grab an interactive node (do not run on head node)
srun -N 1 -n 1 --time=12:00:00 -p interactive --mem=8gb  --cpus-per-task=4 --pty bash
module purge
module load singularity snakemake

# Step 1.) Dry run cache to see what will be pulled
./rna-seek cache --sif-cache /data/$USER/cache \
                 --dry-run  

# Step 2.) Cache remote resources locally 
./rna-seek cache --sif-cache /data/$USER/cache