weave cache

Objective¶

The weave pipeline utilizes a number of large file resources including containers, reference genomes, reference databases, and indexes. This command allows for the user to download all these files serially in one-shot. This execution method will updated to include a parallel cluster option for faster execution.

Execution¶

Example command¶

# starting from install
./weave cache ./output_directory/

Output¶

Warning: cache download only implemented in serial local mode currently
Getting docker resource bcl2fastq...
...singularity output...
Getting docker resource weave...
...singularity output...
Getting web resource kraken...
...progress bar...
Getting web resource kaiju...
...progress bar...
Cache downloads complete!

Contents¶

The current contents of what all is downloaded via the cache command are:

1. All pipeline containerized images in read-only Singularity Image Format (SIF)
2. Kraken2 kmer databases
3. Kaiju kmer databases
4. FastQ_Screen genome indexes