Adding values that aren't file paths

[nsheff]

We recently removed the file checks on the seek function, which allows us to store things in refgenie that aren't file paths, like we are now doing for the bowtie2_index asset.

But it's still impossible to use add on a string that is not a filepath.

1. the value is called path:

refgenie add x/y
usage: refgenie add [-h] [-c GENOME_CONFIG] [-g GENOME] -p PATH
                    asset-registry-paths [asset-registry-paths ...]
refgenie add: error: the following arguments are required: -p/--path

2. It has to be a path, can't be an arbitrary string:

refgenie add x/y -p 1,500
Using 'default' as the default tag for 'x/y'
Traceback (most recent call last):
  File "/home/nsheff/.local/bin/refgenie", line 10, in <module>
    sys.exit(main())
  File "/home/nsheff/.local/lib/python3.7/site-packages/refgenie/refgenie.py", line 638, in main
    refgenie_add(rgc, asset_list[0], args.path)
  File "/home/nsheff/.local/lib/python3.7/site-packages/refgenie/refgenie.py", line 274, in refgenie_add
    format(abs_asset_path, rgc[CFG_FOLDER_KEY]))
OSError: Absolute path '/home/nsheff/code/refgenie_sandbox/x/1,500' does not exist. The provided path must be relative to: /home/nsheff/code/refgenie_sandbox

Should we change add to reflect the changes? I'd suggest:

1. change the name of the arg from path to value.
2. don't enforce that the path must exist or make it absolute

perhaps there could be a -p/--path flag that would flag your value as a path, and then behave as it currently does?

[nsheff]

PS Looks like they also use this capability in nextflow:

https://github.com/nf-core/tools/blob/ebf63095ab222e4df987c4e950ce3839e8784d3e/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/igenomes.config#L22-L23

so it's not just galaxy...