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Usage

refchef-cook

refchef-cook reads master.yaml and executes the commands that will retrieve and/or process the references, indices, or annotations.

usage:

refchef-cook [*arguments*]

arguments:

--help, -h         Show this help message and exit. 

--execute, -e      Executes the YAML file (master or new if specified).  

--append, -a       Will append commands to the master YAML.

--new, -n          Full path to the new YAML.      

--git, -g          Git commands to use, choose from `commit` or `push`.

--outdir, -o       Output folder where references will be stored. 

--git_local, -gl   Required, git folder where the `master.yaml` is stored.  

--git_remote, -gr  Remote git repository (in the format `user/project_name`). 

--config, -c       Path to config file (.yaml or .ini format).     

--logs, -l         Whether to save the log files.

examples:
1. This will read in new.yaml file, append to master.yaml and commit the changes using git: refchef-cook --config /path/to/cfg.yaml --execute --new new.yaml --git commit.
2. This will process master.yaml, commit and push changes to the remote repository:
refchef-cook --execute -o /path/to/output/dir --git_local /path/to/git/dir --git_remote user/project_name --git push.

Refchef-menu provides a way for the user to list all references present in the system, based on master.yaml, as well as filter the list of references based on metadata options. You must specify either --master, -m or --config, -c.

usage:

refchef-menu [*arguments*]

arguments:

--help, -h         Show this help message and exit. 

--filter           Field:value pair for filtering menu.    

--master, -f       Path to `master.yaml` file, needed if `-c` argument unused.    

--config, -c       Path to config file in .yaml or .ini format.    

--full             Will show full table (including files and their locations).    

--meta, -m         Return metadata for a specific reference.

example:
1 - This will look at all primary genome references available in the current system:
refchef-menu -f /Users/jwalla12/remote_references/master.yaml --filter component:primary

┌ 🐶 RefChef Menu ────────────────────────┬───────────┬───────────────────────────────────────────┬──────────────────────────────────────┐
│ name         │ organism                 │ component │ description                               │ uuid                                 │
├──────────────┼──────────────────────────┼───────────┼───────────────────────────────────────────┼──────────────────────────────────────┤
│ S_cerevisiae │ Saccharomyces cerevisiae │ primary   │ corresponds to ganbank id GCA_000146045.2 │ dff337a6-9a1d-3313-8ced-dc6f3bfc9689 │
└──────────────┴──────────────────────────┴───────────┴───────────────────────────────────────────┴──────────────────────────────────────┘