Extend --make_config into --setup

ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

https://ewels.github.io/clusterflow/

GNU General Public License v3.0

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Closed ewels closed 9 years ago

ewels commented 9 years ago

At the moment, CF recommends that you manually add a bash alias to use qs and qsa instead of cf --qstat and cf --qstatall

Could be nice to get the cf --make_config wizard to look for these aliases using which and then append them to .bashrc if the user would like.

ewels commented 9 years ago

There's more we can do here..

[x] Rename --make_config to the more sensible --setup
[x] Check for a system level config file in the installation directory
- [x] If none there, copy the example file as a new config
- [x] Ask about the cluster environment and set this
- [x] Ask about environment modules, and set this (@ignore_modules)
[x] Do user level config file as usual
[x] Set up bash aliases if not there already and wanted