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MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes
GNU General Public License v3.0
18 stars 4 forks source link

Add install script #63

Closed kristyhoran closed 1 year ago

kristyhoran commented 1 year ago

Additions to bohra to provide installation of dependencies as a option bohra init or bohra check will check for the presence of the correct environments and if not present install them. Also modified the name of the bohra envs to represent that they are for bohra (to prevent wierd clashes with users other envs). If the user does not provide a conda path then nextflow will simply default to generating the conda envs in the work directory - so will not fail.

Also addressed #61 so bohra results in printing of help - not a python error. NO CHANGES to accredited tools or versions.

kristyhoran commented 1 year ago

Approved by @abcdtree and @JA-Lacey