theodorross/gwas_tools repository overview

This image contains the following conda virtual environments:

• pyseer contains pySEER⁠, unitig-caller⁠, and unitig-counter⁠
• mandrake contains Mandrake⁠
• panaroo contains Panaroo⁠
• scoary contains Scoary⁠
• kraken2 contains Kraken2⁠
• fastbaps contains fastbaps⁠
• rhierbaps contains rhierBAPS⁠
• panstripe contains Panstripe⁠

In order to use any command within one of the included environments, use the following syntax: conda run -n <env> <command> <args>

Notes:

• All conda environments are the most recent available as of 7 September, 2022.
• the pySEER github repository is also cloned into the directory /pyseer to allow access to the annotation and postprocessing scripts found in /pyseer/scripts
• rhierBAPS and Panstripe (as of 2 September, 2022) are only available as r packages. So each of them are installed as such in their own conda environments.