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bcgsc / orca

:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
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Documentation that Steve asked (for users) #42

Closed tmozgach closed 6 years ago

tmozgach commented 6 years ago

@sjackman could you please review the documentation that Steve asked, do I need add something more?

sjackman commented 6 years ago

Include link to this list of available software: http://formulae.brew.sh Describe a few useful paths, such as

/home/linuxbrew/.linuxbrew/bin
/home/linuxbrew/.linuxbrew/opt
/home/linuxbrew/.linuxbrew/Cellar
sjackman commented 6 years ago

I think we should describe how to mount their local home directory inside the ORCA container.

docker run -it -v $HOME -w $HOME bcgsc/orca
tmozgach commented 6 years ago 
Include link to this list of available software: http://formulae.brew.sh

but it is a list for homebrew for Mac? Should we add that?

sjackman commented 6 years ago

Yep, it's fine. Those formulae are available for both macOS and Linux.

tmozgach commented 6 years ago

@sjackman I didn't find exact definitions for those folders, could you please briefly describe?

/home/linuxbrew/.linuxbrew/bin
/home/linuxbrew/.linuxbrew/opt
/home/linuxbrew/.linuxbrew/Cellar
sjackman commented 6 years ago

/home/linuxbrew/.linuxbrew/bin includes the executables and scripts in your PATH. /home/linuxbrew/.linuxbrew/opt includes symlinks to the most recent version of each software package. /home/linuxbrew/.linuxbrew/Cellar includes all versions of the installed software packages.

tmozgach commented 6 years ago

@sjackman thanks! I edited the text.