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Overview

Since November 2018 it's mandatory to custom install the Ricopili pipeline. Please follow custom installation document. (this is regularly updated).

Requirements

After installation please have a look at the section Required Computation Skills. Most topics are probably familiar to you but we still recommend going through them to refresh your knowledge.Some familiarity with Unix is required to successfully install Ricopili. The trickiest step is adding a directory to the default search path in a Unix/Linux environment, which should be done permanently if possible. Otherwise, you will have to add the directory with the Ricopili binaries to your search path every time you start a new login session.

Helpful Tips

- For Broad users, $HOME/.my.bashrc and $HOME/.my.cshrc are hidden files in your home directory on Broad that allow you permanently add paths to the search path. Note .my.bashrc is different than .bashrc and .my.cshrc is different than .cshrc. NEVER modify .bashrc or .cshrc files.

- You can determine which shell you are using with this command:

env | grep SHELL

- To see hidden files, use the following command:

ls -la .

- To find out the full path of the current directory, use the following command:

pwd

- To edit a file while viewing it in text editor vim, press "i". To write changes (save) and exit, press escape followed by ":wq". To exit without saving any changes press escape then ":q"