Thanks for taking an interest in our pipeline. We hope you find the resources we provide here useful in getting you set up to analyse and interpret your data.
To reference VESPA: https://peerj.com/preprints/1895/
Documentation is now hosted on ReadTheDocs
The main VESPA wrapper is written in Python, while the CodeML wrapper is written in Perl.
To begin, we recommend downloading a versioned tarball from the releases page.
Once downloaded, install as follows:
$ tar -xvzf VESPA.tar.gz
$ cd VESPA
$ chmod +x vespa.py
$ sudo mv vespa.py /usr/local/bin
Perl dependencies
VESPA requires several Perl scripts and modules to be fully operational.
The Perl dependencies may be found alongside vespa.py within the tarball.
The following will install these modules on most systems.
$ tar -xvzf VESPA.tar.gz
$ cd VESPA
$ chmod +x \*Codeml\*.pl
$ sudo mv \*Codeml\*.pl /usr/local/bin
$ sudo mv CodemlWrapper/ /Library/Perl/5.XX/
Note: Replace “5.XX” in the following command to the version of perl used by your system. (perl –v)
DendroPy
VESPA requires users to install the DendroPy Python library (version 4.0). Instructions for installing DendroPy
We have written a manual that will take you through the process step by step. This is constantly evolving with feedback with feedback from our users, and the latest version is hosted as vespa-evol on ReadTheDocs.
If you encounter an issue with VESPA, please open a GitHub issue and we'll do our best to help.