Create repository for external apps - Linux Admin Experience

[sdhutchins]

We need to create a repository for the external apps we're using with this package for users to easily install them.
See ETE's repository

Apps to add:

• Guidance2
• Muscle
• ClustalOmega
• IQTree
• PhyML
• PAML
• Phylip
• Pal2Nal
• MAFFT

[grabear]

Others:

• Pal2Nal
• Mafft

[sdhutchins]

Thanks!

[grabear]

Binaries: http://www.lfd.uci.edu/~gohlke/pythonlibs/
ETE3 for Windows requires SciPi Binary installation, which rquires a special numpy installation.

[sdhutchins]

Created the repository https://github.com/datasnakes/external-apps

[sdhutchins]

Use https://github.com/etetoolkit/ete/blob/master/ete3/tools/ete_upgrade_tools.py for this package to make upgrading tools easy. It uses compile_all.

[grabear]

Once we start pipelining, we need to make sure this works. Shouldn't be too hard.

For a project that uses the full ProjectManagement capabilities, we can put everything in the top level:
(e.g. ~/Test-Repo/bin). Having everying in the top level bin, will make everything much less demanding on the systems hard drive space.