Roary not using packaged executables

[bachev]

Hi there,

maybe this is due to preliminary status of Roary.

Bug report

The prepackaged download .tar.gz file on http://sanger-pathogens.github.io/Roary/ apparently comes with binaries for Linux and OSX. However, if the user does not actively take them up in the $PATH, Roary will not use them (and fail if there are no other versions of them in the $PATH).

Suggested resolution

Test whether a tool is in the current PATH (see #214) and if not, make sure the prepackaged version is used.

[andrewjpage]

Good spot!

The recommended installation method for the dependancies is using homebrew/linuxbrew, apt or from source.
I dont document that these binaries are available anymore (because as you point out in your other issue, they are a pain) but they have solved the odd installation issue in the past when other methods have failed. In the past I checked and used these bundled dependancies after the installed ones, but it proved to be unreliable in practice.

I would be leaning towards deleting them entirely to avoid confusion.
Andrew