Yeah, on most linux distros that I work with, I use apt or yum or rpm, or some other package management program...but in this case there will potentially (most likely) be no externel network access so none of those update programs would work.
I think in my case using PAR will definitely help with the perl dependencies. I think most of the Linux boxes I will be installing on will be redhat or fedora, which usually come with Apache,MySql and Perl but it would probably be best (as advised before) if I install in another set of directories.
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