Thanks for replying.
So far, I’ve been asked to look at a few issues including an existing Prokka installation that didn’t work–which I fixed when I realized it’s basically just a conda environment so I just manually reinstalled the environment using conda.
Assemblystats, which turned out assumed gnuplot is always present: so I manually installed this, then edited the perl script to update $PATH. In this instance I can see many packages have a location under under ‘database/dependencies’ where often there is is an env.sh, though not in the case of Assemblystats (just wondering if there is a way to tweak an installation to make these kinds of changes).
At the moment I’m going round in circles over a gatk installation (from toolshed.g2.bx.psu.edu, avowinkel, b80ff7f43ad1). It’s listed as ‘Installed, missing tool dependencies’–seem to be problem with package_r_for_gatk_3_4_0, which seem to have some issue with R 3.1.2. When I tried to ‘Activate or reinstall repository’ via the ‘Repository Actions’ button, all I get after a long-ish delay is the message ‘There is no repository being installed’.
Hence I wish to get a better understanding about how the process works under the hood.