timkahlke/LongRead_tutorials

Installation of packages, tools and data

Closed this issue · 4 comments

rachko1 commented

after running the following command as per your tutorial:
sudo bash ~/Downloads/install_script.sh
and 1 h later (appeared successful installation) i reopened terminal and typed:
guppy_basecaller --print_workflows
i got the message:
" guppy_basecaller: command not found"
any inputs are welcome. All of the above i have run in my stand alone Ubuntu 20.04 laptop

timkahlke commented

Hi rachko1,

This has happened before when trying to install it outside the VM on a 20.04 system. I'm not exactly sure which dependency it is that breaks it but it does. I think there was also a problem with a missing directory that is required but not created under 20.04. Not only that, guppy will not be the only tool that's not properly installed.

A quick but rather annoying fix for you is the following:

  1. Check each tool/software by typing "which TOOL" on the command line (where TOOL is the name of the tool you check). If it's installed properly it will show you a path. Otherwise it won't show anything

  2. For those tools that are not properly installed it was enough to

  • open the install_script.sh
  • look for the lines that install the particular script (each tool install should have a comment line starting with # and it's name before the install commands)
  • copy-paste them to the command line (potentially with a leading "sudo")

This should either install them nicely or at least tell you why they don't install.

I will leave ticket open and at one point will debug this properly although it's not actually part of the tutorial.

rachko1 commented
timkahlke commented

Hmm, that's a little cryptic. Only thing I can think of is to check whether pip3 is actually installed ... or trying to call it without sudo (as pip should usually be called).

rachko1 commented