I installed galaxy on Ubuntu and I try to keep it as simple as possible so do not use any other program in combination with galaxy. I followed all installation steps and managed to set-up the tools depency as described. However, I keep running into issues with various tools, (I managed to solve another issue related to samtools by installing it using sudo apt-get install samtools).
I completed the following accordingly: https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
I got completely stuck with the following: https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
By using realigner target creator I get error:
/bin/sh: 1: java: not found.
my $PATH seems to give incorrect results:
bash: /bin:/usr/bin: /usr/X11R6/bin:/usr/local/bin: File does not exist
I tried to do various adjustments to the path but did not seem to work OK.. Help would be greatly appreciated! and sorry but my knowledge is very limited, I am definitely no expert!
Many thanks in advance,