I ran into the same problem twice : on my freshly installed local Galaxy server, Bowtie2, and RNA-Star couldn't finish because samtools is not found. I installed both tools through main tool shed and chose automatic dependency handling and installation seemed to go well. While an apparent solution to this is to locate the binary of the required package and manually add its path to system PATH variable, it doesn't seem to be a good solution because 1) from what it seems, tool dependency should be handled automatically. 2) Different program may only work with a certain version of samtools, for example, Bowtie2 requires samtools 1.2 while RNA-Star requires samtools 0.1.19. Setting PATH variable to force the two programs to use the same samtools just doesn't seem right.
So I came up with these two general questions :
1) Is tool dependency automatically handled when a new tool is installed in Galaxy? Or is manual setup usually necessary? How, especially to set up different tool dependencies for different tools? (How to make sure env.sh is run correctly by each program?)
2) In my case, I see that the env.sh file is actually located under tool_dependency/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f rather than tool_dependency/samtools/0.1.19 Is this supposed be correct? Since according to this post, the env.sh should be under tool_dependency_dir/name/x.y.z ?