Fix setup.sh script and add check for samtools in PATH

[tinyheero]

This PR

• Fixes a bug in the setup.sh script where it doesn't update the hisat2 submodule and build it:
  • To commands git submodule init; git submodule update need to run from the root directory of the repository. The current setup.sh script changes to the hisat2 folder and then tries to run these commands throwing an error, which doesn't get caught by the script.
• Adds a small check for whether samtools is in the PATH or not and throws an error if not.

[chbe-helix]

Looks good! Thanks for the fix.