Verify sha256sum checksums in planemo dependency_script

[peterjc]

In addition this fixes a problem trying to run the script without setting $DOWNLOAD_CACHE (documented as defaulting to ./download_cache) or if the local cache folder did not exist.

[peterjc]

This has been tested locally while updating the MIRA tool_dependencies.xml files:

peterjc/galaxy_mira@a7c7640
peterjc/galaxy_mira@7eb9dbe

Once incorporated into an official planemo release this would get tested on TravisCI via https://github.com/peterjc/galaxy_mira and (once I record more checksums in their tool_dependencies.xml files) my other repositories.

[jmchilton]

Thanks a bunch - I'll try to do a release today.

[peterjc]

Thanks John - I'll keep an eye on my TravisCI tool tests using planemo dependency_script once the next planemo release is out - just in case it flags are any side effects.

[peterjc]

Performance issue addressed in #541.

Also found this is missing checksum verification in the dep_install.sh from a download_file action, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/effectiveT3/tool_dependencies.xml