Changing maven package for protein-comparison-tool to shade

Rather than copy all the jars individually using the maven assembly
plugin, we use the shade plugin to combine them all into a single jar
file, then assemble that. Since all our dependencies are
lgpl-compatible, this should be OK.

This fixes #197.

I've also included improvements to the run scripts which let you run
them from any directory, not just the current one. Maven handles
replacing the jar filename at assembly time.

Finally, I changed the name of the assembly. They are now named like
'protein-comparison-tool-4.0.0.jar' rather than including a timestamp.
Merge pull request #198 from sbliven/master

Changing maven package for protein-comparison-tool to shade
Removing warnings
More #111
Removing ad-hoc logger verbosity control
Fixing #193
- also some improvement for #191: now a TranslationException will be
thrown when compound not known
- a few improvements for other issues: #111, #155, #185
Merge pull request #199 from josemduarte/master

Exception handling and logging improvements, solves #193
started to work on a parser for Phosphosite data (data under CCBY_NC) http://www.phosphosite.org
upgrading to latest log4j
added uniprot id pattern matching to fail-fast on wrong uniprot ids, added retrying netwrok request if id is not available immediately, bubbling-up the error codes in case uniprot servers are down
making access method public
corrected the fetch url, not writing into cache when cache directory not specified and breaking correctly after fetching the entry xml
changed CompoundNotFoundException into IllegalArgumentException, removed MalFormedUrlException, added RemoteException when failing to fetch the uniprot entry
Fixing test to fail only if CompoundNotFound, otherwise will go to error
Merge pull request #2 from josemduarte/fixToTest

Fixing test to fail only if CompoundNotFound, otherwise will go to error
Merge pull request #200 from parit/uniprotRMI

Improvements in fetching uniprot entry using uniprot accession id