Travis-CI builds fail for pal_finder tool (Galaxy 17.01)

[pjbriggs]

The Travis-CI builds are now failing for the pal_finder tool, see:

https://travis-ci.org/fls-bioinformatics-core/galaxy-tools/jobs/197609334

This has first been observed with Galaxy 17.01 release but the problems might predate this release. All the tests fail.

The logs contain multiple occurrences of

|  ### Running filtering & assembly script ###
|  File "/home/travis/build/fls-bioinformatics-core/galaxy-tools/tools/pal_finder/pal_filter.py", line 129
|  print "\n~~~~~~~~~~"
|  ^ 
| SyntaxError: Missing parentheses in call to 'print'

which looks like a Python 3 error trying to run the pal_filter.py utility.

There might also be issues with the Perl version but it's not clear if these are causing errors or are just warnings:

Use of uninitialized value $ampedLoci in concatenation (.) or string at /home/travis/build/fls-bioinformatics-core/galaxy-tools/test.tool_dependencies.pal_finder/pal_finder/0.02.04/bin/pal_finder_v0.02.04.pl line 718.
Use of uninitialized value $ampedBases in concatenation (.) or string at /home/travis/build/fls-bioinformatics-core/galaxy-tools/test.tool_dependencies.pal_finder/pal_finder/0.02.04/bin/pal_finder_v0.02.04.pl line 718.

[pjbriggs]

Fixed with migration to conda (PR #49).