I've downloaded, compiled and installed HyPhy
I've copied the contents of the installation folder to .../galaxy-dist/tool-data/HYPHY
I've symlinked HYPHYMP in that folder to HYPHY
I uncommented the print statement in /usr/local/galaxy/develop/galaxy-dist/tools/hyphy/hyphy_nj_tree_wrapper.py and the standard output from running in Galaxy now reads:

Single Alignment Analyses
Error:
Could not read command file in ExecuteAFile.
Original path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/TemplateBatchFiles/chooseDistanceFormula.def'.
Expanded path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/TemplateBatchFiles/chooseDistanceFormula.def'
Function call stack
1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"chooseDistanceFormula.def" using basepath /tmp/.
Standard input redirect:
1 : TN93
2 : /galaxy_data/develop/files/000/dataset_285.dat
3 : /tmp/tmpuKVPrQ
-------
2 : InferTreeTopology(0)
Standard input redirect:
1 : TN93
2 : /galaxy_data/develop/files/000/dataset_285.dat
3 : /tmp/tmpuKVPrQ
-------
3 : ExecuteAFile from file "/tmp/tmpdu4x8_" using basepath /tmp/. reading input from _genomeScreenOptions
{"0":"/galaxy_data/develop/files/000/dataset_260.dat",
"1":"TN93",
"2":"/galaxy_data/develop/files/000/dataset_285.dat",
"3":"/tmp/tmpuKVPrQ"}
-------

Any help would be greatly appreciated!

Thanks!

Julian