Hi all,
Could someone please point me to helpful ressources for installing HYPHY in
Galaxy?
- 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
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