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