On Sep 10, 2012, at 6:29 PM, Julian Pradinuk wrote:
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'
Hi Julian,
Did you copy the TemplateBatchFiles directory to the installation directory from the source directory? The buildFromSVN.sh script contains the following:
cp -R trunk/{ChartAddIns,DatapanelAddIns,GeneticCodes,Help,SubstitutionClasses,SubstitutionModels,TemplateBatchFiles,TopologyInference,TreeAddIns,UserAddIns} $installDirectory
--nate
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: