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
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