Hi Pablo, About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy – we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418
The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable. I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken too…. -John
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