Hello. I am an undergraduate working on a tool very similar to Tophat. My question is probably very basic, but I am having issues displaying the output. I am assuming is giving me the failed run boxes, even though my tool completes execution and generates its files.

Note that I am not working on a cluster, as I am simply trying out galaxy with this tool.

I have modified universe_wsgi.ini "cleanup_job = onsuccess" to keep the output from being deleted due to the failure. Every file that is queued up in the history pane for each run appears in the working directory after execution, and I confirm successful runs with stdout and logs. If you click on the boxes in the history pane, you can download the output files correctly. I just cannot see previews of them or see them in the middle screen.


output in my tool XML is specified as follows:
<data format="sam" name="alignments" label="${tool.name} on ${on_string}: alignments" from_work_dir="mapsplice_out/alignments.sam" />

where mapsplice out is a sub directory created to contain all output of my command line tool. The reason I have it contained is because it runs its own combine and clean-up jobs before it is done executing, and you are left with logs. If you do not specify 'from_work_dir' in the output, the output files are there, but if you do specify, galaxy seems to be moving them into the database.

stderr prints: (also I am aware stderr causes galaxy failures, I have nothing printing to stderr)
"/home/XXXX/galaxy-dist/database/files/000/dataset_387.dat is fasta format"

which suggests to me that galaxy is trying to copy the contents of the output files into this particular file which is not what needs to happen. If I do not include the optional "from_work_dir" in the <data> tag I am not able to download the files that are created.

On the wiki, the output tag set says that " You specify the number and type of your output files using the contained <data> tags. You must pass them to your tool executable through using line variables just like the parameters described in the previous sections."
    For this, I have created variables to hold the output and pass them in the command string, but my tool takes no parameters to specify output. It simply creates various output files based on the parameters passed in. However it still runs regardless.

The preview I get after execution is the print to stdout (exact copy of the log) that indicate a successful run.

I apologize for the length, I am just trying to give most the helpful information. If more is needed, let me know. I am running my own instance of galaxy.

John P - Undergraduate Research
University of Kentucky Bioniformatics