Hi,
I wrote a pipeline (xml attached) that, from what I can gather, succeeds, but galaxy shows it as an error and doesn't make the output file accessible as a new data set.
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured the output, but in the display of the web browser, it just shows up in the error state. The script being run exits (0) on success. Any ideas?
Here's what the output section of my xml file looks like:
<outputs> <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: coord-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/> </outputs>
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job dispatched galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453 executing: alignReads.pl --target /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat -o alignment --aligner bowtie --single /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat --seqType fq
galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam to /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat as directed by from_work_dir
Again, as far as I can tell, everything worked - but the browser doesn't think so.
I've run the exact command above on the command-line, and it exits(0) indicating success. Also, I've verified that when run through my galaxy instance, the galaxy-relocated output file is as expected.
Many thanks for your help. I'm still getting my feet wet with galaxy, reading through all the documentation and searching the mailing list for additional help.
best regards,
-brian