I managed to fix my problem. I modified the CCAT wrapper to output the CCAT log file to Galaxy, then got this at the end: reading tag files...... 0 tags in L1, 0 tags in L2. tag file error! So there was an error when running the CCAT binary, but the CCAT wrapper thinks it succeeded and tries to move the output files. I looked at the CCAT source and it turns out it is returning 0 on error, which seems bizarre. The cause of the real error was my chromosome names were "1", "2", "Y", etc. instead of "chr1", "chr2", "chrY", etc. Kyle On Fri, Oct 12, 2012 at 3:59 PM, Kyle Chessman <knchess@gmail.com> wrote:

When running CCAT I get:

Error running CCAT. Traceback (most recent call last): File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 44, in <module> if __name__ == "__main__": main() File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 41, in main return stop_err( tmp_dir, e ) File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 15, in stop_err raise exception IOError: [Errno 2] No such file or directory: '/tmp/tmpc3sfYR/CCAT in Galaxy.significant.peak'

I'm using the latest galaxy-dist and have the CCAT binary in /usr/local/bin. Nothing gets put into the temp directory while CCAT is running.

Any ideas?

Thanks, Kyle