Hello, Please don't set your bug report address (error_email_to in universe_wsgi.ini) to the user mailing list. This should be set to a local address at your site. --nate galaxy-user@lists.bx.psu.edu wrote:

GALAXY TOOL ERROR REPORT ------------------------

This error report was sent from the Galaxy instance hosted on the server "192.168.0.36:8080" ----------------------------------------------------------------------------- This is in reference to dataset id 377 from history id 2 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item

176: Cuffcompare on data 175: transcript accuracy

by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.

192.168.0.36:8080/history/view?id=f597429621d6eb2b ----------------------------------------------------------------------------- The user 'johnwu@ibms.sinica.edu.tw' provided the following information:

While executing cuffcompare, I encountered this error message:

Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'

I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data.

I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare.

how should i solve this problem?

thanks a lot! ----------------------------------------------------------------------------- job id: 126 tool id: cuffcompare ----------------------------------------------------------------------------- job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat ----------------------------------------------------------------------------- job stderr: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'

----------------------------------------------------------------------------- job stdout: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fa ./input1

----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/