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 316 from history id 2 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item

121: Cufflinks on data 92: gene expression

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:

Hi galaxy dev team:

I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

however, I encountered following error messages when I was trying to execute Cufflinks in galaxy..

----------------------------------------------------------------------------- job id: 106 tool id: cufflinks ----------------------------------------------------------------------------- job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cufflinks_wrapper.py --input=/home/galaxy/software/galaxy_dist/database/files/000/dataset_287.dat --assembled-isoforms-output=/home/galaxy/software/galaxy_dist/database/files/000/dataset_318.dat --num-threads="4" -I 300000 -F 0.05 -j 0.05 -b --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data ----------------------------------------------------------------------------- job stderr: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'

----------------------------------------------------------------------------- job stdout: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b

----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).