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 'joh...@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). ___________________________________________________________ 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/
