Hi Carlos: After I replaced cuffcompare_wrapper.py & cuffcompare_wrapper.xml with code provided by Jeremy, now I can execute cuffcompare on my local galaxy. You can check following link: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 hope this helps. Best John Wu 1. Re: cuffcompare error in galaxy (Carlos Javier Borroto) ---------------------------------------------------------------------- Message: 1 Date: Mon, 20 Jun 2011 14:01:15 -0400 From: Carlos Javier Borroto <carlos.borroto@gmail.com> To: ??? <johnwu@ibms.sinica.edu.tw> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cuffcompare error in galaxy Message-ID: <BANLkTi=jtR88L_X5-SZpgnU4=oVqao=epQ@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combine d.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 ??? <johnwu@ibms.sinica.edu.tw>:

Dear galaxy team:

I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy?s RNA-seq tutorial.

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

I could run TopHat, cufflinks, and cuffdiff and got results correctly,

but when I executed cuffcompare through galaxy, the following error occurred:

Tool execution generated the following error message:

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

The tool produced the following additional output:

cuffcompare v1.0.3 (2403)

cuffcompare -o cc_output? -s /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1

and error messages in log file (galaxy.log) are:

galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched

galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: 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_398.dat

galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: 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_398.dat

galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c c_output to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i nput1.tmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i nput1.refmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c c_output.combined.gtf to /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:28,174

job 130 ended

I?ve tried to manually execute cuffcompare to analyze dataset_398.dat (which is the output of tophat) and I could get correct cuffcompare output.

$ cuffcompare -o cc_output? -s /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat

It seems that the coffcompare_wrapper might have something to do with this error?

Thanks in advance for your help!

Best

John Wu

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