It turns out this problem may also arise from a mismatch between the version of Cuffcompare that Galaxy expects and the version of Cuffcompare actually present on the system.
Specifically, up to galaxy-central changeset 4789:d258d5bf9843, Galaxy expects Cuffcompare version 0.9.2 or lower. If you were using Cuffcompare version 0.9.3, you would get this error. As of galaxy-central changeset 4780:8273a8243639, Galaxy expects and works correctly with Cufflinks/Cuffcompare version 0.9.3 You can get this changeset by pulling directly from our in-development repository at: http://bitbucket.org/galaxy/galaxy-central or by waiting for our next stable release, which should hopefully be out later this week. Thanks, J. On Dec 24, 2010, at 11:09 PM, Nate Coraor wrote: > Hi, > > Because your cuffcompare tool runs on a cluster, please ensure that > $TEMP on your Galaxy server is set to a directory which is shared across > the cluster. By default temporary files will be created in /tmp, and > this directory is local to each system. > > --nate > > vasu punj wrote: >> I get the error message run Cuff compare with Cufflinks- GTF file and >> Ensembl file downloaded to Galaxy. To download Ensembl file Is used >> following procedure: >> Get Data --> UCSC Main >> select clade/genome/assembly >> for group, use 'Genes and Gene Prediction Tracks' >> for track, use Ensembl >> for table, choose the default (enGene) >> region: genome >> output format: GTF >> >> The error message is:Error in cuffcompare: >> [Errno 2] No such file or directory: >> '/tmp/9935868.hpc-pbs.usc.edu/tmpGXnESn/input1.tmap' >> Begin PBS Prologue Thu Dec 23 16:29:09 PST 2010 >> Job ID: 9935868.hpc-pbs.usc.edu >> Username: ramjan >> Group: hsc-ar >> Name: [email protected] >> Queue: laird >> Shared Access: yes >> Nodes: hpc2712 >> TMPDIR: /tmp/9935868.hpc-pbs.usc.edu >> End PBS Prologue Thu Dec 23 16:29:09 PST 2010 >> ---------------------------------------- >> Warning: no access to tty (Bad file descriptor). >> Thus no job control in this shell. >> ---------------------------------------- >> Begin PBS Epilogue Thu Dec 23 16:29:21 PST 2010 >> Job ID: 9935868.hpc-pbs.usc.edu >> Username: ramjan >> Group: hsc-ar >> Job Name: [email protected] >> Session: 29712 >> Limits: neednodes=1:ppn=8,nodes=1:ppn=8,walltime=100:00:00 >> Resources: cput=00:00:09,mem=62512kb,vmem=288372kb,walltime=00:00:12 >> Queue: laird >> End PBS Epilogue Thu Dec 23 16:29:21 PST 2010 >> ---------------------------------------- >> >> >> >> > >> _______________________________________________ >> galaxy-user mailing list >> [email protected] >> http://lists.bx.psu.edu/listinfo/galaxy-user > > _______________________________________________ > galaxy-user mailing list > [email protected] > http://lists.bx.psu.edu/listinfo/galaxy-user J.
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