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: 84_cuffcompare_ramjan@usc.edu 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: 84_cuffcompare_ramjan@usc.edu 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 ----------------------------------------

...

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J.