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.