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_ram...@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_ram...@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
>> ----------------------------------------
>> 
>> 
>> 
>> 
> 
>> _______________________________________________
>> galaxy-user mailing list
>> galaxy-user@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-user
> 
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user

J.



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