John, Questions about local installs are best directed to galaxy-dev, so I've moved the question to this list.

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While executing cuffcompare, I encountered this error message:

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

I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data.

I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare.

how should i solve this problem?

thanks a lot!

A recent change set has made Cuffcompare compatible with v1.0.3: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 You'll need to update your Galaxy instance with this change set for Cuffcompare to work; also note that the change set is in galaxy-central, not galaxy-dist. Best, J.