When we run cuffdiff from the command line we get this;

[galaxy@q ~]$ /bin/cuffdiff
/bin/cuffdiff: /usr/lib64/libz.so.1: no version information available
(required by /bin/cuffdiff)
cuffdiff v2.0.2 (3522)

It looks like we are using a more recent version of cuffdiff than is
supported by the galaxy tool wrappers (0.0.5 and 0.0.6).

Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in
runs that last for five days without terminating. Has this behavior been
seen before? How can we get good outputs to feed into cummeRbund?

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