lets.see the.data, i would be surprised if there was much cross hyb
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To: "Bidwell, Christopher A." <email@example.com>
Cc: "firstname.lastname@example.org" <email@example.com>
Subject: [galaxy-user] Latest supported Cufflinks?
Date: Mon, Oct 29, 2012 1:31 pm
Cufflinks 1.3 is currently supported. However, this may be
unrelated, or rather you may need so solve another problem first.
The error seems to be related to how you have the reference data set
up and some of the tool options you are using (bias correction = Y
?). Difficult to tell the root cause with the given data, but here
is the information for both so that you can troubleshoot. The goal
would be to make sure that the reference genome is in place with
indexes, it is in the builds.txt list and configured correctly, and
that the same genome is used for all steps in the analysis.
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Next time, posting to the firstname.lastname@example.org mailing list would
be best for questions about local instances.
On 10/29/12 12:42 PM, Bidwell,
I am interested in using Cufflinks 2.0
on our local instance of Galaxy but I am not sure if it is
supported yet. We did Galaxy update in early October and
we tried to install cufflinks V2.0 and it seems to run. I
get the output files and they have the genes listed but
0.000 for all results (using files that worked on previous
The output file summaries contain the
Info: ERROR: Unable to read builds
file: [Errno 2] No such file or directory:
ERROR: Unable to read builds file:
[Errno 2] No such file or directory: '/opt/galaxy/galaxy-d
Is there a fix for this error or do we
need to go back to the latest supported version of
Cufflinks and if so which version?
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