Hi Chris,
There is an update - I was in error about the supported Cufflinks
versions - this is 1.3.0-2.0.2 for all in the tool package.
Wiki corrected - Tool dependencies:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
Hopefully you have solved the problem! (did appear to be unrelated to
Cufflinks)
Take care,
Jen
Galaxy team
On 10/29/12 1:31 PM, Jennifer Jackson wrote:
Hello Chris,
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.
Data setup:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
Tool dependencies:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
More about distributions:
http://bitbucket.org/galaxy/galaxy-dist (source)
http://wiki.g2.bx.psu.edu/News (has RSS feed, all news)
http://wiki.g2.bx.psu.edu/DevNewsBriefs (only releases)
http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter
http://wiki.g2.bx.psu.edu/MailingLists
You can follow us on Twitter, watch the wiki/RSS feed or join the
galaxy-dev/user/annouce mailing lists to get notice when a new
distribution is released along with a News Brief describing key
updates and changes, including wrapper updates.
Next time, posting to the galaxy-...@bx.psu.edu mailing list would be
best for questions about local instances.
Thanks!
Jen
Galaxy team
On 10/29/12 12:42 PM, Bidwell, Christopher A. wrote:
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 version).
The output file summaries contain the following:
Info: ERROR: Unable to read builds file: [Errno 2] No such file or
directory:
'/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt'
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?
Thanks
Chris Bidwell
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please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
