Hi Jennifer,
I am now trying to run MACS 1.3.7.1. in Galaxy.
I also ran python setup.py install and set variables $PATH and
$PYTHONPATH for the commandline run. Nevertheless, MACS gives error:
/ImportError: No module named MACS.OptValidator/
I checked - library OptValidator.py exists in the file system, and path
to the folder is both in $PATH and $PYTHONPATH
Any ideas?
best regards,
Jerzy
On 10/17/2012 04:18 PM, Jennifer Jackson wrote:
Hello Jerzy,
The MACS wrapper in Galaxy currently supports version 1.3, which
explains the problems with 1.4. Tool dependencies are noted on this wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
For the other errors, are you trying to run MACS on the command line
or within Galaxy? For command line, some environment variables need to
be set up, the MACS documentation has the details:
http://liulab.dfci.harvard.edu/MACS/INSTALL.html
Hopefully this helps,
Jen
Galaxy team
On 10/17/12 2:09 AM, Jerzy Dyczkowski wrote:
Hello,
I cannot run MACS on the local Galaxy. When I install MACS version 1.4.,
it gives error something like cannot find macs. When I install version
1.3.7.1 it gives error /line 34, in module from MACS.OptValidator
import opt_validate ImportError: No module named MACS.OptValidator/
I sourced PATH to the directory with this module. Any ideas?
best regards,
Jerzy
--
Dr Jerzy Dyczkowski
Bioinformatician
Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
Grisebachstr. 5
D-37077 Göttingen
Email:jerzy.dyczkow...@eni-g.de
Phone: +49 (0)551 39-12352
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--
Dr Jerzy Dyczkowski
Bioinformatician
Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
Grisebachstr. 5
D-37077 Göttingen
Email: jerzy.dyczkow...@eni-g.de
Phone: +49 (0)551 39-12352
___
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/
