Error Installing Macs On Local Galaxy

Question: Error Installing Macs On Local Galaxy

6.1 years ago by

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.Dyczkowski@eni-g.de Phone: +49 (0)551 39-12352

macs • 1.6k views

ADD COMMENT • link •

modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.1 years ago by Jerzy Dyczkowski • 40

6.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: Jerzy.Dyczkowski@eni-g.de Phone: +49 (0)551 39-12352

ADD REPLY • link written 6.1 years ago by Jerzy Dyczkowski • 40

Solved it already. For future users' benefit: One should not add to the PYTHONPATH the MACS folder with libraries, but the longer address of the subfolder created by the installation: export PYTHONPATH=/xxx/xxx/xxx/xxx/MACS-1.3.7.1/lib/lib64/python2.6/site- packages:$PYTHONPATH best and thanks for help, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: Jerzy.Dyczkowski@eni-g.de Phone: +49 (0)551 39-12352

ADD REPLY • link written 6.1 years ago by Jerzy Dyczkowski • 40

Similar posts • Search »