installation issues ?

[parlar]

Hi Måns,

Thought I'd give genmod a go, but something seems to be failning when I execute it. This is the error (traceback) that I get:

[genetik@v01s979 genmod]$ genmod
Traceback (most recent call last):
  File "/usr/bin/genmod", line 9, in <module>
    load_entry_point('genmod==3.4', 'console_scripts', 'genmod')()
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 378, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2566, in load_entry_point
    return ep.load()
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "build/bdist.linux-x86_64/egg/genmod/commands/__init__.py", line 8, in <module>
  File "build/bdist.linux-x86_64/egg/genmod/commands/annotate_variant.py", line 35, in <module>
  File "build/bdist.linux-x86_64/egg/genmod/annotate_variants/__init__.py", line 3, in <module>
  File "build/bdist.linux-x86_64/egg/genmod/annotate_variants/read_tabix_files.py", line 3, in <module>
ImportError: cannot import name TabixError

Am I at fault here or is there some other issue?

cheers,

Pär L, Klin gen, Umeå

[moonso]

Hi Pär,

I'm glad to hear that you want to try it. Will have a look at this as soon as possible, We run genmod everyday but I haven't seen this error. What system are you using?

Måns

[moonso]

How did you install genmod? Was it successfull? It seems like you are missing pytabix, I know there has been some issues with pytabix on windows...

[parlar]

Solved! There was a conflict with a tabix module under CrossMap. Now, though, I just have to figure out how to avoid problems with CrossMap .... I'm not a python expert.

No need for the phone call now.

//Pär

[henrikstranneheim]

Use conda! http://conda.pydata.org/docs/

[parlar]

probably a good idea