[miso-users] MISO installation issue

[Yarden Katz]

Great to hear, I'm CCing the mailing list so that other users may find the answer if they run into the same issue.



On Jul 25, 2013, at 7:56 PM, Zhou Qi wrote:

> It is working! Thanks a lot!
> On Jul 25, 2013, at 12:23 PM, Yarden Katz <yarden at mit.edu> wrote:
> 
>> Hi,
>> 
>> It sounds like this might be a Python version difference between the root account and the user account.  When you log in as root versus as the user, and type:
>> 
>> $ python --version
>> $ which python
>> 
>> do you get the same version and same path to Python?  If not, just pick the path that's in the root account and place it first in your PATH environment variable.  Similarly for PYTHONPATH if needed -- you want to make sure that you are using the same set of Python packages read by the root Python.  This means that if you log in as root and do:
>> 
>> (as root)$ python
>>>>> import numpy
>>>>> numpy
>> 
>> You get the same path to numpy as you do when you log in as a user:
>> 
>> (as user)$ python
>>>>> import numpy
>>>>> numpy
>> 
>> --Yarden
>> 
>> On Jul 25, 2013, at 2:52 PM, Zhou Qi wrote:
>> 
>>> Dear MISO-users:
>>> 
>>> I have a silly question about installing MISO on a linux cluster. When I test the installation or test the MISO run, I can pass with root account but not with certain user's account. It says:
>>> 
>>> "Looking for required Python modules..
>>> Checking for availability of: numpy
>>> - Module numpy not available!
>>> Checking for availability of: scipy
>>> - Module scipy not available!
>>> Checking for availability of: json
>>> Checking for availability of: matplotlib
>>> - Module matplotlib not available!
>>> matplotlib is required for sashimi_plot
>>> Checking for availability of: pysam
>>> Total of 3 modules were not available. Please install these and try again.
>>> Looking for required executables..
>>> Checking if samtools is available
>>> - samtools is available
>>> Checking if bedtools is available
>>> - bedtools is available"
>>> 
>>> 
>>> "Traceback (most recent call last):
>>> File "test_miso.py", line 7, in <module>
>>>  import sam_utils
>>> File "/jbods/data00/zhouqi/soft/misopy-0.4.9/misopy/sam_utils.py", line 8, in <module>
>>>  from misopy.Gene import load_genes_from_gff
>>> File "/usr/local/lib/python2.7/site-packages/misopy/Gene.py", line 2, in <module>
>>>  from scipy import *
>>> File "/usr/local/lib/python2.7/site-packages/scipy/__init__.py", line 64, in <module>
>>>  from numpy import show_config as show_numpy_config
>>> File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
>>>  import add_newdocs
>>> File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
>>>  from numpy.lib import add_newdoc
>>> File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
>>>  from type_check import *
>>> File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
>>>  import numpy.core.numeric as _nx
>>> File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
>>>  import multiarray
>>> ImportError: /usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double"
>>> 
>>> 
>>> Can someone tell me how to add the dependent and miso packages into my path?
>>> 
>>> Thanks a lot!
>>> 
>>> Qi
>>> _______________________________________________
>>> miso-users mailing list
>>> miso-users at mit.edu
>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>> 
>