Error during installation

[jerowe]

[root@6d3896cca719 metAMOS-1.5rc3]# python INSTALL.py core
<<Welcome to metAMOS install>>
Traceback (most recent call last):
  File "INSTALL.py", line 68, in <module>
    import workflow
  File "/anaconda/conda-bld/work/metAMOS-1.5rc3/src/workflow.py", line 8, in <module>
    from utils import readConfigInfo
ImportError: cannot import name readConfigInfo

If I just do

python setup.py build
python setup.py install

Running initPipeline.py (not initPipeline, btw, as it says in the docs)

[root@6d3896cca719 metAMOS-1.5rc3]# initPipeline.py 
Traceback (most recent call last):
  File "/anaconda/bin/initPipeline.py", line 4, in <module>
    __import__('pkg_resources').run_script('metAMOS==1.0b0', 'initPipeline.py')
  File "/anaconda/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script
  File "/anaconda/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/anaconda/lib/python2.7/site-packages/metAMOS-1.0b0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/initPipeline.py", line 13, in <module>

ImportError: No module named workflow

[skoren]

The install will copy initPipeline.py to initPipeline, you shouldn't be running initPipeline.py, that won't (and shouldn't) work.

My guess is you have a conflicting package that is being loaded instead of metAMOS's utils package. Try adding

import utils
print utils.__file__
import workflow
print workflow.__file__

on lines 67-68 in INSTALL.py. It should be

/anaconda/conda-bld/work/metAMOS-1.5rc3/src/utils.py
/anaconda/conda-bld/work/metAMOS-1.5rc3/src/workflow.py

If it's not try updating your python path to remove the offending utils package and try again.

[skoren]

Closing, inactivity