Installation cellprofiler on ubuntu


#1

Hi, I am trying to install cellprofiler 2.2.0 on ubuntu locally but when I run the following command, ```
pip install --user --editable .

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/export/home1/users/biocomp/weill/CellProfiler/setup.py", line 279
        for ext in ".ui", ".png"])]
                        ^
    SyntaxError: invalid syntax

Do you have any ideas? 
Thanks 
Solene

#2

Hm, other may know better than me.

But which python version are you using?

And can you try:

pip install --upgrade --user --editable .


#3

Thank you for your help. I found the solution, I had to use pip2.7 because I have both pip2.7 and pip3 and by default everything was done with python 3. But Now I have new problem with ilastik. I cannot launch cellprofiler:

Exception fetching new version information from http://cellprofiler.org/CPupdate.html: HTTP Error 404: Not Found
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/usr/local/src/CellProfiler/cellprofiler/modules/classifypixels.py”, line 71, in
from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/usr/local/src/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py”, line 70, in
import ilastik_main
ImportError: No module named ilastik_main
Failed to stop Ilastik

Do you have ideas of what I can do? I tried downloading some ilastik package but didn’t have luck.

Thank you,
Solène


#4

That error is a known bug in 2.2, but shouldn’t stop you from running CellProfiler- you don’t get any error message after that or any output window?


#5

Hi,
I know there was some error about Ilastik and that shouldn’t be a problem but no I do not have nothing after this error and no output window…


#6

Hi, @solene:

Try running:

$ python2 CellProfiler.py --log-level=DEBUG

from the CellProfiler directory and paste the output.