let me slightly depict the described compilation problems – actually, I’m installing the josefjar’s CP within our grid environment – in more detail.
Our infrastructure runs Debian 6/7 clusters – for the first attempt, I’ve tried to use the Makefile.CP2.ubuntu.64 and follow the compilation steps described at github.com/CellProfiler/CellPro … -for-Linux . And using this, I run into the problems described by JosefJar (there were also several compilation problems, which I managed to overcome). In fact, the file CpmeasurementsXXXXX was created, however with no content (and that coused the error).
Nevertheless, based on your reactions, I’ve tried the Makefile.CP2.64 compilation – now, the compilation went more smoothly, and I managed to prepare much more stable/better version.
Now, I’m facing hopefully a last problem – when starting CP (Version: 2014-06-14T17:02:06 4e6ec2c / 20140614170206), it shows:
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 "/afs/ics.muni.cz/software/cellprofiler/2.1.0/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 81, in <module>
ImportError: No module named ilastik_main
Does anybody know where the problem could be? I’ve tried different versions of ilastik with no luck. It seems to me that there’s something wrong with the ilastik_pixel_classification.py script…
Thanks a lot for your hints.
PS: For David: in the future, we’ll definitely prepare the workflow based on batch jobs. However, since our infrastructure supports interactive jobs as well (including the ones with GUI apps), we’re currently testing the installation this way. Once we overcome all problems, we’ll try to optimize the whole processing workflow – so, thank you very much for your hints, we’ll definitely use them…