Installing CP2 on RH


hopefully I am right here with my topic. I try to install CP2 on a Red Hat machine.

I did the following steps:

svn export

wget … kefile.CP2 --no-check-certificate

export HOSTTYPE=x86_64

make -f Makefile.CP2 PREFIX="/cs/CellProfiler"

make: *** No rule to make target /.tar.bz2', needed by/bin/pcre-config’. Stop.

I looked at the line
pcre: (PCREPREFIX)/bin/pcre-config (PCREPREFIX)/bin/pcre-config: (SRCDIR)/(PCREVERSION).tar.bz2

And it seems to me, that (PCREVERSION) is not set. But sadly I have no clue what should be the valued of (PCREVERSION).
It would be great if anyone could help me with this issue.

Many thank!

I simply copied the files from the repository and it worked for me. But sadly ilastik won’t work. Can anybody please help me with ilastik? I installed the current ilastik version from the ilastik homepage and all environment variabled are set correctly.

In I see the line

but the file doesn’t exist. CP runs without ilastik but we need “classify pixels”.

If I try to run ilastik with cellprofiler I get

python /cs/CellProfiler/ --ilastik Traceback (most recent call last): File "/cs/CellProfiler/", line 195, in <module> import ilastik ImportError: No module named ilastik

It would be great if someone could help us with this!


One of our other users, Nick Holway (username: nickholway), is or is associated with folks using ilastik on Red Hat (as indicated this issue on GitHub , and this forum post). He’s been willing to chime in at times. Perhaps you could PM him and ask how he installed it on his system?

It’s also worth noting that not any release of Ilastik will work with CellProfiler, as noted here.