Getting CP2 running a batch job on Amazon EC2


#21

I would be happy to try your suggestion, but I’m stuck on an unrelated problem. I’m unable to compile cellProfiler from source.
I went here: CellProfiler Developer’s version installation for Linux
I downloaded the Makefile.CP2:

Then I launched the compilation like that:

I had a lot of outdated libs failling to download. I’ve updated the Makefile with the correct urls.
Now I’m facing this error:

[code]./xconfig -d s /root/soft/cellProfiler/tmp/ATLAS/x86_64/…/ -d b /root/soft/cellProfiler/tmp/ATLAS/x86_64 -Fa alg -fPIC -b 64 -Ss flapack /root/soft/cellProfiler/tmp/lapack-3.3.0/lapack_LINUX.a -Ss pmake ‘make -j4’ -Si cputhrchk 0

ERROR around arg 19 (cputhrchk).
USAGE: ./xconfig [flags] where flags are:[/code]
So I guess I’m not using the correct file/method to build cellProfiler from source and the wiki is maybe outdated.
Please be kind enough to give me any hint to be able to build from source.


#22

I would try using github.com/CellProfiler/CellPro … rofiler.sh instead.


#23

I just tested the above patch and can confirm it does indeed solve the problem. I can now initiate an analysis using the “-l” command and everything seems fine. Many thanks for your help.

I am still, however, unable to start an analysis using the “-g” flag as I described in my post above (Thu Feb 06, 2014) and get the same error [ValueError: The grouping keys specified on the command line (Metadata_Site, Metadata_Well) must be the same as those defined by the modules in the pipeline ()]. This isn’t really a problem for me as I was planning to use the -f and -l commands anyways for my analysis, but unless I am doing something wrong, there may be another bug lurking there somewhere that I wanted to bring to your attention.

In any case, thank you again for the patch and all your development work in general!

cscott


#24

Hi cscott,
Glad to hear at least one bug is fixed!

As for the ‘-g’ flag, would you first confirm this: if you run with the GUI, does the Groups module report the proper groups when you click the Update button?

Thanks,
David