Overcoming objections to installing CP2 on a cluster


#1

Hello! We have previously used CellProfiler 1 with great success in our lab (http://www.sciencedirect.com/science/article/pii/S0022282811004755 by ) and are enjoying the improvements in version 2. We are going to be analyzing about 2.5 million 3-channel image sets, so we are working on installing CP2 onto the Linux cluster here (http://www.uvacse.virginia.edu/resources/itc-clusters/).

We love CellProfiler and haven’t experienced any problems with it, but we’re having a hard time convincing the personnel in charge of the cluster to be willing to install it. Part of the objection to installing either the prebuilt or the step-by-step version of CellProfiler was the following:

Do you have any comments that might help explain why the current installation process works the way it does, or advice regarding what might make the cluster personnel more willing to move forward with installation?

Many thanks!

Philip Tan
Cardiac Systems Biology Lab (Dr. Jeff Saucerman)
University of Virginia


#2

It’s certainly feasible to build CellProfiler yourself, if you prefer; several universities, institutes, and companies have done so for their clusters. Like any large, complicated system with many dependencies, the build process is complicated and time consuming. I wish we could streamline the build process more, but our resources are very limited. Also, some institutional users have wanted to customize the build (e.g., to use dotkit).

If the Makefile is not working for you and you find it hard to debug, we’ll do our best to help answer simple questions here on the forum. If you have (or want to sign up for) the CellProfiler Annual Support and Training Plan (cellprofiler.org/supportplan.shtml), we can get more heavily involved with build and configuration for your cluster.

As for the prebuilt RPMs, we provide them as a yum repository simply because there are so many RPMs. There are so many because we have a separate RPM for each dependency that CentOS 6 does not already provide. (As you know, CentOS 6 has old versions of many packages, and we need newer version.) We build them separately to simplify the build process and also to make download and installation more manageable. If you decide to use our prebuilt RPMs, you can maintain change control by making a local mirror of the yum repository. I have also included the URLs below in case you want to download the individual RPMs. Finally, you can rebuild the RPMs yourself. Let me know if you choose to go this route, and I can give you what you need.

cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm
cellprofiler.org/linux/cento … x86_64.rpm


#3

Thank you! This explanation was helpful. We’ll investigate the individual RPMs and see if the people running the cluster are more comfortable using those. If this doesn’t work, we’ll look into the other options you mentioned.

Thanks again!
Philip