Docker installation and --file-list

Hi.
Short mention to tell you guys how much I like cellprofiler. I use it for years now and its great!
So great I want to install a modest Linux server running cellprofiler pipes remotely. Without going into the details, I want to send to the server, through a socket orders to analyze a list of images using a specified Pipe. So the option that is interesting to me is –file-list, which I read replaces –image-set-file. I guess I could use –data-file, but the module LoadData seems to be deprecated.
It all looks to me like I should setup a docker installation. And here is where I get confused.

I created two docker images, one by pulling cellprofiler/cellprofiler from the oficial docker repository:

$docker pull cellprofiler/cellprofiler
and another one by building from your github repository

$docker build -t cellprofiler .
That looks fine:

# docker images REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE cellprofiler latest 9746f9cd5bd8 4 minutes ago 1.408 GB centos centos6 a30bc9f3097e 8 days ago 215.8 MB cellprofiler/cellprofiler latest e005e0a4e4b5 5 weeks ago 1.927 GB

However, when I run the proposed tests, the –file-list option is not working.

[code][root@localhost CellProfilerTest]# mkdir input
[root@localhost CellProfilerTest]# cd input/
[root@localhost input]# curl -O http://cellprofiler.org/svnmirror/ExampleImages/ExampleHumanImages/ExampleHuman.cppipe
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 17033 100 17033 0 0 17802 0 --:–:-- --:–:-- --:–:-- 17798
[root@localhost input]# curl -O http://cellprofiler.org/svnmirror/ExampleImages/ExampleHumanImages/AS_09125_050116030001_D03f00d0.tif
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 227k 100 227k 0 0 127k 0 0:00:01 0:00:01 --:–:-- 128k
[root@localhost input]# curl -O http://cellprofiler.org/svnmirror/ExampleImages/ExampleHumanImages/AS_09125_050116030001_D03f00d1.tif
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 235k 100 235k 0 0 117k 0 0:00:02 0:00:02 --:–:-- 117k
[root@localhost input]# curl -O http://cellprofiler.org/svnmirror/ExampleImages/ExampleHumanImages/AS_09125_050116030001_D03f00d2.tif
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 286k 100 286k 0 0 146k 0 0:00:01 0:00:01 --:–:-- 146k
[root@localhost input]# for a in *.tif; do echo file:///input/a; done > filelist.txt [root@localhost input]# cd .. [root@localhost CellProfilerTest]# mkdir -m 777 output [root@localhost CellProfilerTest]# docker run --rm -v (pwd)/input:/input -v $(pwd)/output:/output cellprofiler -i /input -o /output -p /input/ExampleHuman.cppipe --file-list=/input/filelist.txt
Usage: CellProfiler.py [options] ])
where is the optional filename for the output file of
measurements when running headless.
The flags -p, -r and -c are required for a headless run.

CellProfiler.py: error: no such option: --file-list
[root@localhost CellProfilerTest]# docker run --rm -v (pwd)/input:/input -v (pwd)/output:/output cellprofiler/cellprofiler -i /input -o /output -p /input/ExampleHuman.cppipe --file-list=/input/filelist.txt
Usage: CellProfiler.py [options] ])
where is the optional filename for the output file of
measurements when running headless.
The flags -p, -r and -c are required for a headless run.

CellProfiler.py: error: no such option: --file-list[/code]

Do you have an idea of what the problem is? Am I getting the wrong version of the docker image?

Hi Julio,
First of all, the LoadData module isn’t deprecated - it’s recommended for usage in screening. It’s widely used and will always be supported.

I think our dockerfile in github is picking up the 2.1.1 release and not the the trunk. Our trunk builds page has an RPM for the current trunk / centos6 - it worked the last I checked:
cellprofiler.org/cgi-bin/trunk_build.cgi

hope this helps.

–Lee

Hi,

Thanks for the help. I was confused by a message when adding the LoadData module.

I’ll look into the trunk RPM package.

Thanks again.

Cheers, Julio