because my setup may not be typical, I thought I would send a small report on my findings so far. There were/are a few bugs but they probably don’t warrant opening an issue on github as they may be too specific to my setup. Anyway, here goes:
- Scientific Linux release 6.2 (Carbon), 64 bit/*]
]I am just a user on the machine, no root privilege/]
]I can only download web packages via a proxy/]
]I am using my own local copy of anaconda linux, which I had updated to the latest version (Python 2.7.10)./]
]PYTHONPATH, HTTP_PROXY, http_proxy, JAVA_HOME, etc… all setup and exported in .bashrc/]
*]CellProfiler cloned from github (but not compiled / installed).
When I launched CellProfiler for the first time (python CellProfiler.py from within the cloned repository), I was asked to manually download apache-maven-3.0.4-bin.zip and unzip it to CellProfiler/imagej/maven
The python-bioformats package was missing, but pip install bioformats installed 0.18.7 (if I remember), which is much older than the version needed by CellProfiler. I then cloned / installed your own version from github.com/CellProfiler/python-bioformats.git
MySQL-python was missing, so I issued a pip install MySQL-python (this works because $http_proxy is defined).
Still missing vigra and cellh5.
If anything else needs clarifying, do ask away.
First problem was that external_dependencies.py (or any module relying on urllib / urllib2) requires a $http_proxy (low case) environment variable to be defined.
Then (at least on my setup), this issue needs to be resolved:
[quote]Updating Java dependencies using Maven.
Traceback (most recent call last):
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 157, in fetch_external_dependencies
aggressive_update = aggressive_update)
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 235, in run_maven
executeable_path = get_mvn_executable_path(maven_install_path)
File “$HOME/projects/CellProfiler/external_dependencies.py”, line 186, in get_mvn_executable_path
TypeError: reduce() of empty sequence with no initial value
Maven failed to update Java dependencies.
Run external_dependencies with the -o switch to get full output.
As a temporary measure, this works:
subdir = reduce(max, [x for x in os.listdir(maven_install_path)
subdir = ''
When CellProfiler downloaded all the packages I needed and opened, I got this exception (after a little while) which was caught by CellProfiler:
[quote]Traceback (most recent call last):
File “$HOME/projects/CellProfiler/cellprofiler/gui/pipelinelistview.py”, line 1695, in on_mouse_move
IndexError: list index out of range
I then tried to import this pipeline via URL: cellprofiler.org/svnmirror/Examp … ple.cppipe
Again, the environment variable $http_proxy needed to be defined for this to work.
This is it for now, I will load some of my own pipelines / images, have a play and report back. Any comments welcome.