Is there support for assigning a temporary directory in CellProfiler?
I have a situation similar to this one: http://forum.cellprofiler.org/t/unable-to-change-temporary-directory-on-cluster/2544, where I have a PBS/Torque cluster and the /tmp/ directory on the nodes is very limited in space. When running a CellProfiler job, two files are written in this directory, a .h5 file that looks something like "CellProfilerImageCache4GQWlo.h5", and an .hdf5 file that looks something like "Cpmeasurements1aoH7l.hdf5"
Running 2.2.0rc3 there seems to be support for a "-t " flag for the command line functionality, but running 2.4.0rc1 and this seems to no longer be supported according to this issue:
The LIMS documentation mentions both the use of the "-t" flag (which is now depricated), and the ability to assign the write path for the .hdf5 file
Using the latter method ("cellprofiler mytmpfile.hdf5 -c -r -p pipeline_file.cppipe --data-file=data_file.csv") the .hdf5 file is written to the correct location but the .h5 file is sill being written in /tmp/
Specifying a /tmp/ file in the CellProfiler GUI does not transfer to the .cppipe file and therefore does not effect the headless run
Any help or work-arounds would be great.