Updates needed to installation instructions and requirements.txt

[Colin Kern]

I recently installed MERlin on a new machine, and discovered that the installation instructions no longer work. I had to make 3 changes to get it to work.

First, I was getting a DLL load failed error when the tables package was trying to import hdf5extension. To fix this, I removed the pytables installed through conda and re-ran the pip install command for MERlin so that pytables was installed through pip. So it seems like the step in the installation instructions that says pip doesn't correctly install tables isn't the case anymore, and following the instructions to install pytables with conda no longer works.

Next, I was getting an error in my DeconvolutionPreprocess tasks saying that it couldn't find the files that should have been created by the FiducialCorrelationWarp tasks, however these files did exist when I checked for them. I believe that the DeconvolutionPreprocess tasks weren't waiting for the FiducialCorrelationWarp tasks to complete. I was able to fix this by reverting my snakemake version to 5.12.0. I don't know exactly which version introduced this bug, but 5.12.0 was the version installed on another machine where MERlin does work, so I just used that version.

Finally, I got an error from tifffile that "ImageJ does not support non-contiguous series". I reverted tifffile to 0.14.0, the minimum version required in requirements.txt, which also required reverting scikit-image to 0.15.0 to avoid dependency issues. Everything seems to be working now.