plotly vs xlmhg version conflict

[mthang]

Hi Author, I have tried to run the celseq2 after installation. However, there is a serious version conflict between plotly and xlmhg. The current version plotly does not work with xlmhg after the upgrade of plotly and vice versa. is there a way to run celseq2 with the latest version of both plotly and xlmhg packages?

Many thanks, Mike

[tzeitim]

I had the same problem and managed to solve it by installing specific versions of the packages that would be compatible. The error messages generally tell you which version you should use.

I did something like the following, which might differ from your setup. Just iterate a bit with the versions that pip suggests to you.

pip install snakemake==5.5.2
pip install genometools
pip install xlmhg==2.4.9

[mthang]

Hi Tim, Thank you for the reply ! I have tried the solution you posted here and plotly will complain as well. I have found a way to get around the version incompatibility. For those who like to use the celseq2, you can follow the quick workaround below.

Create a vritualenv using python 3 and install the genometools and celseq2 in the virtualenv

Download CelSeq and Genometools https://github.com/yanailab/celseq2 https://github.com/flo-compbio/genometools

Genometools Installation
The solution is to change the plotly version to <=3 in the setup.py of genometools.

• download genometools 0.4.1 tarball from https://pydigger.com/pypi/genometools
• untar the genometools tarball
• cd into the genometools directory
• change the plotly version in setup.py to <=3 e.g 'plotly>=2, <=3'
• pip setup.py install
• note: make sure xlmhg version is 2.4.9 and it is the requirement of genometools 0.4.1