Installing Enrich2

Installing Enrich2 / using a Conda environment

I have a couple of new Macs in the lab that need Enrich2 installed. The goal today is to go through the steps of making a Conda environment specifically for running Enrich2 (and installing Enrich2), developed by Alan Rubin.

The Enrich2 repository

The Enrich2 docs

Alan instructions for making a Conda environment specifically for Enrih2

Alan’s instrucitons for doing this is pretty good, if I remember correctly. But, Alan is a seasoned programmer / computational scientist, while people like me are novices and far less familiar with these steps. Furthermore, depending on the specifics of your computer / system, you may get different errors in the installation process. Thus, here’s my interpretation of this process for the benefit of others like me.

0) This supposes that you have already installed an updated version of Anaconda on your Mac. Go back and do this now, if you haven’t done so already.

1) Download the Anaconda Enrich2 environment file and put it somewhere you can access using Terminal.

2A) Update to the newest version of Anaconda, just in case. Hit “y” if prompted.

conda update conda

2B) OK, so now was installing the right version of Pandas it needs. To do this, I first went into Anaconda Navigator and made a new environent called python2, that uses Python 2. Then in terminal, I called:

conda activate python2

2C) This activated python2, so that now the prompt didn’t say “base”, but now it said “(python2)”. Cool. Envinroment activated. I then installed pandas 0.19.2 by typing in:

pip install pandas==0.19.2

2D) OK, this seemed to work too. I got an error when trying to re-run the “enrich2_env.yml file”, so I removed the “=0.19” part form the .yml file and ran “conda env create -f enrich2_env.yml”. This actually seemed to work giving me a list of packages being extracted. Now to actually test it out.

conda activate enrich2

3) Cool, that worked, and the terminal prompt now says “(enrich2)”. Now we’re in business. Next is actually installing Enrich2 now that we’re in the enviroment. Go to the Enrich2 repository, download the file, unzip it, and then move to its directory in terminal. Then run:

python install

That seemed to work since it didn’t throw any errors.

4) Next is actually trying to run the application. Type in the following:


Oh Jesus christ. It literally crashes the Finder due to the following errors:

CGSTrackingRegionSetIsEnabled returned CG error 268435459
CGSTrackingRegionSetIsEnabled returned CG error 268435459
CGSTrackingRegionSetIsEnabled returned CG error 268435459
HIToolbox: received notification of WindowServer event port death.
port matched the WindowServer port created in BindCGSToRunLoop

Looks like this may have been a problem with the MacOS operating system. Updating my OS to Catalina and then trying again.

5) OK, MacOS has been updated to Catalina. Now let’s try running Enrich again. (You’ll likely want to run this command after you’ve navigated to the directory with your raw files to simplify the file locating process).


Awesome. It worked!

PS. I followed these instructions for my second Mac and it worked like a charm. I even went straight for the Cataline update early on and didn’t run into the error in Step4.