# IMPORTANT - Ignore carriage returns when using a Cygwin environment. # Proxy Servers & Network Setup (if needed) # containing the base installation of anaconda/miniconda.Įxport CONDA_BASE_DIR=/cygdrive/c/Users/Patrick/Miniconda3 # Anaconda Environment Selection - Plese set CONDA_BASE_DIR to the directory Using this setup, I am able to use cyg-conda and cyg-activate in the same way I would typically use conda and activate at the Anaconda command prompt, while making the environments available to my Cygwin bash shell.Ĭertainly open to suggestions for improvements, etc. Please note that the variable name $CONDA_DEFAULT_ENV is special, and used internally by the actual conda command. And finally, we define an alias cyg-conda and a function cyg-activate to be used as replacement commands for the standard conda and activate commands. bash_profile to keep track of the current conda environment using a shell variable $CONDA_DEFAULT_ENV. First, the user needs to explicitly set the directory $CONDA_BASE_DIR to be the location where the base environment for conda/anaconda/miniconda was installed. This setup essentially does three things. hoping I did not miss something inadvertently.) bash_profile relevant to the integration.

Assuming you have both Cygwin and Anaconda working independently, to access all of the Anaconda tools from Cygwin, the following setup in. After wrestling with the problem for quite some time, I think I've achieved a reasonable and workable method to integrate Anaconda's python (and associated environments) into Cygwin.

Install pybedtools cygwin anaconda