Probable Bug Bytes

When you run in the situation that you want to run all of your R scripts in a jupyter notebook, within a conda environment, you will have to take some slight detours to install non-conda R packages. This is assuming that you have already installed R and jupyter through conda.  For information, checkout this awesome post . For an example, let's take a look at how one would install the ecodist package in R. We will need to pass in 3 arguments, (1) the name of the package, (2) the location of the conda R version and (3) the cran repository we will want to download from. install.packages('ecodist', '/Users/mortonjt/miniconda3/envs/bio/lib/R/library/', repos="http://cran.cnr.berkeley.edu") So, just modify the path to your environment in the second argument, and you should be good to go :)

First set of posts on conda.  Its becoming increasingly difficult to sift through my inbox to find all of the proper commands, so here it goes :) Anyways, conda has proven to be quite a powerful tool.  It enables _all_ of the capabilities provided by virtualenv, plus more.  It can install C libraries such as hdf5, is my personal go-to whenever I'm installing software on a new system.  Heck you can even install different versions of Python - how cool is that? That being said, the fastest way I know of to install qiime on a new cluster is through conda. To get started, you'll first want to install Miniconda .  The reason way is because you want a minimal conda install, otherwise you'll end up breaking some of the dependencies required by qiime. After getting into your root directory, you can download python (for python 3) for linux wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh If you have a mac you can use the following URL instead