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Installing qiime through conda



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. 
wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
Now you can install conda on your machine. 
chmod a+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc
Once this is complete, try restarting your session. This can also be done by opening up a new terminal. Now we can start to setup our environment, let's call it qiime_env.  And we'll first install the required packages (including python2)


conda create -n qiime_env pip python=2 numpy scipy matplotlib pandas h5py
source activate qiime_env
pip install qiime

And bam. That should install qiime for you on your machine in a contained, local conda environment

Comments

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