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Table of Contents

On O2, we encourage cluster users to install the packages and software they need. One method to install packages and manage environments is to use conda, which is available through the conda2/4.2.13 or miniconda3/4.10.3 module. our miniconda modules. Conda manages dependencies by default when you install packages, which can make it easier to install software. Packages that can be installed with conda include Python modules, libraries, or executable programs.

Commonly used commands, examples

Command

Meaning

module spider

conda

miniconda3

shows the versions of conda installed on O2

module load miniconda3/version

loads an individual conda module

(replace version with an actual version)

conda info --envs

see available conda environments

conda create -n test_env

create conda environment named test_env

(name the environment whatever you'd like)

conda create -n aligners_env bwa bowtie star

create conda environment, and install some packages (bwa, bowtie, and star) on the fly

source activate /path/to/test_env

"activate" a conda environment

named

located at /path/to/test_env

source deactivate

exit current conda environment

conda-env remove -n test_env

delete a conda environment named test_env (may also require full path if installed to nonstandard location)

conda search numpy

search for a package

(replace numpy with the package of your choice)

conda install numpy

install a package, and must be within a conda environment or this command will fail.

(replace numpy with the package of your choice)

Setup

To install packages on O2 using conda, you must first create a conda environment. Environments are simply directories in ~/.conda/envs/ that contain packages you installed. You "source" an environment to use those packages, and can "deactivate" to exit the environment. You can have multiple environments, and can switch between them. 

...

Code Block
mfk8@compute-a-01-01:~$ module load miniconda3/423.101.30

Then the conda command will be available:

Code Block
mfk8@compute-a-01-01:~$ which conda
/n/app/miniconda3/423.101.30/bin/conda

Running conda info will return information about the current conda installation:

...

You can see available conda environments with conda info --envs. If you have not created any conda environments yet, the only listing you will see is the root environment in /n/app/conda2miniconda3. Cluster users do not have access to alter this. 

...

Code Block
(test_env) mfk8@compute-a-01-01:~$ which python
/n/app/miniconda3/423.101.30/bin/python

The default version of Python that's available through the conda module is Python 2.7.12:

Code Block
(test_env) mfk8@compute-a-01-01:~$ python --version
Python 3.9.5

If you want to use a specific version of Python with conda (strongly recommended), you can create a conda environment and install it. For example to create an environment using Python 3.6.5:

...

Code Block
mfk8@login01:~$ srun --pty -p interactive -t 0-2 bash
mfk8@compute-a-01-01:~$ module load miniconda3/423.101.30
mfk8@compute-a-01-01:~$ module list

Currently Loaded Modules:
  1) miniconda3/423.101.30 (E)

  Where:
   E:  Experimental

mfk8@compute-a-01-01:~$ conda create -n my_env
# truncated
mfk8@compute-a-01-01:~$ source activate my_env

# install example python package, scipy, which is available through conda:
(my_env) mfk8@compute-a-01-01:~$ conda install scipy
# truncated

# see list of packages available in this conda environment:
(my_env) mfk8@compute-a-01-01:~$ conda list
# truncated
# will report scipy in the list

# test importing scipy in python to verify it is installed correctly
(my_env) mfk8@compute-a-01-01:~$ python -c "import scipy"
(my_env) mfk8@compute-a-01-01:~$ 

# exit environment
(my_env) mfk8@compute-a-01-01:~$ source deactivate
mfk8@compute-a-01-01:~$

...