The scope of this manual is a brief introduction on how to manage Python packages.
Different Python versions do not play nice with each other. It is best to only load one Python module at any given time. For more information regarding our module system please refer to Environment Modules. The miniconda2 module for Python is the new default version. This will enable users to leverage the conda installer. The older version of Python (python/2.7.5 ) is still available, however you must explicitly load this version if you wish to use it.
To revert back to the older 2.7.5 version of python, do the following:
module unload miniconda2 module load python/2.7.5
To load the pre-installed Python packages, do the following:
conda activate hppc-base #This may take a few seconds
It is best to create your own environment in which you have full control over package installs.
Installing many packages can consume a large (ie. >20GB) amount of disk space, thus it is recommended to store conda environments under your bigdata space.
If you have bigdata, create the
.condarc file (otherwise conda environments will be created under your home directory).
Create the file
.condarc in your home, with the following content:
channels: - defaults pkgs_dirs: - ~/bigdata/.conda/pkgs envs_dirs: - ~/bigdata/.conda/envs
Then create your Python 2 conda environment, like so:
conda create -n NameForNewEnv python=2.7.14 # Many Python versions are available
For Python 3, please use the miniconda3, like so:
module unload miniconda2 module load miniconda3 conda create -n NameForNewEnv python=3.6.4 # Many Python versions are available
Once your virtual environment has been created, you need to activate it before you can use it, like so:
conda activate NameForNewEnv
In order to exit from your virtual environment, do the following:
Here is a simple example for installing packages under your Python virtual environment via conda:
conda install -n NameForNewEnv PackageName
You may need to enable an additional channel to install the package (refer to your package’s documentation):
conda install -n NameForNewEnv -c ChannelName PackageName
It is possible for you to copy an existing environment into a new environment:
conda create --name AnotherNameForNewEnv --clone NameForNewEnv
Run the following to get a list of currently installed conda evironments:
conda env list
If you wish to remove a conda environment run the following:
conda env remove --name myenv
We also have a service for interactive Python development, Jupyter-Hub. In order to enable your environemnt within Jupyter you will need to do the following:
# Create a virtual environment, if you don't already have one conda create -n ipykernel_py2 python=2 ipykernel # Load the new environment conda activate ipykernel_py2 # Install kernel python -m ipykernel install --user --name myenv --display-name "JupyterPy2"
Now when you visit Jupyter-Hub you should see the option “JupyterPy2” when you click the “New” dropdown menu in the upper left corner of the home page.
Multiple versions of Python and R are supported. For instructions on how to configure your R environment please visit IRkernel. Since we should already have IRkernel install in the latest version of R, you would only need to do the following within R:
IRkernel::installspec(name = 'ir44', displayname = 'R 3.5.0')
This section is a automatically on how to manage R packages
Current R Version
Currently the default version of R is 3.5.0 and loaded automaticly for you. This can be seen by running:
Older R Versions
You can load older versions of R with the following:
module unload R module load R/3.4.2
Installing R Packages
The default version of R has many of the most popular R packages available all ready installed. It is also possible for you to install additional R packages in your local environments.
source("https://bioconductor.org/biocLite.R") biocLite("package-to-install") Update all/some/none? [a/s/n]: n
library(devtools) install_github("duncantl/RGoogleDocs") # replace name with the GitHub account/repo
install.packages("http://hartleys.github.io/QoRTs/QoRTs_LATEST.tar.gz",repos=NULL,type="source") # replace URL with your URL or local path to your .tar.gz file
For more information regarding conda please visit Conda Docs.