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Installing new packages

Since Polus Notebooks are running in the container environment it has a fixed set of packages and libraries installed into it for all users. Of course, it cannot possibly include all existing libraries, so you might want to install something necessary for your research. Here is the walkthrough explaining how to install new package for each of the supported language kernels.

Python 3

Python packages are managed with conda package manager. You can use both conda or pip to install and update new packages

With conda

  1. Use Anaconda Cloud to search for package you are interested in
anaconda_cloud_1

anaconda_cloud_1

  1. Choose the package you are looking for. Most of the community packages are published through conda-forge account
anaconda_cloud_2

anaconda_cloud_2

  1. Copy the install command and paste it to the notebook cell
anaconda_cloud_3

anaconda_cloud_3

You have to append --yes to the end of the command

anaconda_cloud_4

anaconda_cloud_4

With pip

  1. Use Python Package Index (PyPi) to search for package you are interested in
pypi_1

pypi_1

  1. Choose the package you are looking for.
pypi_2

pypi_2

  1. Copy the install command and paste it to the notebook cell
pypi_3

pypi_3

You have to use exclamation mark before the command to let Jupyter know that this is shell command

pypi_4

pypi_4

You can specify the version to install using =<version> afer name of the package

!pip install opencv-python=4.1.1.26

R

You can use both conda or R to install and update new packages

With Anaconda

  1. Use Anaconda Cloud to search for R packages you are interested in
anaconda_cloud_1

anaconda_cloud_1

  1. Choose the package you are looking for. Many R packages are published through r/ or conda-forge/ repos and their names start with r-
r_anaconda_cloud\_

r_anaconda_cloud_

  1. Copy the install command and paste it to the notebook cell
r_anaconda_cloud_3

r_anaconda_cloud_3

You have to append --yes to the end of the command

system("conda install -c r r-tidyverse --yes", intern=TRUE)

From CRAN

Install packages from CRAN-like repositories or from local files using install.packages("<PACKAGE_NAME>") command

install.packages("tidyverse")

More documentation on install.packages available here: https://www.rdocumentation.org/packages/utils/versions/3.6.1/topics/install.packages

Julia

Install packages using Pkg as shown below

using Pkg
Pkg.add("CSV")

then load them with using statement:

using CSV

Java

You can add maven dependencies at runtime using magic command %maven. Full list of supported magic commands is here.

%mavenRepo scijava.public https://maven.scijava.org/content/groups/public
%maven net.imagej:imagej:2.0.0-rc-71
%maven net.imagej:imagej-notebook:0.7.1

You can search Maven Central for available packages

Octave

Octave Forge is a central location for development of packages for GNU Octave, similar to Matlab’s toolboxes. To install a package, use the pkg command from the Octave prompt by typing:

pkg install -forge package_name
pkg load package_name

C++

C++ does not have a built-in package manager. There are multiple existing package manager and if you are interested we may support one of them in the future.