A Brief Example

Owned by tianche5
Last updated: Nov 15, 2024
3 min read

This example is about installing and using a Python package called multiqc on Sol.

Step 1 - Search

Go to anaconda.org and search for multiqc in the search bar:

Screenshot 2024-11-13 at 1.53.54 PM.png

Click on one of the search results, usually the first one:

Screenshot 2024-11-13 at 1.55.18 PM.png

 

Exam the details on the following page, especially the version of the package:

The “conda install” on the above page gives the installation commands:

The conda part in the red circle needs to be changed to mamba, and the bioconda part in the blue box is the channel name of this multiqc package. Channel is similar to the name of an online folder, that mamba can find and download the correct package. This is important for the next step.

 

Step 2 - Install

  1. Connect to the VPN

  2. Open a terminal app or a command line interface on a personal laptop or pc, or in a Sol desktop session. And then type in the commands:

  3. ssh asurite@sol.asu.edu

  4. interactive -p htc -c 4 -t 30

  5. module load mamba/latest

  6. mamba create -n myENV -c bioconda multiqc

  7. And answer Y to the promoted question, if everything looks fine

  8. Wait till the installation finish

The -c flag in the mamba create command (#6) means “channel". The channel name must be correct to install the correct package. In our case, the channel of multiqc is bioconda, as found in “Step 1 - Search” section.

More information can be found here: Managing Python Modules Through the Mamba Environment Manager

 

Step 3 - Use

Once the myENV environment is ready, multiqc can be used directly or within a python session/script.

  1. Connect to the VPN

  2. Open a terminal app or a command line interface on a personal laptop or pc, or in a Sol desktop session. And then type in the commands:

  3. ssh asurite@sol.asu.edu

  4. interactive -p htc -c 4 -t 30

  5. module load mamba/latest

  6. source activate myENV

  7. python

  8. import multiqc

 

Step 4 - What about pip?

As explained in Python Package Installation Method Comparison , if a package is not found on anaconda.org, but found on pypi.org , pip can be used inside a mamba env. This is the only correct way to use pip on the ASU supercomputers.

Almost all of the Python packages can be found on anaconda.org, and mamba is always preferred.

 

Here is an example of such a special package called q2-greengenes2:

The commands to have this package installed to a mamba env are:

  1. Connect to the VPN

  2. Open a terminal app or a command line interface on a personal laptop or pc, or in a Sol desktop session. And then type in the commands:

  3. ssh asurite@sol.asu.edu

  4. interactive -p htc -c 4 -t 30

  5. module load mamba/latest

  6. source activate myENV

  7. pip install q2-greengenes2

 

Step 5 - Jupyter Notebook

After multiqc and q2-greengenes2 have been installed to myENV, we want to use this mamba env in the Jupyter Notebook session on the Sol web portal. So we need to make a Jupyter kernel from this mamba env. More details are covered in Preparing Python Environments for Jupyter and here are the example steps:

  1. Connect to the VPN

  2. Open a terminal app or a command line interface on a personal laptop or pc, or in a Sol desktop session. And then type in the commands:

  3. ssh asurite@sol.asu.edu

  4. interactive -p htc -c 4 -t 30

  5. module load mamba/latest

  6. mkjupy myENV "myENV_kernel"

  7. Find and use myENV_kernel

    1. Log in to the Sol web portal

    2. On the top bar: Interactive Apps > Jupyter > Fill out request form > Connect to Jupyter

    3. Inside the Jupyter Notebook: Open a Launcher page > Click on myENV_kernel icon

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