A Brief Example

Aim

Install and use a Python package called multiqc on Sol.

Step One: Search

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

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

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 Two: Install

1. 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:

2. ssh someone@sol.asu.edu

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

4. module load mamba/latest

5. mamba create -n myENV -c bioconda multiqc

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

In step 5, the -c flag 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 Two.

Step Three: Use

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

1. 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:

2. ssh someone@sol.asu.edu

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

4. module load mamba/latest

5. source activate myENV

6. python

7. import multiqc

Step Four: 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.

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. 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:

2. ssh someone@sol.asu.edu

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

4. module load mamba/latest

5. source activate myENV

6. pip install q2-greengenes2