3. Installing PM4NGS

Read PM4NGS published manuscript in GIGAScience

3.1. What is a Python virtual environment?

A python virtual environment is a "new Python installation" with their own site directories, optionally isolated from system site directories. Each virtual environment has its own Python binary (which matches the version of the binary that was used to create this environment) and can have its own independent set of installed Python packages in its site directories.

Creation of virtual environments is done by executing the command venv:

Note

python3 -m venv /path/to/new/virtual/environment

Running this command creates the target directory (creating any parent directories that don’t exist already), a common name for the target directory uses as suffix _venv. It also creates a bin subdirectory containing a copy/symlink of the Python binary/binaries. It also creates an (initially empty) lib/pythonX.Y/site-packages subdirectory for the new packages. If an existing directory is specified, it will be re-used.

Once a virtual environment has been created, it can be “activated” using a script in the virtual environment’s binary directory. The invocation of the script is platform-specific (<_venv> must be replaced by the path of the directory containing the virtual environment):

Note

$ source /path/to/new/virtual/environment/bin/activate

3.2. Installing PM4NGS

Creates a Python virtual environment named: pm4ngs_venv for installing PM4NGS.

veraalva@instance-veraalva:~$ which python3
/usr/bin/python3
veraalva@instance-veraalva:~$ python3 -m venv pm4ngs_venv
veraalva@instance-veraalva:~$ source pm4ngs_venv/bin/activate
(pm4ngs_venv) veraalva@instance-veraalva:~$ which python3
/home/r78v10a07/pm4ngs_venv/bin/python3
(pm4ngs_venv) veraalva@instance-1:~$ pip install wheel
(pm4ngs_venv) veraalva@instance-1:~$ pip install pm4ngs

These commands need to be executed only one time during the tutorial.

3.3. Testing PM4NGS

Test PM4NGS RNA-Seq module:

(pm4ngs_venv) veraalva@instance-veraalva:~$ pm4ngs-rnaseq