pegi3s/biopython repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of Biopython⁠, a group of multipurpose Python tools for computational molecular biology. This includes file parsing, with support for many file formats such as FASTA, GenBank and Swiss-Prot, alignment operations, graphical analysis and interfaces with other commonly used bioinformatics tools and databases.

⁠Using the Biopython image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/biopython bash -c "python3 /data/your_script.py"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the python script you want to run.
• your_script.py to the actual name of your python script.

⁠Using the Biopython image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/biopython bash -c "python3 /data/your_script.py"