pegi3s/mauve 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 Mauve⁠, a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

⁠Using the Mauve image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/mauve bash -c "progressiveMauve --output=/data/output /data/input1 /data/input2"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• output to the actual name of your output file.
• input1 to the actual name of your first input genome file.
• input2 to the actual name of your second input genome file.

⁠Running the Mauve GUI in Linux

This docker image can be also used to run the Mauve GUI. To do so, just run: docker run --rm -ti -e USERID=$UID -e USER=$USER -e DISPLAY=$DISPLAY -v /var/db:/var/db:Z -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" pegi3s/mauve

If the above command fails, try running xhost + first. In this command, you should replace:

• /your/data/dir to point to the directory that you want to have available at Mauve.

Running this command opens the Mauve Graphical User Interface. Your data directory will be available through the file browser at /data.

⁠Using the Mauve 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/mauve bash -c "progressiveMauve --output=/data/output /data/input1 /data/input2"