pegi3s/goalign 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 allows the usage of Goalign⁠, a set of command line tools to manipulate multiple alignments.

By running the command docker run --rm pegi3s/goalign goalign help you can list the commands included in Goalign.

To obtain the help of a particular application, you just need to run: docker run --rm pegi3s/goalign goalign <goalign-application-name> -h (e.g. docker run --rm pegi3s/goalign goalign random -h)

⁠Using the Goalign image in Linux

To run an application, you should adapt and run the following command: docker run -v /your/data/dir:/data --rm pegi3s/goalign goalign <goalign-application-name> -i /data/input -o /data/output

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <goalign-application-name> to the name of the Goalign application you want to use.
• <input> to the actual name of your input file.
• out to the actual name of your output file.

For instance, to use the subseq application, you should run: docker run -v /your/data/dir:/data --rm pegi3s/goalign goalign subseq -i /data/align.fasta -s 2 -l 3 -o /data/align.sub.fasta

A sample align.fasta file can be this file⁠:

>Sequence1
AAAAAAAATTTTTTTT
>Sequence2
AAAAA-A-TTTTT-T-
>Sequence3
AAAAA-ATTTTTT-T-

⁠Using the Goalign 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/).

As in the Linux case, to run an application, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/goalign goalign <goalign-application-name> -i /data/input -o /data/output