pegi3s/alter 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 ALTER⁠ (ALigment Transformation EnviRonment), a public tool for MSA (Multiple Sequence Alignment) file format conversion. It performs a program-oriented conversion between different DNA and protein MSA formats.

⁠Using the ALTER image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/alter -i /data/input -o /data/output -ia -of <out_format> -oo Linux -op GENERAL

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file you want to align.
• input to the actual name of your input file.
• output to the actual name of your output file.
• <out_format> to the output format you intend to obtain. The allowed standard formats are: ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP and PIR.

For instance, in order to convert a NEXUS file into a FASTA file, you should run: docker run --rm -v /your/data/dir:/data pegi3s/alter -i /data/input.nexus -o /data/output.fasta -ia -of FASTA -oo Linux -op GENERAL

To see the ALTER help, just run docker run --rm pegi3s/alter help.

⁠Running the ALTER GUI in Linux

This docker image can be also used to run the ALTER 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/alter

If the above command fails, try running xhost + first.