pegi3s/alter
ALTER (http://www.sing-group.org/ALTER/) docker image.
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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.
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
.
To test the previous command, you can copy and paste this sample data into the input
file.
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.
docker pull pegi3s/alter