pegi3s/alter

Sponsored OSS

By i3S

Updated 9 months ago

ALTER (http://www.sing-group.org/ALTER/) docker image.

Image
Data Science
Machine Learning & AI

821

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.

Test data

To test the previous command, you can copy and paste this sample data into the inputfile.

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.

Docker Pull Command

docker pull pegi3s/alter