pegi3s/seda

Sponsored OSS

By i3S

Updated 24 days ago

SEDA (www.sing-group.org/seda) docker image.

Image
Data Science
Integration & Delivery
Machine Learning & AI

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This image facilitates the usage of SEDA (SEquence DAtaset builder), an open source application for processing FASTA files containing DNA and protein sequences.

Running the SEDA GUI in Linux

Due to changes in the structure of the NCBI website, the "NCBI rename" option no longer works in versions prior to 1.6.1

You should adapt and run the following command: 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" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda

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 SEDA.

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

To increase the RAM memory that the dockerized version of SEDA for Linux systems uses, simply add -e SEDA_JAVA_MEMORY='-Xmx6G' (change 6G to the amount of RAM memory you want to use) to the docker run command:

docker run --rm -ti -e SEDA_JAVA_MEMORY='-Xmx6G' -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" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda

Running the SEDA CLI in Linux

SEDA 1.6.0 introduced a new Command-Line Interface (CLI).

To see the SEDA help and obtain the list of available commands, just run docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help.

And to obtain the help of a specific command, just run docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help <command> (e.g. docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help sort)

You should adapt and run the following command: 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" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh <command> -if /data/input.fasta -od /data/output <command_parameters>

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input file you want to process with SEDA.
  • input.fasta to the actual name of your input FASTA file.
  • output to the actual name of your output directory (i.e. where the output FASTA will be created).
  • <command> to the SEDA command you want to execute.
  • <command_parameters> to the list of command parameters.

For instance, in order to sort a FASTA file, you should 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" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh sort -if /data/input.fasta -od /data/output --sort-on header --descending --criteria alphabetical

Docker Pull Command

docker pull pegi3s/seda