pegi3s/seda repository overview

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

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.

⁠Running the SEDA CLI in Linux

SEDA 1.6 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 /opt/SEDA/run-cli.sh help.

And to obtain the help of a specific command, just run docker run --rm pegi3s/seda/opt/SEDA/run-cli.sh help <command> (e.g. docker run --rm pegi3s/seda /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 /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 /opt/SEDA/run-cli.sh sort -if /data/input.fasta -od /data/output --sort-on header --descending --criteria alphabetical

⁠Advanced usage

⁠Increase RAM memory

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. For instance, this would be the command for the GUI:

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

⁠Debugging external software execution

If external software execution fails or raises unexpected results, add the following to the docker run command to see in the console which commands are executed: -e JAVA_USER_D_ARGS="-Dseda.execution.showcommands=true"