pegi3s/seda
SEDA (www.sing-group.org/seda) docker image.
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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.
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 $HOME/.Xauthority:/home/developer/.Xauthority -v "/your/data/dir:/data" -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp pegi3s/seda
SEDA 1.6.0 introduced a new Command-Line Interface (CLI).
To see the SEDA
help and obtain the list of available commands, just run docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help
.
And to obtain the help of a specific command, just run docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help <command>
(e.g. docker run --rm pegi3s/seda:1.6.0 /opt/SEDA/run-cli.sh help sort
)
You should adapt and run the following command: docker run --rm -ti -e USERID=$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 pegi3s/seda