pegi3s/agat repository overview

⁠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 AGAT⁠, a GFF/GTF annotation handling toolkit.

⁠Using the AGAT image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/agat agat_convert_sp_gxf2gxf.pl -g /data/gffFile -o /data/output.gff3

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file(s).
• agat_convert_sp_gxf2gxf.pl to the actual agat command you want to run.
• gffFile to the actual name of your GTF/GFF file.
• output.gff3 to the actual name of your output file.

To see the AGAT⁠ help, just run docker run --rm pegi3s/agat agat --help.