pegi3s/bioconvert 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 bioconvert⁠, a collaborative project that supports the interconversion of life science data from one format to another.

You can see the full list of conversions with: docker run --rm pegi3s/bioconvert --help. To obtain the help of a conversion, you just need to run: docker run --rm pegi3s/bioconvert <bioconvert-conversion-name> --help (e.g. docker run --rm pegi3s/bioconvert fastq2fasta --help)

⁠Using the bioconvert image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/bioconvert <bioconvert-convesion-name> /data/input /data/output

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file you want convert.
• <bioconvert-convesion-name> to the name of the conversion command (e.g. fastq2fasta).
• input to the actual name of your input file.
• output to the actual name of your output file.

⁠Using the bioconvert image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/bioconvert <bioconvert-convesion-name> /data/input /data/output