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BFL-lab / Mfannot

MFannot is a program for the annotation of mitochondrial and plastid genomes
GNU General Public License v3.0
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mf2sqn does not work in Docker container #64

Open Adamtaranto opened 8 months ago

Adamtaranto commented 8 months ago

MFannot throws an error when run with the --sqn option in the Docker container.

Running mf2sqn also fails.

When I try to run mf2sqn directly I get the error Accepted value for author is Lang or Burger but neither of these work

I have tried creating Lang.sbt in the mf2sqn/lib/mf2sqn_Submitters/ dir and using "SubmitterGeneric" (to match "mf2sqn/lib/mf2sqn_Submitters/SubmitterGeneric.sbt"). Neither are recognised as valid authors.

Adamtaranto commented 8 months ago

For future travellers, you need a .sbt file in $MF2SQN_LIB/mf2sqn_Submitters with a name formatted as 'Submitter[name].sbt` where [name] matches the author arg.

i.e. To use the SubmitterGeneric.sbt template info, run: mf2sqn -d -t -a Generic -m mfannot_outfile.masterfile

See mf2sqn code here: https://github.com/BFL-lab/Mf2sqn/blob/6faf9f444dd54cddfc1ac625c7099001c5736428/mf2sqn#L279