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shohei-kojima / MEGAnE

MEGAnE
MIT License
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Usage of call_genotype with no sex gene #1

Closed piosierra closed 2 years ago

piosierra commented 2 years ago

Hello,

I am trying to run the pipeline for a species with no sex gene (or not determined so far). Is there a way to by pass the requirement for a name for -female_sex_chr?

Thanks

shohei-kojima commented 2 years ago

Thank you for your feedback.

From v1.0.1beta, MEGAnE has -no_sex_chr option. Please pull the new version from DockerHub and use that option. With this option, MEGAnE treats all chromosomes as autosomes. An example usage of this option is available in the wiki page.

piosierra commented 2 years ago

Thanks a lot. I had missed this comment on the wiki.

piosierra commented 2 years ago

I am using the singularity version. Should it update all the same? (I just downloaded it today)

shohei-kojima commented 2 years ago

Yes, a singularity container and a docker container built from the DockerHub will be the same. Did you specify the tag? If not, please try the build again.

sudo singularity build MEGAnE.sif docker://shoheikojima/megane:v1.0.1.beta
# or
singularity build --fakeroot MEGAnE.sif docker://shoheikojima/megane:v1.0.1.beta
piosierra commented 2 years ago

Updated. Thanks!