PEMAbase needs to be indenpendent from any local files

hariszaf / pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes

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Closed hariszaf closed 2 years ago

hariszaf commented 2 years ago

A new version of the pemabase images needs to be built making sure that:

everything that is needed is publicly available
updates and upgrades that have been suggested to be included, e.g. ref databases updates (see #21) or pseudogene step (#27 )

hariszaf commented 2 years ago

To this end, it needs:

[x] to find a way to install OBITools // or just replace obiuniq step with something else
[ ] update CREST to CREST4 and thus support updated Silva and PR2 databases
[x] check RDPTools and staff how not to depend on local files
[x] remove CROP at all

edit if more will come

hariszaf commented 2 years ago

A zenodo repo was built to host the classifiers pema uses along with the databases that have been trained with.

hariszaf commented 2 years ago

Crest will not be upgraded for the time being. Instead the files required for the case of PR2 and Silva 138

hariszaf commented 2 years ago

Since pemabase:v.2.1.0 all precompiled dependencies for pema are on the zenodo repo already mentioned.

New databases wiil have to be added in those directories based on the current pemabase architecture.

We ll consider about upgrading the CREST classifier in a future version.

This issue is now resolved.