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Currently, the pipeline uses NCBI's `rankedlineage.dmp` taxdump file for taxonomic standardisation, which only has the ranks `kingdom`, `phylum`, `class`, `order`, `family`, `genus` and `species`. How…
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Hi,
For the SU students, thanks to Nathalie Picot, you now have access to useful sequence databases on the TME machines :
uniref90 : /Infos/BIM/MU5IN757/uniref90/uniref90.fasta
uniref50 : /Infos/…
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Currently, memefish fails unknown option key in some `OPTIONS`.
`OPTIONS` key can be added without notification, and it is even possible to have undocument options.
I think it is better to have "s…
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WI-V5.0.1.1469 Firebird 5.0
the sequence of actions:
1) I am creating a database using the ddl.sql script
2) I save the database in fbk
3) I restore from fbk with the option "Deactivate indexes"…
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Hello,
I was hoping you might have some advice about understanding an issue I am running into with some microbiome samples (fungal community in soybean at ITS region).
The issue has to do with i…
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I encountered the following error when I test example data. Is there any solution to this error? Thanks.
[PEM-Q] primerChrom: chr15
[PEM-Q] primer_start: 61986633
[PEM-Q] primer_end: 61986652
[P…
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Users needs to be able to search a repository by an URL.
We need a route that will accept a repository URL, and:
1. Search for an existing repository in our database
2. If we don't have the reposit…
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- VEuPathDB had JBrowse instances set up so that each config and tracks are done dynamically (not typical); REST service sits in front of database to write config files and extract data dynamically to…
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Currently we use `0` all over the place in the codebase, implicitly because it is the sentinel value that means "replace me when I am inserted in to a table with a sequence defined on my column". We s…
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Today, plugins are collections of functions that perform atomic actions. This design is beneficial as it exposes the Large Language Model (LLM) to a variety of specific actions it can perf…