IMP issueshttps://git-r3lab.uni.lu/IMP/IMP/-/issues2018-10-04T14:26:35+02:00https://git-r3lab.uni.lu/IMP/IMP/-/issues/141IMP-specific prokka conda recipe needed2018-10-04T14:26:35+02:00Cedric LacznyIMP-specific prokka conda recipe needed`prokka` comes by default with `tbl2asn`.
While this makes sense when using prokka for isolate genomes, the use of this step for metagenomes is less apparent.
In particular, this step is very time-consuming, i.e., can take 10 hours or mo...`prokka` comes by default with `tbl2asn`.
While this makes sense when using prokka for isolate genomes, the use of this step for metagenomes is less apparent.
In particular, this step is very time-consuming, i.e., can take 10 hours or more.
Moreover, the output is currently not used at all by the IMP pipeline.
Hence, creating a dedicated recipe for prokka is suggested.
A dedicated recipe would allow us to apply a patch to prokka's perl script to disable the tbl2asn step.
While it could also be described in the installation instructions of IMP to comment-out the respective line when using the prokka bioconda recipe, having a dedicated recipe seems to be the cleaner solution.