Mercurial > repos > galaxyp > eggnog_mapper
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
author | galaxyp |
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date | Thu, 07 Sep 2023 18:51:23 +0000 |
parents | 844fa988236b |
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This folder contains three tools: 1. eggnogg_mapper: which runs the search and annotation phase in a single tool 2. eggnogg_mapper_search: which implements the search phase 3. eggnogg_mapper_annotate: which implements the annotation phase While the search phase of eggnog_mapper is very CPU intense and is efficient also for a larger number of threads, the annotation phase is very IO intensive and can be very inefficient (depending on the configuration, e.g. if the reference data is located on a slow partition). While for most applications eggnogg_mapper will be sufficient to separate the two phases can be more efficient: - sending eggnogg_mapper_search to a destination using many threads - and eggnogg_mapper_annotate to a destination using a small number of threads Admins can choose to set the environment variable ``EGGNOG_DBMEM=--dbmem`` which will copy the complete EggNOG annotation DB into memory which is usually much faster than using multiple cores (but needs approx. 37GB of RAM).