annotate README @ 13:844fa988236b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb

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).