diff README @ 13:844fa988236b draft

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

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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).
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