Mercurial > repos > galaxyp > eggnog_mapper

annotate README @ 12:a5d5e84eed93 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
author galaxyp
date Mon, 19 Jan 2026 22:22:38 +0000
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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1 This folder contains three tools:
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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3 1. eggnogg_mapper: which runs the search and annotation phase in a single tool
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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4 2. eggnogg_mapper_search: which implements the search phase
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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5 3. eggnogg_mapper_annotate: which implements the annotation phase
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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7 While the search phase of eggnog_mapper is very CPU intense and is efficient
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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8 also for a larger number of threads, the annotation phase is very IO intensive
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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9 and can be very inefficient (depending on the configuration, e.g. if the
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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10 reference data is located on a slow partition).
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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12 While for most applications eggnogg_mapper will be sufficient to separate the
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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13 two phases can be more efficient:
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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15 - sending eggnogg_mapper_search to a destination using many threads
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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16 - and eggnogg_mapper_annotate to a destination using a small number of threads
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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18 Admins can choose to set the environment variable ``EGGNOG_DBMEM=--dbmem``
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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19 which will copy the complete EggNOG annotation DB into memory which is usually
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
galaxyp
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20 much faster than using multiple cores (but needs approx. 37GB of RAM).