Mercurial > repos > jjohnson > eggnog_mapper
comparison tool-data/eggnog_mapper_db.loc.sample @ 6:090802703234 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
author | jjohnson |
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date | Thu, 07 Nov 2019 12:40:37 -0500 |
parents | a74d61dbd155 |
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5:a093b9061498 | 6:090802703234 |
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1 #This is a sample file distributed with Galaxy that enables tools | |
2 #to use a directory of eggnog_mapper data files. | |
3 # | |
4 # eggnog-mapper requires the following files to be installed in the data directory: | |
5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz | |
6 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz | |
7 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz | |
8 # In addition individual HMM DBs can be installed from: | |
9 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ | |
10 # A complete diamond database is available from: | |
11 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz | |
12 # | |
13 # The python script download_eggnog_data.py, | |
14 # included with eggnog_mapper, can be used to download the files to the correct directory | |
15 # | |
16 # The near-equivalence of columns "value" and "db" is needed for the tests to work, | |
17 # and for the setting of --data_dir to the parent directory of eggnog.db | |
18 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. | |
19 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases | |
20 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, | |
21 # value and db should be the same (in the example, both should be "thaNOG") | |
22 # | |
23 # | |
24 #db_version name path | |
25 #4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db |