Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath

annotate tool-data/eggnog_mapper_db_versioned.loc.sample @ 1:46d2e3ed9530 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:52:23 +0000
parents
children 3d12bbd5c0ba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
2 #to use a directory of eggnog_mapper data files.
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
3 #
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
4 # eggnog-mapper requires the following files to be installed in the data directory:
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
6 # http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
7 # A complete diamond database is available from:
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
8 # http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
9 #
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
10 # The python script download_eggnog_data.py,
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
11 # included with eggnog_mapper, can be used to download the files to the correct directory
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
12 #
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
13 # The near-equivalence of columns "value" and "db" is needed for the tests to work,
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
14 # and for the setting of --data_dir to the parent directory of eggnog.db
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
15 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
16 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
17 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
18 # value and db should be the same (in the example, both should be "thaNOG")
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
19 #
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
20 #
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
21 #db_version name path
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff changeset
22 #5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db