annotate tool-data/eggnog_mapper_db_versioned.loc.sample @ 7:4e4c6329f6cd draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:54:25 +0000
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children 96cac424c870
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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1 #This is a sample file distributed with Galaxy that enables tools
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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2 #to use a directory of eggnog_mapper data files.
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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3 #
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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4 # eggnog-mapper requires the following files to be installed in the data directory:
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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6 # http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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7 # A complete diamond database is available from:
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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8 # http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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9 #
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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10 # The python script download_eggnog_data.py,
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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11 # included with eggnog_mapper, can be used to download the files to the correct directory
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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12 #
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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13 # The near-equivalence of columns "value" and "db" is needed for the tests to work,
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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14 # and for the setting of --data_dir to the parent directory of eggnog.db
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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15 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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16 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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17 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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18 # value and db should be the same (in the example, both should be "thaNOG")
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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19 #
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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20 #
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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21 #db_version name path
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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22 #5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db