Mercurial > repos > jjohnson > data_manager_eggnog_mapper

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 288c3043b10594647e9f6e5de56bf98a38779f75-dirty
author jjohnson
date Fri, 08 Nov 2019 14:32:49 -0500
parents 6abbdf623176
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6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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1 #This is a sample file distributed with Galaxy that enables tools
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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2 #to use a directory of eggnog_mapper data files.
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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3 #
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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4 # eggnog-mapper requires the following files to be installed in the data directory:
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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6 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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7 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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8 # In addition individual HMM DBs can be installed from:
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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9 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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10 # A complete diamond database is available from:
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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11 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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12 #
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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13 # The python script download_eggnog_data.py,
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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14 # included with eggnog_mapper, can be used to download the files to the correct directory
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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15 #
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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16 # The near-equivalence of columns "value" and "db" is needed for the tests to work,
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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17 # and for the setting of --data_dir to the parent directory of eggnog.db
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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18 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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19 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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20 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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21 # value and db should be the same (in the example, both should be "thaNOG")
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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22 #
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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23 #
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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24 #db_version name path
6abbdf623176 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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25 #4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db