Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath
diff tool-data/eggnog_mapper_hmm_dbs.loc.sample @ 0:9d5f039c637f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
| author | galaxyp |
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| date | Mon, 11 Nov 2019 11:49:47 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_hmm_dbs.loc.sample Mon Nov 11 11:49:47 2019 -0500 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#key db_version value name path +#4.5.1_NOG 4.5.1 NOG Full eggNOG database (NOG) +#4.5.1_euk 4.5.1 euk Eukaryotes (euk) +#4.5.1_aproNOG 4.5.1 aproNOG Proteobacteria_alpha (aproNOG) +#4.5.1_aproNOG 4.5.1 ENOG411CB2I ENOG411CB2I (custom) /path/to/custom/hmmdb/ENOG411CB2I