Mercurial > repos > galaxyp > data_manager_eggnog_mapper
changeset 3:5a2ffc486246 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
| author | galaxyp |
|---|---|
| date | Tue, 25 Jan 2022 13:50:50 +0000 |
| parents | 3d82020b1e3b |
| children | 516eb4e1cf8e |
| files | data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml data_manager/eggnog_macros.xml test-data/cached_locally/eggnog.db test-data/cached_locally/eggnog.taxa.db test-data/cached_locally/eggnog_mapper_db_versioned.loc tool-data/eggnog_mapper_db_versioned.loc.sample |
| diffstat | 7 files changed, 25 insertions(+), 14 deletions(-) [+] |
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--- a/data_manager/data_manager_eggnog.py Fri Feb 19 18:53:40 2021 +0000 +++ b/data_manager/data_manager_eggnog.py Tue Jan 25 13:50:50 2022 +0000 @@ -42,13 +42,21 @@ data_table = 'eggnog_mapper_db_versioned' dm_dict['data_tables'][data_table]\ = dm_dict['data_tables'].get(data_table, []) - # Versionning is super confusing: + # DB versionning was super confusing for eggnog-mapper 2.0.x: # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) - # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) - # db v4.5 are not compatible with eggnog-mapper 2.0 + # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0) + # (db v4.5 are not compatible with eggnog-mapper 2.0) + # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2 version = "2.0" if "4.5" in db_version: + # special case: eggnog-mapper 1.x version = "1.0" + elif db_version.startswith('2.'): + # special case: eggnog-mapper 2.0.x + version = "2.0" + else: + # normal case or eggno-mapper >= 2.1 + version = db_version data_table_entry = dict(value=db_version, name=db_version, path=args.install_path, version=version) dm_dict['data_tables'][data_table].append(data_table_entry)
--- a/data_manager/data_manager_eggnog.xml Fri Feb 19 18:53:40 2021 +0000 +++ b/data_manager/data_manager_eggnog.xml Tue Jan 25 13:50:50 2022 +0000 @@ -21,7 +21,7 @@ <help><![CDATA[ This tool downloads eggnog data using download_eggnog_data.py and populates the data tables: eggnog_mapper_db_versioned. -The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.0/ +The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.2/ can vary from 1G to 80G in size. This will install data relative to the galaxy_data_manager_data_path declared in config/galaxy.yml
--- a/data_manager/eggnog_macros.xml Fri Feb 19 18:53:40 2021 +0000 +++ b/data_manager/eggnog_macros.xml Tue Jan 25 13:50:50 2022 +0000 @@ -1,14 +1,15 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">2.0.1</token> - <token name="@EGGNOG_DB_VERSION@">2.0</token> + <token name="@VERSION@">2.1.6</token> + <token name="@EGGNOG_DB_VERSION@">5.0.2</token> <!-- - # Versionning is super confusing: + # DB versionning was super confusing for eggnog-mapper 2.0.x: # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) - # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) - # db v4.5 are not compatible with eggnog-mapper 2.0 + # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0) + # (db v4.5 are not compatible with eggnog-mapper 2.0) + # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2 --> - <token name="@IDX_VERSION@">2.0</token> + <token name="@IDX_VERSION@">5.0.2</token> <xml name="citations"> <citations> <citation type="doi">10.1093/nar/gkv1248</citation> @@ -26,6 +27,8 @@ <xml name="data_manager_params"> <param name="test" type="hidden" value="false" /> <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/> + <param name="mmseqs_database" type="boolean" truevalue="-M" falsevalue="" checked="true" label="Install the MMseqs2 database" help="Required for mmseqs seed ortholog search mode. Takes ~11Gb, you most probably want it."/> + <param name="pfam_database" type="boolean" truevalue="-P" falsevalue="" checked="true" label="Install the Pfam database" help="Rquired for de novo annotation or realignment. Takes ~3Gb, you most probably want it."/> </xml> <xml name="data_manager_outputs"> <outputs> @@ -40,7 +43,7 @@ #end if mkdir -p '${install_path}' && download_eggnog_data.py - $diamond_database -y -q + $diamond_database $mmseqs_database $pfam_database -y -q #if $test == 'true' -s #end if
--- a/test-data/cached_locally/eggnog_mapper_db_versioned.loc Fri Feb 19 18:53:40 2021 +0000 +++ b/test-data/cached_locally/eggnog_mapper_db_versioned.loc Tue Jan 25 13:50:50 2022 +0000 @@ -1,2 +1,2 @@ #value name path version -2.0 eggNOG_2.0 ${__HERE__} 2.0 +5.0.2 eggNOG_5.0.2 ${__HERE__} 5.0.2
--- a/tool-data/eggnog_mapper_db_versioned.loc.sample Fri Feb 19 18:53:40 2021 +0000 +++ b/tool-data/eggnog_mapper_db_versioned.loc.sample Tue Jan 25 13:50:50 2022 +0000 @@ -3,9 +3,9 @@ # # 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://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz +# http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz # A complete diamond database is available from: -# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz +# http://eggnog5.embl.de/download/emapperdb-5.0.2/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