Update ncbi fcs gx #6307
Update ncbi fcs gx #6307
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…these fields to the ncbi_fcs_gx_databases table.
| @@ -1,7 +1,7 @@ | |||
| <tables> | |||
| <!-- Locations of NCBI FCS GX databases --> | |||
| <table name="ncbi_fcs_gx_databases" comment_char="#"> | |||
| <columns>value, source_manifest, name</columns> | |||
| <columns>value, name, source_manifest, use_source_manifest, phone_home, phone_home_label, node_cache_dir, local_manifest</columns> | |||
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We can not change the columns in a already existing data-table. I think you need to create a new one. e.g. ncbi_fcs_gx_databases_ext
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Thanks! I'll rename it.
| <param name="use_source_manifest" type="boolean" label="Should the tool use the source manifest"/> | ||
| <param name="phone_home" type="boolean" label="Should phone home be enabled"/> | ||
| <param name="phone_home_label" type="text" label="Phone home label"/> | ||
| <param name="node_cache_dir" type="text" label="Directory to copy database to local node"/> |
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Can you explain what this is doing? I can not see that anything is copied in the data manager.
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I've added some documentation to the Help section that hopefully clears some of this up. The Galaxy Admin chooses a manifest file (for example: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/latest/all.manifest). The data manager then uses sync_files.py from the ncbi-fcs-gx bioconda package to download a local copy of the database described in the manifest. It then adds the location of the local manifest file to the ncbi_fcs_gx_databases_ext table.
The data manager then parses the downloaded taxa.tsv file to create a lookup table mapping GX divisions to descriptions that will be seen and selected by the user.
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This parameter is optional? Its an implementation details, a TMP_DIR? In that case, I would not even expose it.
The problem I see is that we put a path in a config-file that might be node/cluster dependent. But we have heterogenous clusters most of the time. The path might be destination dependent. Usually, we work with those use-cases by setting $TEMP or related envs via Galaxy for a particular tool.
My question: Do we really need this parameter and the value set in the loc file, or can we just go with the default value (assuming that is some TMP dir).
...cbi_fcs_gx_database_downloader/data_manager/data_manager_ncbi_fcs_gx_database_downloader.xml
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added more content to the help section
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@bernt-matthias can you have a look at this one? It LGTM. |
Updating NCBI FCS GX.. Removed the ncbi_fcs_gx_config table and added those fields to the ncbi_fcs_gx_databases table. Made sure both the tool and the data manager are using version 0.5.4.
FOR CONTRIBUTOR: