Compleasm: use busco_database_options for lineages instead of hardcoded ones#7915
Compleasm: use busco_database_options for lineages instead of hardcoded ones#7915Delphine-L wants to merge 2 commits intogalaxyproject:mainfrom
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@Delphine-L could you please adapt the tests according to the recent modifications? |
bernt-matthias
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bernt-matthias
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You need to add entries for the options data table here https://github.com/Delphine-L/tools-iuc/blob/5b45ca3f0bfd94f83918b77c57a45a88bd35fa2b/tools/compleasm/tool_data_table_conf.xml.sample and here https://github.com/Delphine-L/tools-iuc/blob/5b45ca3f0bfd94f83918b77c57a45a88bd35fa2b/tools/compleasm/tool_data_table_conf.xml.test
| ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' && | ||
| ## Create a compleasm-specific empty file to avoid redownloading the lineage data (https://github.com/huangnengCSU/compleasm/blob/0.2.6/compleasm.py#L165) | ||
| touch 'galaxy_db/${lineage_dataset}.done' && | ||
| echo ${__HERE__} && |
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I do not think that this part is needed. Instead you need to add an entry to the options data table test file.
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I mean the whole block and the hidden test variable
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@SaimMomin12 I am not sure how to write tests for data tables. busco doesn't use them . Could you take a look ? |
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For using the new data table you will need to add an entry for the data table in tool_data_table_conf.xml.sample. This will refer to a sample sample loc in the You can copy from here:
For the tests you need:
I guess you can draw inspiration from the busco tool as well. |
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