Add bwa-mem2 data manager #6376
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Can I persuade you to drop the python wrapper? If there is non much logic involved datamanagers can (and maybe should) be much simpler.
An example might be https://github.com/galaxyproject/tools-iuc/blob/main/data_managers/data_manager_metaphlan_database_downloader/data_manager/data_manager_metaphlan_download.xml
Edit: Besides being simpler we also would not need the mulled container because we con drop the python requirement.
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Thanks, I didn't know there were already examples that dropped the wrapper, I'll convert it. |
| <tables> | ||
| <!-- Locations of indexes in the BWA-MEM2 mapper format--> | ||
| <table name="bwa_mem2_indexes" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> |
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Maybe we want to include the bwa-mem2 version here (that has been used for the generation).
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The index format has been stable since 2020 and the Galaxy version of the tool was added after that index format change, so it should be compatible with all versions. For tools that have changed it in the past (e.g. STAR) we added a new versioned data table once that happens, but I guess if we want to be safe I could add a version column, even if it's unused for now?
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I think we should add a version column to all DM. Its just more future-proof and does not cost anything.
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Makes sense, but wouldn’t adding a column make it incompatible with the existing bwa-mem2 tool’s data table?
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This is true. I rephrase it, ideally, we should have a version column. Lets get it in for now without the version column and hope it will never change.
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In that case I think this is ready to go.
| "value": "${value}", | ||
| "dbkey": "${all_fasta_source.fields.dbkey}", | ||
| "name": "${name}", | ||
| "path": "${fasta_file_name}" |
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should this be ${out_file.extra_files_path}/${fasta_file_name}?
In the DMs that I created recently I just crated a directory (e.g. DIR) in the working dir and used this. I guess using out_file.extra_files_path is not really necessary.
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Doing so seems to cause the index to be referenced from the object store after the DM completes: the path in the loc file points to /path/to/galaxy/database/objects/c/0/f/dataset_c0ffee_files/fooBar1.fa. Whereas if it is just the relative name inside the extra_files_path, then the index is referenced from tool_data_dir as expected for a DM. Possibly just an artifact of os.path.join([tool_data_dir, intermediate_dirs, '/path/to/galaxy/database/objects/c/0/f/dataset_c0ffee_files/fooBar1.fa']) clobbering the earlier path elements, but either way that's not the desired outcome.
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Great. Thanks a lot for the contribution. |
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Thanks @bernt-matthias @bgruening! |
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