Usage issues with downloaded snpeff 5.N databases ORG and EU

[jennaj]

The download tool is not downloading versions of the database that are compatible. Is there something we can do to make the usage clearer to users? Or can these tool wrappers be modified to be less strict about the database versions? It seems that the 5.2 version is available but we are pulling in the last archive in the path instead (which is a mismatch for the tool versions available in Galaxy).

Thanks!

Workaround for end users

1. Consider using the version 4.3+T.galaxy2 of the SnpEFF tools instead
2. How to navigate tool versions https://training.galaxyproject.org/training-material/faqs/galaxy/tools_change_version.html
3. Example usage https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html#variant-annotation-and-reporting

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy0

The tool's claim to list and download 5.2 databases, but it is indexed as a 5.1 or 5.0 database then tools cannot use the index.

We want https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh37.p13.zip

But are pulling in https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh37.p13.zip

GRCh37.p13	HumangenomeGRCh37usingRefSeqtranscripts			[https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh37.p13.zip,https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.p13.zip,https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh37.p13.zip]

{
    "history_id": "bbd44e69cb8906b5de59df1089dac477",
    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/5.2+galaxy0",
    "tool_version": "5.2+galaxy0",
    "inputs": {
        "snpDb|genomeSrc": "history",
        "snpDb|snpeff_db": {
            "batch": false,
            "product": false,
            "values": [
                {
                    "id": "f9cad7b01a472135c07307f0db837008",
                    "src": "hda",
                    "map_over_type": null
                }
            ]
        }
    }
}

Reproducible at ORG and EU.

https://usegalaxy.org/u/jen-galaxyproject/h/bug-snpeff-5-2 https://usegalaxy.eu/u/jenj/h/test-snpeff-download