clair3 breaks galaxy due to discrepancy in all_fasta columns

[cat-bro]

Galaxy Australia's staging server failed to restart this morning. This entry in the shed_tool_data_table_conf.xml

    <table name="all_fasta" comment_char="#">
        <columns>value, name, path</columns>
        <file path="/mnt/galaxy/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/clair3/c8ba8286e7c0/all_fasta.loc"/>
        <tool_shed_repository>
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>clair3</repository_name>
            <repository_owner>iuc</repository_owner>
            <installed_changeset_revision>c8ba8286e7c0</installed_changeset_revision>
        </tool_shed_repository>
    </table>

has the wrong columns in columns. Each other entry for all_fasta has <columns>value, dbkey, name, path</columns> and galaxy would not start until this new entry was commented out.

[bernt-matthias]

I would consider this a bug in galaxy (and Clair).

[mvdbeek]

We can't really do anything there in Galaxy, failing to boot is probably the correct thing to do.

[bernt-matthias]

We can't really do anything there in Galaxy, failing to boot is probably the correct thing to do.

We could just fail to load the tool, like we do for xml parsing errors, etc.

[mvdbeek]

This is a server misconfiguration that might have a huge impact, this needs to be fixed, failing is the right thing to do.

[wm75]

is all_fasta even the right table to use? wouldn't fasta_indexes be the correct one?

[bernt-matthias]

Still don't get why this break on au and not eu?

[mvdbeek]

all_fasta is for fasta files, fasta_indexes would be for .fai files as produced by samtools faidx

[wm75]

all_fasta is for fasta files, fasta_indexes would be for .fai files as produced by samtools faidx

tools-iuc/tools/clair3/clair3.xml

Line 20 in 6da96d8

samtools faidx reference.fasta &&

yes, that's why

[mvdbeek]

I guess the idea was that all_fasta is more widely populated ? I have no particular problem with this, of course it would be a little faster to go with fasta indexes.

[wm75]

Still don't get why this break on au and not eu?

so for sure all three versions of the tool that we have installed on .eu carry that faulty tool data table file with them, but the these tables are not listed in our installed data tables.
Maybe @bgruening has cleaned this up and fixed .eu when we first installed the tool?

[cat-bro]

this PR might be enough #6311