bump blast

[bernt-matthias]

With 2.15 comes the nice option to select non-leaf nodes to filter taxonomically

https://www.ncbi.nlm.nih.gov/books/NBK131777/

[peterjc]

And a lot of housekeeping work on top (I assume based on IUC updates in similar repos?). This is looking good!

Linting is failing on some URLs, e.g.

.. ERROR: Error '('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))' accessing https://www.ncbi.nlm.nih.gov/pubmed/16796549
.. ERROR: Error '403 Client Error: Forbidden for url: https://academic.oup.com/gigascience/article/doi/10.1186/s13742-015-0080-7/2707769' accessing https://doi.org/10.1186/s13742-015-0080-7

For the first, we could use the DOI instead - https://doi.org/10.1089/cmb.2006.13.1028

And for the second one quoted, that's not very nice of OUP to block a DOI!

[Edit: Switched DUST paper URL to DOI in 5a33f24 on master]

[bernt-matthias]

Do you know by any change what the msa datatype is. Is there a Galaxy datatype? For now I removed it: 454488e. xref https://www.ncbi.nlm.nih.gov/books/NBK569842/

[bernt-matthias]

Linting is failing on some URLs, e.g.

.. ERROR: Error '('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))' accessing https://www.ncbi.nlm.nih.gov/pubmed/16796549
.. ERROR: Error '403 Client Error: Forbidden for url: https://academic.oup.com/gigascience/article/doi/10.1186/s13742-015-0080-7/2707769' accessing https://doi.org/10.1186/s13742-015-0080-7

For the first, we could use the DOI instead - https://doi.org/10.1089/cmb.2006.13.1028

And for the second one quoted, that's not very nice of OUP to block a DOI!

Yeah this is annoying us also in other repos. Since I would that @REFERENCES@ and the <citations> were redundant I hope that removing @REFERENCES@ is an acceptable hack d65268d

[peterjc]

I would guess "msa" in this context was aligned multiple sequence FASTA (all same length with "-" for gaps). But that is only a guess without looking back at Galaxy datatypes in the core or toolshed.

[peterjc]

I've not checked the Galaxy GUI recently enough to recall how and where the <CITATIONS> block is now rendered, but in the early days as I recall having this repeated in the tool text was pragmatic for visibility. Dropping the redundant reference text seems fine to me.

[peterjc]

Linting now failing with:

 .. ERROR: Error '403 Client Error: Forbidden for url: https://www.liebertpub.com/doi/10.1089/cmb.2006.13.1028' accessing https://doi.org/10.1089/cmb.2006.13.1028

Not just OUP being silly here - perhaps a planemo user agent tweak would be pragmatic here?

[peterjc]

Or we revert 5a33f24 for the NCBI pubmed URL instead of the DOI? Or we move this to a citation block?

[peterjc]

You'll need to add test-data/three_human_mRNA.fasta.gz to https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/.shed.yml (this is setup manually rather than automatical includes; there are pros and cons).

[peterjc]

I'm confused now. test-data/three_human_mRNA.fasta.gz was in the manifest but not in the repository? Oops - but why didn't this get flagged earlier if so?

[bernt-matthias]

I'm confused now. test-data/three_human_mRNA.fasta.gz was in the manifest but not in the repository?

Good thing is that it's fixed now.

Oops - but why didn't this get flagged earlier if so?

Seems that planemo just checks, but does not much with that information. Maybe its hidden somewhere in the logs?

[peterjc]

Thank you!

This looks ready to squash-and-merge, or rebase?

[bernt-matthias]

squash-and-merge seems fine for me. Can you do this here?

[peterjc]

Done, thank you! I don't recall right now if this will automatically deploy to the main Tool Shed, or not...

[bernt-matthias]

Done, thank you! I don't recall right now if this will automatically deploy to the main Tool Shed, or not...

Should happen automatically in the deploy job here: https://github.com/peterjc/galaxy_blast/actions/runs/14088420616

[peterjc]

Confirmed - I got the update email from the Tool Shed shortly afterwards. Thank you!

[nsoranzo]

Linting now failing with:

 .. ERROR: Error '403 Client Error: Forbidden for url: https://www.liebertpub.com/doi/10.1089/cmb.2006.13.1028' accessing https://doi.org/10.1089/cmb.2006.13.1028

Not just OUP being silly here - perhaps a planemo user agent tweak would be pragmatic here?

@peterjc I updated the user agent a few weeks ago in galaxyproject/planemo#1495 but it wasn't in a Planemo release until today, should hopefully be solved now.

[peterjc]

Wow - I didn't even have to open an issue 🤣

Thank you!