The Docker container is not compatible with recent BLAST DB versions

[bgruening]

ERROR for blast call 'blastn -outfmt "6 qseqid saccver qstart qend sstart send evalue staxids" -query ./id.7.tmp1 -db /data/db/databases/blast/nt/2024-08-15/nt -evalue 1 -max_target_seqs 500 -num_threads 1 -task blastn':
        return code = 2
        error cmd = blastn -outfmt "6 qseqid saccver qstart qend sstart send evalue staxids" -query ./id.7.tmp1 -db /data/db/databases/blast/nt/2024-08-15/nt -evalue 1 -max_target_seqs 500 -num_threads 1 -task blastn
        error stderr = BLAST Database error: Error: Not a valid version 4 database.

[bgruening]

xref: https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/24/have-you-tried-blast-2-9-0-and-version-5-blast-databases-dbv5/

[bgruening]

I tried updating to a new ubuntu, but then the deb package of viennarna is not available and newer once fail because they depend on liblapack which is not available in ubuntu, its called liblapacke or liblapack3 ... I also don't know why this tool needs python2.

ping @lotts @riasc @martin-raden

[martin-raden]

eventually, Steffen @lotts is the only one alive who knows the code.. maybe @JensGeorg has an idea...

is it possible to create softlinks of the lapack libs or to use conda to install the viennalib?

[bgruening]

I think we could use conda for everything, BUT someone would need to test this container/tool intensively afterwards :(

[JensGeorg]

I think we could ask Fayyaz to look into it, he has a good insight

…

On Fri, Sep 27, 2024 at 10:59 AM Björn Grüning ***@***.***> wrote: I think we could use conda for everything, BUT someone would need to test this container/tool intensively afterwards :( — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH44J4JJ22ANHQKQGB7IHZTZYUM57AVCNFSM6AAAAABOTJXN2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZYG44TKMJTGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[riasc]

Thanks for reporting this. It's been a minute since I looked into this code. I'd appreciate it if Fayyaz would be able to look into this? I probably won't have time until November.

Will try to get ahold of Steffen