I’m trying to recover a fasta file from a blast search run in galaxy but blastdbcmd doesn’t recognize the database.
I made the blast database with makeblastdb in galaxy and I have tried it with and without parse_seq_ids - it is not recognized as a database either way.
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Hi @ajnaram
This is an older tool wrapper that was not designed to work with BLAST+ results associated with mapping against a custom blast database. Only natively indexed genomes can be parsed, and which are available vary by Galaxy server. You could set up your own local Galaxy, index the genome, and use the tool but I am guessing that is not your goal.
Parsing this data from custom/created databases without having it specifically indexed on the server certainly seems like useful functionality. There is also likely a workaround to achieve similar results without using this exact tool.
More feedback soon – I’m going to review all options (not those already available at Galaxy Main https://usegalaxy.org), consult with our developers, then will write back with the best way forward. Thanks for your patience!
Update: the tool now works on results from makeblastdb as run in Galaxy and is quite forgiving about which “index” identifier is used.
Great thank you! I am trying to build a workflow that my students can use with minimal external tools and without downloading many files/programs onto their computers. They will each be starting with different SRA databases.