Example documentation to download and list database

[phrh]

Hello,

I am following the documentation to download a ncbi database nt. The files are dowloaded but when I try to check the available databases in local nothing appears. I try also with the pdbaa database as shown in the example but it does not work. Is there any step missing?

Download Protein Data Bank amino acid database (pdbaa)

docker run --rm \ -v $HOME/blastdb:/blast/blastdb:rw \ -w /blast/blastdb \ ncbi/blast \ update_blastdb.pl pdbaa

Display database(s) in $HOME/blastdb

docker run --rm \ -v $HOME/blastdb:/blast/blastdb:ro \ ncbi/blast \ blastdbcmd -list /blast/blastdb -remove_redundant_dbs

[tom6931]

Hi, Thank you for your interest in BLAST+ Docker. I've just tried this on GCP and it worked (see below).

Some questions:

• Are you on a cloud provider? If so, which one?
• Which OS are you using?
• Did you create a $HOME/blastdb directory?
• Is there anything in $HOME/blastdb?

Regards,

Tom

`madden@cwl-madden:~$ docker run --rm -v $HOME/blastdb:/blast/blastdb:rw -w /blast/blastdb ncbi/blast update_blastdb.pl pdbaa

madden@cwl-madden:~$ ls blastdb/ pdbaa.pdb pdbaa.pin pdbaa.pos pdbaa.ppd pdbaa.psq pdbaa.pto taxdb.bti pdbaa.phr pdbaa.pog pdbaa.pot pdbaa.ppi pdbaa.ptf taxdb.btd `

[phrh]

Hi, Thank you for your answer

Are you on a cloud provider? If so, which one?

No, I am at a local pc

Which OS are you using?

Description: Ubuntu 18.04.4 LTS

Did you create a $HOME/blastdb directory?

I did not, but when I run update_blastdb.pl It was created.

Is there anything in $HOME/blastdb?

Yes, the files are there.

nt.00.tar.gz nt.03.tar.gz.md5 nt.07.tar.gz nt.10.tar.gz.md5 nt.14.tar.gz nt.17.tar.gz.md5 nt.21.tar.gz nt.24.tar.gz.md5 pdbaa.tar.gz nt.00.tar.gz.md5 nt.04.tar.gz nt.07.tar.gz.md5 nt.11.tar.gz nt.14.tar.gz.md5 nt.18.tar.gz nt.21.tar.gz.md5 nt.25.tar.gz pdbaa.tar.gz.md5 nt.01.tar.gz nt.04.tar.gz.md5 nt.08.tar.gz nt.11.tar.gz.md5 nt.15.tar.gz nt.18.tar.gz.md5 nt.22.tar.gz nt.25.tar.gz.md5 nt.01.tar.gz.md5 nt.05.tar.gz nt.08.tar.gz.md5 nt.12.tar.gz nt.15.tar.gz.md5 nt.19.tar.gz nt.22.tar.gz.md5 nt.26.tar.gz nt.02.tar.gz nt.05.tar.gz.md5 nt.09.tar.gz nt.12.tar.gz.md5 nt.16.tar.gz nt.19.tar.gz.md5 nt.23.tar.gz nt.26.tar.gz.md5 nt.02.tar.gz.md5 nt.06.tar.gz nt.09.tar.gz.md5 nt.13.tar.gz nt.16.tar.gz.md5 nt.20.tar.gz nt.23.tar.gz.md5 nt.27.tar.gz nt.03.tar.gz nt.06.tar.gz.md5 nt.10.tar.gz nt.13.tar.gz.md5 nt.17.tar.gz nt.20.tar.gz.md5 nt.24.tar.gz nt.27.tar.gz.md5

[tom6931]

Thanks for the details. The instructions assume you are on AWS or GCP. In order to get your files nicely delivered, you should add --decompress to your command-line (see below). First, you may want to remove the files that are currently present. Sorry that this is unclear. I'll make a note to update the documentation.

regards,

Tom

docker run --rm -v $HOME/blastdb:/blast/blastdb:rw -w /blast/blastdb ncbi/blast update_blastdb.pl pdbaa --decompress

[phrh]

thank you!