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Getting BLAST databases
How one may go about accessing BLAST databases on the cloud varies depending on where the data comes from and the environment in which it runs.
| Environment | Origin: NCBI | Origin: User-provided |
|---|---|---|
| VM/AMI | Pre-configured in /blast/blastdb
|
Build your own using: Install in /blast/blastdb_custom
|
| Docker | Obtain via: Install in /blast/blastdb_custom
|
Same as above cell |
The BLAST databases available in Google Cloud Storage (GCS) can be found here.
The BLAST databases listed above are pre-configured and available on
/blast/blastdb. Any user-provided BLAST databases can be installed in
/blast/blastdb_custom for ease of integration with BLAST tools on that
VM/AMI.
Please see data provisioning in our Docker image documentation.
If you want to BLAST against your own BLAST databases (in any enviroment),
please build your BLAST databases using either makeblastdb4cloud or makeblastdb,
and make those BLAST databases available in /blast/blastdb_custom.
The BLAST VM/AMI comes pre-configured with BLAST databases retrieved by this program. It is configured to download the most recent version of these BLAST databases at the time of the first search, but these BLAST databases will not be automatically updated as newer databases become available.
remote-fuser downloads the BLAST database over the network, so the first
BLAST search against a new database will be slow. remote-fuser caches the
database on disk and subsequent searches will be faster.
remote-fuser is part of the NCBI SRA Toolkit.
You can download and install remote-fuser following these instructions or via
a Docker container.