Skip to content

CLI Usage

After installation of blast2galaxy you can use the blast2galaxy CLI to perform BLAST and DIAMOND searches against the Galaxy servers you have configured in the .blast2galaxy.toml file

You can find all possible subcommands and parameters in the CLI reference.

List available and compatible BLAST+ and DIAMOND tools of a Galaxy server

After configuration of at least one default server you can use the list-tools command of the CLI to get a table with all NCBI BLAST+ tools and DIAMOND available on that Galaxy server. The table also contains the Tool-IDs for configuration of the blast2galaxy profiles.

List all available tools of the default server: 

blast2galaxy list-tools

List all available tools of the server with the ID SERVER_ID: 

blast2galaxy list-tools --server=SERVER_ID

List available tools and sequence databases of a Galaxy server

After configuration of at least one default profile you can use the list-dbs command of the CLI to get a table with all available sequence databases for a specific tool.

List all available databases of the tool with ID TOOL_ID on the default server: 

blast2galaxy list-tools --tool=TOOL_ID

If you have configured multiple servers in the config file .blast2galaxy.toml, you can also obtain the available databases for a tool on a specific server other than the default server.

List all available databases of the tool with ID TOOL_ID on the server with ID SERVER_ID: 

blast2galaxy list-tools --server=SERVER_ID --tool=TOOL_ID

Perform search requests

blast2galaxy blastn --profile=blastn --query=dna.fasta --db=vertebrata_cds --out=blastn_vertebrata.txt --outfmt=6

blast2galaxy diamond-blastp --profile=diamond_blastp --query=protein.fasta --db=uniprot_swissprot_2023_03 --out=result_diamond_blastp.txt --outfmt=6

Output result to stdout

If the --out parameter of the CLI is omitted, the result of the search request is forwarded to stdout.