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Configuration

blast2galaxy provides two ways to configure servers and profiles to be used with blast2galaxy.

  • TOML file based configuration
    This type of configuration can be used when using the CLI or Python API of blast2galaxy.

  • Python API based configuration
    This type of configuration can only be used when using the Python API of blast2galaxy.

Both ways of configuration are described in the following sections of this page.

TOML file based configuration

blast2galaxy uses the TOML file format for configuration of one or multiple Galaxy servers and one or multiple profiles. The default filename of the config file is .blast2galaxy.toml and blast2galaxy looks for it in the current working directory. If it can't find a configuration file in the current working directory it looks for one in the home-directory of the current user. If it can't find any configuration file an error message will be displayed.

An individually named configuration file at a storage location of your choice can be set via the following parameter of the CLI: 

--configfile=PATH

Example: 

--configfile=/opt/myapps/config/app1.blast2galaxy.toml


General Structure of the config TOML file

The configuration file has two types of sections:

  • [servers.###]
  • [profiles.###]

Where ### has to be replaced with either default or a unique server-ID / profile-ID.

Note

A config file must consist at least one [servers.] entry and one [profiles.] entry. If you provide [servers.default] and [profiles.default] the --server= and --profile= parameter of the CLI commands can be omitted.


Servers

The servers section holds one or multiple Galaxy server instances with their corresponding URLs and API-Keys.

Note

To connect to an API of an existing Galaxy server, the user of blast2galaxy has to provide API access credentials in the form of a Galaxy API key. How you can obtain an API key is described in the Tutorial

Example: 

[servers.default]
server_url = "https://usegalaxy.eu"
api_key = "65dcb*******************************"

Tip

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

List all available tools of the default server: 

blast2galaxy list-tools

List all available tools of the server with ID SERVER_ID: 

blast2galaxy list-tools --server=SERVER_ID


Profiles

The profiles section holds one or multiple profiles where each profile configures at least the Galaxy server and the Tool-ID to be used.

Mandatory fields for each profile are:

  • server   An ID of an configured server in the servers section
  • tool   Tool-ID for the tool on the Galaxy server

Optional fields for each profile are:

  • db   The ID of the BLAST or DIAMOND database to be used when using this profile. The --db parameter of the CLI or the db= argument of the methods of the Python API can be then omitted.

Example: 

[profiles.default]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2"

Tip

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-dbs --tool=TOOL_ID

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

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



Example of a complete configuration file with two servers and multiple profiles

[servers.default]
server_url = "https://usegalaxy.eu"
api_key = "65dcb*******************************"

[servers.my_institutes_server]
server_url = "https://galaxy.myinstitute.org"
api_key = "1k32z*******************************"

[profiles.default]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2"

[profiles.blastp]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2"

[profiles.blastp_plantae_genes]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2"
database = "plant_proteins"

[profiles.diamond_blastp_plantae_genes]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0"
database = "plant_proteins"

[profiles.blastn_vertebrata]
server = "default"
tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2"
database = "vertebrata_proteins"

Python API based configuration

If you use the Python API of blast2galaxy it is also possible to provide the configuration programmatically without the need for an .blast2galaxy.toml file.

Example for API based configuration during runtime for setting a default server and a default profile: 

import blast2galaxy

blast2galaxy.config.add_default_server(
    server_url = 'https://usegalaxy.eu', 
    api_key = 'your_api_key'
)

blast2galaxy.config.add_default_profile(
    server = 'default', 
    tool = 'toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2'
)

blast2galaxy.blastp(
    query = 'prot.fasta',
    db = 'database_id',
    out = 'result_blastp.txt',
    outfmt = '6'
)

If you want to add further servers and profiles beside the defaults you can use blast2galaxy.config.add_server() and blast2galaxy.config.add_profile(): 

import blast2galaxy

blast2galaxy.config.add_server(
    server = 'myserver',
    server_url = 'https://usegalaxy.eu', 
    api_key = 'your_api_key'
)

blast2galaxy.config.add_profile(
    profile = 'diamond',
    server = 'myserver',
    tool = 'toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0'
)

blast2galaxy.diamond(
    profile = 'diamond',
    query = 'prot.fasta',
    db = 'database_id',
    out = 'result_diamond_blastp.txt',
    outfmt = '6'
)