tbtools

TBtools

Overview

TBtools-II is a Java-based bioinformatics toolkit that runs on Windows and macOS. Prefer TBtools' own bundled Java/RPC/CLI tools. Do not introduce Python, R, Conda, or other dependencies unless the user explicitly asks.

Honor TBTOOLS_HOME or TBTOOLS_JAR if set; fall back to the platform default.

Setup

Windows (PowerShell)

$TbtoolsHome = if ($env:TBTOOLS_HOME) { $env:TBTOOLS_HOME } else { "C:\Program Files\TBtools" }
$TbtoolsJar = if ($env:TBTOOLS_JAR) { $env:TBTOOLS_JAR } else { Join-Path $TbtoolsHome "TBtools_JRE1.6.jar" }
$env:Path = "$(Join-Path $TbtoolsHome 'bin');$env:Path"

Test-Path $TbtoolsJar
java -version

macOS / Linux (bash)

TBTOOLS_HOME="${TBTOOLS_HOME:-/Applications/TBtools-II}"
TBTOOLS_JAR="${TBTOOLS_JAR:-$(find "$TBTOOLS_HOME" -name 'TBtools*.jar' -maxdepth 4 2>/dev/null | head -1)}"
export PATH="$TBTOOLS_HOME/bin:$PATH"

[ -f "$TBTOOLS_JAR" ] && echo "jar: $TBTOOLS_JAR" || echo "TBtools jar not found — set TBTOOLS_JAR"
java -version

Use bin/ (bin\ on Windows) tools directly when the task is a standard external tool workflow:

blastn -query query.fa -db db_prefix -out results.tsv -outfmt 6
muscle -in input.fa -out aligned.fa
iqtree -s aligned.fa -m MFP -bb 1000 -nt AUTO
diamond blastp -d proteins.dmnd -q query.fa -o matches.tsv

RPC Server

Windows (PowerShell)

.\scripts\start_rpc_server.ps1 -Background

Direct form:

java -cp $TbtoolsJar biocjava.rpc.RpcServer

macOS / Linux (bash)

java -cp "$TBTOOLS_JAR" biocjava.rpc.RpcServer &

Default URLs:

rpcPort is configurable in TBtools config. rpcBindAddress is normalized to loopback only (127.0.0.1 or ::1); do not expose the RPC server on 0.0.0.0.

RPC Helper

Windows (PowerShell)

function Invoke-TBtoolsRpc {
    param(
        [Parameter(Mandatory=$true)][string]$Method,
        [hashtable]$Params = @{},
        [string]$Uri = "http://127.0.0.1:8765/rpc",
        [int]$TimeoutSec = 600
    )

    $body = @{
        jsonrpc = "2.0"
        method = $Method
        params = $Params
        id = [guid]::NewGuid().ToString()
    } | ConvertTo-Json -Depth 50

    $response = Invoke-RestMethod -Method Post -Uri $Uri -ContentType "application/json" -Body $body -TimeoutSec $TimeoutSec
    if ($null -ne $response.error) {
        $reason = if ($response.error.data -and $response.error.data.reason) { " ($($response.error.data.reason))" } else { "" }
        throw "TBtools RPC error $($response.error.code): $($response.error.message)$reason"
    }
    return $response.result
}