Java compiler¶

javacompiler · 0 contributors · 1 version

No documentation was provided: contribute one

Quickstart¶

from janis_unix.tools.compile import Compile

wf = WorkflowBuilder("myworkflow")

wf.step(
    "javacompiler_step",
    Compile(
        file=None,
    )
)
wf.output("out", source=javacompiler_step.out)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for javacompiler:

# user inputs
janis inputs javacompiler > inputs.yaml

inputs.yaml

file: file

Run javacompiler with:

janis run [...run options] \
    --inputs inputs.yaml \
    javacompiler

Information¶

ID:	`javacompiler`
URL:	No URL to the documentation was provided
Versions:	v1.0.0
Container:	openjdk:8
Authors:
Citations:	None
Created:	None
Updated:	None

Outputs¶

name	type	documentation
out	File

Additional configuration (inputs)¶

name	type	prefix	position	documentation
file	File		1

Workflow Description Language¶

version development

task javacompiler {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File file
  }
  command <<<
    set -e
    javac \
      -d '.' \
      '~{file}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "openjdk:8"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = glob("*.class")[0]
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Java compiler

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: openjdk:8

inputs:
- id: file
  label: file
  type: File
  inputBinding:
    position: 1

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: '*.class'
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: javac
arguments:
- prefix: -d
  position: 0
  valueFrom: .

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: javacompiler