Getting Started

Installing Martian

Official binary distributions of the Martian toolchain are available for Linux. We hope to have MacOS and Windows support soon.

Download OS Arch SHA256
martian-v4.0.4-linux-x86_64.tar.xz Linux x86-64 d37f8d4f17d5fa4192223a900af0ef29e97c9ac96b3bc820c2ad49162fec1584
martian-v4.0.4-linux-x86_64.tar.gz Linux x86-64 1083f0cbd4fae609f469b780cad76bddd2c1ef9e7e086312844b001d47aad5ae
martian-v3.2.5-linux-x86_64.tar.gz Linux x86-64 3b3fb295c120014be344a548670c68a8463e8fe338e84955728e74886c3b5762
martian-v3.2.5-linux-x86_64.tar.xz Linux x86-64 3ff65723d7c238c3f92680bf0c688d0506343f3415c89692802ebfb183b9d23f
martian-v3.1.0-linux-x86_64.tar.gz Linux x86-64 669d6722563dc23834162993fcb29d2471317a993b3ca30782fa879b8a6f94ff
martian-v3.0.0-linux-x86_64.tar.gz Linux x86-64 f0708a27113417d8d69ad61835930dba8a8fd827f11d4fb6ce5c6108e773a57e
martian-v2.3.2-linux-x86_64.tar.gz Linux x86-64 657eb6018a9371ac6af7267191945fd5ca590963d93d5d8096078f37d92b1107
Coming soon macOS x86-64
Please contribute! Windows x86-64

System Requirements

  • Currently, running pipelines requires a Linux system with kernel version 2.6.23 or later.
    • Martian 2.x has been confirmed working on Linux versions as far back as RHEL/CentOS 5.5 or Ubuntu 10.
    • Martian 3.0 and higher are supported on RHEL/CentOS 6 or Ubuntu 12 or higher.
    • For the time being, mrp only functions on Linux.
    • Ancillary tools such as mro and mrstat are expected to work on MacOS.
  • Martian was designed for large bioinformatics pipelines. One may run into issues on systems with less than 6GB of available memory. Editing jobmanagers/config.json to reduce the default memory request for jobs may alleviate some of those issues.

Building from Source

Prerequisites

  • Go 1.14 or higher is required to build Martian.
  • The Python adapter for wrapping stage code requires Python 2.7 or 3.6 or higher.
  • To build the user interface, Node 10 or higher is required, along with NPM.

Building the source

Build with make

To build the Martian toolchain from source, clone the Martian GitHub repository, run make all, and the compiled binaries will be generated in bin/.

$ git clone --recursive https://github.com/martian-lang/martian.git
$ cd martian
$ make all
$ ls bin
mrjob mro mrp mrstat

To test that everything is working, make longtests runs a few simple test pipelines and verifies that their output is correct, including tests that pipeline failures are handled correctly.

Build with bazel

Clone the repository and run

bazel test //...

Build with go

You can use

$ go get golang.org/x/tools/cmd/goyacc
$ go install golang.org/x/tools/cmd/goyacc
$ go get github.com/martian-lang/martian/cmd/...
$ go generate github.com/martian-lang/martian/...
$ go install github.com/martian-lang/martian/cmd/...

However that will not you’ll still need to run make web in the repository directory in order to build the web UI. Furthermore, the martian binaries expect various data files to be located in specific relative locations. Building with make is therefore recommended.

Environment Setup

Martian Executables

The Martian toolchain comprises five core executables:

Executable Role Details
mro check Compiler/Checker Parses and validates Martian code
mro format Formatter Canonicalizes Martian code formatting and whitespace
mro graph Analysis Supports queries, e.g. tracing inputs/outputs, as well as formatting the call graph.
mro edit Refactoring Rename or remove stages/pipelines/inputs/outputs.
mrp Pipeline Runtime Executes a Martian pipeline or stage.
mrjob Stage wrapper Wraps user stage code, ensuring it obeys the contracts mrp expects.
mrstat Progress query CLI tool for querying mrp’s API and issuing commands.

Make these executables available on your PATH and then confirm that you can run them. If you unpacked or cloned Martian into /home/user/git/martian, for example, then:

$ export PATH=$PATH:/home/user/git/martian/bin
$ mro --version
v4.0.2

Martian Project Path – MROPATH

The code for a Martian pipeline project typically lives under a single directory. Set MROPATH to this directory to allow the Martian executables to find the project code without the need for absolute paths.

When developing multiple projects, switch between them by changing MROPATH.

To give you an idea of how a Martian project looks in practice, here’s an example:

martian_project/
    bin/
        hello_go
        hello_rust
    lib/
        go/
            vendor/github.com/martian-lang/martian
                src/martian/adapter/adapter.go
            src/
                hello_go.go
        rust/
            Cargo.lock
            Cargo.toml
            src/
                hello_rust.rs
    mro/
        _hello_stages.mro
        hello.mro
        stages/
            hello/
                hello_py/
                    __init__.py

Stage code (or binaries) are searched for relative to - the mro file defining the stage - the MROPATH - the PATH