Getting Started

Installing Martian

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

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 1.18 or higher is required to build Martian.
• The Python adapter for wrapping stage code requires Python 2.7 (until version 4.0.9) or 3.6 or higher.
• To build the user interface, Node 14 or higher is required, along with yarn.

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:

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