## 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-v4.0.10-linux-x86_64.tar.xz](https://github.com/martian-lang/martian/releases/download/v4.0.10/martian-v4.0.10-linux-x86_64.tar.xz)|Linux|x86-64|e1e1a8550594a2f8008fadb1a8800e11ed297f8cf004143457dd8e1a186ad01d| |[martian-v4.0.4-linux-x86_64.tar.xz](https://github.com/martian-lang/martian/releases/download/v4.0.4/martian-v4.0.4-linux-x86_64.tar.xz)|Linux|x86-64|d37f8d4f17d5fa4192223a900af0ef29e97c9ac96b3bc820c2ad49162fec1584| |[martian-v4.0.4-linux-x86_64.tar.gz](https://github.com/martian-lang/martian/releases/download/v4.0.4/martian-v4.0.4-linux-x86_64.tar.gz)|Linux|x86-64|1083f0cbd4fae609f469b780cad76bddd2c1ef9e7e086312844b001d47aad5ae| |[martian-v3.2.5-linux-x86_64.tar.gz](https://github.com/martian-lang/martian/releases/download/v3.2.5/martian-v3.2.5-linux-x86_64.tar.gz)|Linux|x86-64|3b3fb295c120014be344a548670c68a8463e8fe338e84955728e74886c3b5762| |[martian-v3.2.5-linux-x86_64.tar.xz](https://github.com/martian-lang/martian/releases/download/v3.2.5/martian-v3.2.5-linux-x86_64.tar.xz)|Linux|x86-64|3ff65723d7c238c3f92680bf0c688d0506343f3415c89692802ebfb183b9d23f| |[martian-v3.1.0-linux-x86_64.tar.gz](https://github.com/martian-lang/martian/releases/download/v3.1.0/martian-v3.1.0-linux-x86_64.tar.gz)|Linux|x86-64|669d6722563dc23834162993fcb29d2471317a993b3ca30782fa879b8a6f94ff| |[martian-v3.0.0-linux-x86_64.tar.gz](https://github.com/martian-lang/martian/releases/download/v3.0.0/martian-v3.0.0-linux-x86_64.tar.gz)|Linux|x86-64|f0708a27113417d8d69ad61835930dba8a8fd827f11d4fb6ce5c6108e773a57e| |[martian-v2.3.2-linux-x86_64.tar.gz](https://github.com/martian-lang/martian/releases/download/v2.3.2/martian-v2.3.2-linux-x86_64.tar.gz)|Linux|x86-64|657eb6018a9371ac6af7267191945fd5ca590963d93d5d8096078f37d92b1107| |[Coming soon](https://github.com/martian-lang/martian/blob/master/.github/CONTRIBUTING.md)|macOS|x86-64| |[Please contribute!](https://github.com/martian-lang/martian/blob/master/.github/CONTRIBUTING.md)|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](https://golang.org) 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](https://nodejs.org) 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](https://github.com/martian-lang/martian), run `make all`, and the compiled binaries will be generated in `bin/`. ```sh $ 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`](https://bazel.build) Clone the repository and run ```sh bazel test //... ``` #### Build with go You can use ```sh $ 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`