# Toplevel Makefile Documentation

## Variables

### `MAKEFLAGS`

**Help:** Add -R to make to clear buitin variables

### `CMAKE_FLAGS`

**Help:** Additional CMake flags for CMake-related tasks

### `JOBS`

**Help:** Number of parallel jobs for building.
Defaults to number of CPU cores detected using `nproc`.

### `BASH`

**Help:** Shell to use for shell scripts

### `PYTHON`

**Help:** Python interpreter to use for Python scripts

### `MPIEXEC`

**Help:** MPI launcher command. Used in MPI-related tests only
NOTE: Setting this target does NOT enable MPI build!
Use release-mpi or debug-mpi targets to build with MPI support.

### `OPT_DIR`

**Help:** Output directory for build artifacts

### `ARCH`

**Help:** System architecture

### `PACKAGE_VERSION`

**Help:** Package version, derived from the latest git tag if not set

## Targets

### `help`

**Depends on:** None

**Help:** Generate help message from Makefile comments

### `dumpvar`

**Depends on:** None

**Help:** List all variables using .VARIABLES

### `build`

**Depends on:** `debug`

**Help:** build as an alias to debug

### `debug`

**Depends on:** None

**Help:** Generates debug build with tests enabled

### `debug-mpi`

**Depends on:** None

**Help:** debug with MPI

### `release`

**Depends on:** None

**Help:** Generates release build with native optimizations

### `release-mpi`

**Depends on:** None

**Help:** release with MPI

### `rel_with_dbg_alpine`

**Depends on:** None

**Help:** Generates RelWithDebInfo build without native optimizations
for fully-static-linked build on Alpine Linux

### `fmt`

**Depends on:** None

**Help:** Run code formatting checks and auto-formatting
Format the code using [`clang-format`](https://clang.llvm.org/docs/ClangFormat.html), [`sh`](https://github.com/mvdan/sh), [Black](https://black.readthedocs.io/en/stable/), [`cmake-format`](https://cmake-format.readthedocs.io/), and [`dos2unix`](https://www.freebsd.org/cgi/man.cgi?query=dos2unix&sektion=1).

### `scc`

**Depends on:** None

**Help:** Run source code counting
Note that this excludes third-party codes so should be preferred over pure `scc` in project root.

### `testsmall`

**Depends on:** `testsmall-debug`

**Help:** Alias to testsmall-debug

### `testsmall-mpi`

**Depends on:** `testsmall-debug-mpi`

**Help:** Alias to testsmall-debug-mpi

### `testsmall-debug`

**Depends on:** `debug`, `raw_data`

**Help:** Run (not necessiarily) small integration tests with debug build. Also tests `art_profile_builder`.
Env. Flags:

- FORMAT_ONLY=1: Stop after testing all output formats is working
- NO_FASTQC=1: Do not run FASTQC

### `testsmall-debug-mpi`

**Depends on:** `debug-mpi`, `raw_data`

**Help:** testsmall with MPI

### `testsmall-release`

**Depends on:** `release`, `raw_data`

**Help:** Run small tests with release build

### `testsmall-release-mpi`

**Depends on:** `release-mpi`, `raw_data`

**Help:** testsmall-release with MPI

### `testsmall-conda`

**Depends on:** `raw_data`

**Help:** Run small tests with conda-installed art_modern

### `testsmall-conda-mpi`

**Depends on:** `raw_data`

**Help:** testsmall-conda with MPI

### `raw_data`

**Depends on:** None

**Help:** Download raw data required for tests

### `clean`

**Depends on:** None

**Help:** Clean all build artifacts

### `testbuild`

**Depends on:** None

**Help:** Test building using diverse conditions

### `testbuild-mpi`

**Depends on:** None

**Help:** testbuild with MPI

### `testbuild-small`

**Depends on:** None

**Help:** Test building using diverse conditions with testsmall configurations

### `testbuild-small-mpi`

**Depends on:** None

**Help:** testbuild with MPI with testsmall configurations

### `doc`

**Depends on:** None

**Help:** Build documentation

### `cleandoc`

**Depends on:** None

**Help:** Clean and build documentation

### `serve-doc`

**Depends on:** None

**Help:** Serve built documentation at <http://localhost:8000>

### `packing`

**Depends on:** None

**Help:** Create binary packages

### `packing-update-containers`

**Depends on:** None

**Help:** Update Docker and Singularity containers used for packing