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Document building additional tools
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asl committed Apr 5, 2024
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Expand Up @@ -90,6 +90,27 @@ which will install SPAdes into `/usr/local/bin`.

After installation you will get the same files (listed above) in `./bin` directory (or `<destination_dir>/bin` if you specified PREFIX). We also suggest adding `bin` directory to the `PATH` variable.

## Building additional tools
SPAdes toolkit includes a number of standalone tools that are built using core
SPAdes algorithms. This includes:

- Binning refining tool BinSPreader
- HMM-to-graph aligning tool Pathracer
- Sequence-to-graph aligning tool SPAligner

These tools are not built by default and therefore must be built separately. One
can pass `-SPADES_ENABLE_PROJECTS="semicolon-separated list of projects"` to enable building only
subset of SPAdes components. The components are:

- `spades`
- `spades_tools` [standalone SPAdes tools](standalone.md)
- `binspareader` [BinSPreader](binspreader.md)
- `pathracer`
- `spaligner`

By default only SPAdes and SPAdes tools are enabled (so
`-DSPADES_ENABLE_PROJECTS="spades;spades_tools"` is the default). Alternatively,
one can simply enable building everything via specifying `SPADES_ENABLE_PROJECTS="all"`.

## Verifying your installation

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