From 667962dd0a3108a193375842e949501643d5c013 Mon Sep 17 00:00:00 2001 From: Anton Korobeynikov Date: Fri, 5 Apr 2024 11:56:40 +0300 Subject: [PATCH] Document building additional tools --- docs/installation.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/docs/installation.md b/docs/installation.md index 1e32dd527..1b48ada32 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -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 `/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