MSTK - The Mass Spectrometry Toolkit

Status

We are currently integrating / relocating libraries into the MSTK framework.

Check out the integration branch for the most recent (and pretty stable) code.

Available MSTK modules

Here is a list of modules/components that are currently available in MSTK:

common: code used by all MSTK components (e.g. error handling, typedefs and logging)
fe: the LC/MS feature extraction module
ipaca: isotope pattern calculation
psf: peak shape function modeling
aas: provides standard elements and its corresponding isotope distributions, amino acids, standard modifications and its specificities, stoichiometries and amino acid sequences

Building MSTK

In brief:

fulfill the MSTK dependencies. You need:

 * boost (>=1.42), http://boost.org/
 * vigra (>=1.5, for MSTK/psf only), http://hci.iwr.uni-heidelberg.de/vigra/
 * libfbi (1.3, for MSTK/fe only), https://github.com/mkirchner/libfbi/

clone git repo / get tar.gz / etc
clone/unzip into MSTK-src directory
cd ..; make MSTK-build; cd MSTK-build

Build all MSTK components, in release mode, include debug info and enable testing

 cmake ../MSTK2-src 
     -DCMAKE_BUILD_TYPE=RelWithDebInfo 
     -DENABLE_TESTING=TRUE
     -DMSTK_COMPONENTS=common;fe;ipaca;psf
     -DVIGRA_INCLUDE_DIR=/path/to/vigra/includes
     -DCMAKE_INSTALL_PREFIX=/my/install/path

Use -DENABLE_EXAMPLES=TRUE to automatically build examples

make && make test
check if all tests succeeded
make install (this will also build the docs)

-M