MSTK - The Mass Spectrometry Toolkit

0. Status

---

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

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

1. 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

2. Building MSTK

---

In brief:

0. 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/
   

1. clone git repo / get tar.gz / etc

2. clone/unzip into MSTK-src directory

3. cd ..; make MSTK-build; cd MSTK-build

4. 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

5. make && make test

6. check if all tests succeeded

7. make install (this will also build the docs)

-M