We use the anaconda 2. Download it from here, choose anaconda 2, then you will get a '.sh' file. To install anaconda2, execute:

$ bash name_of_the_file.sh

Then, add anaconda's bin directory into your path:

$ export PATH="/home/path_to_anaconda/anaconda2/bin:$PATH"

Next, install dependencies:

$ conda install setuptools
$ conda install nose
$ conda install numpy
$ conda install wheel
$ pip install autowrap

To clone and then build contrib, execute:

$ mkdir -p ~/BaseOpenMS
$ cd ~/BaseOpenMS

$ git clone  https://github.com/OpenMS/contrib.git
$ mkdir -p ~/BaseOpenMS/contrib-build
$ cd ~/BaseOpenMS/contrib-build

$ cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 ../contrib

If you encounter any problems, please refer to the instructions page.

Next, we clone the OpenMS repository. Note that you have to provide the absolute path to the contrib-build directory for cmake command. The absolute path should look like /home/your_user_name/BaseOpenMS/contrib-build.

$ cd ~/BaseOpenMS

$ git clone https://github.com/OpenMS/OpenMS.git
$ cd ~/BaseOpenMS/OpenMS
$ mkdir ~/BaseOpenMS/OpenMS-build
$ cd OpenMS-build

$ cmake -DOPENMS_CONTRIB_LIBS="/home/your_user_name/BaseOpenMS/contrib-build" -DBOOST_USE_STATIC=OFF ../OpenMS

Next, enter the make command to start the build process for OpenMS library. -j4 ensures that the job is done in parallel on 4 CPU's.

$ make -j4

Again, if you encounter any errors, refer to the official build instructions of OpenMS.

Edit ~/.bashrc to add the following two lines. Make sure you edit the absolute paths in both lines according to your system. The first line adds the path to lib folder of OpenMS-build to the environment variable LD_LIBRARY_PATH. The second line puts the path to bin folder of OpenMS-build to the environment variable PATH. This allows the user to use the commands for TOPP tools from anywhere on the system.

export LD_LIBRARY_PATH="/home/your_user_name/BaseOpenMS/OpenMS-build/lib:LD_LIBRARY_PATH"
export PATH=PATH:/home/your_user_name/BaseOpenMS/OpenMS-build/bin

Afterwards, restart the terminal for a new session or execute source ~/.bashrc so that the changes can take effect for the current session.

Execute the following command to test your installation.

$ make test

If everything went well, you should see the following lines at the end of the execution message:

100% tests passed, 0 tests failed out of 2017

Total Test time (real) = xxx.xx sec

The recommended way to install pyOpenMS is using pip tool, simply execute the following line and it's done:

$ pip install pyopenms

Optionally: If you want to install the pyopenms into a specific location, use:

$ pip install pyopenm --target="/home/path_to_destination/pyopenms"

Then add that directory into the PYTHONPATH:

$ export PYTHONPATH="/home/path_to_destination/pyopenms:$PYTHONPATH"

Of course you can also build pyopenms from source, please refer to instructions for pyOpenMS. We recommend to use pip tool, it's easier and faster.

To check your installation, the following command should not give any errors.

$ python -c "from pyopenms import BilinearInterpolation, MzMLFile, FeatureXMLFile, FeatureMap, MSExperiment, SplineSpectrum"

$ pip install pillow==4.2.1
$ pip install h5py==2.7.0
$ pip install scipy==0.19.1