Installation on GNU/Linux

Install Debian package

If you are using a Debian-based Linux we suggest to use the deb-package provided by us in our archive. It is most easily installed with "gdebi" which automatically resolves the dependencies if they are available in your repositories.

sudo apt-get install gdebi
sudo gdebi /PATH/TO/OpenMS.deb

If you encounter errors with unavailable packages, you can try the following steps:
When Qt5 (or one of its packages, e.g. qt5xbase) is missing, usually your Debian is too old to have a recent enough version in its official repositories. We suggest to use the same packages that we use for building (make sure to adapt the Qt version and your Debian/Ubuntu version, here Xenial):

sudo add-apt-repository ppa:beineri/opt-qt59-xenial
sudo apt-get update

and try the installation again. If after the successful Qt installation above, ICU with its libicu is missing in a certain version, we suggest to find the missing version on https://pkgs.org/ and install it with gdebi, too. You can safely have multiple versions of ICU installed.
To ensure the tool functionality please add the OPENMS_DATA_PATH variable to your environment as follows (you will get an error advising you this when executing a tool):

export OPENMS_DATA_PATH=/usr/share/OpenMS 

If you used a thirdparty repository to install Qt5 (through the workaround above), do not forget to source the provided environment file like this (mind the version number again)

source /opt/qt59/bin/qt59-env.sh

Executables for THIRDPARTY applications can be found in:

/usr/share/OpenMS/THIRDPARTY

Add the folders inside to your PATH for a convenient use of our adapters.

Install via package managers

Currently there are also packaged versions of OpenMS provided for Fedora, OpenSUSE, Debian, and Ubuntu available in the corresponding package managers of these distributions (they might require a lookup in thirdparty "science" repositories). For other GNU/Linux distributions or to obtain the most recent version of the library you need to build your own OpenMS.

Note

Please note that these packages are not directly maintained by us and we can not guarantee the same behaviour as when building it on your own. Also their availability and version is subject to change and support might be limited (due to unforeseen or untested behaviour). We also suggest not to install them parallel to our Debian package.

Build it on your own

Get the source code from Github and see Building OpenMS on GNU/Linux on how to build OpenMS.

Note

Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.

Run a (Bio)Docker image

We are also constantly updating our Docker support. Images can be obtained via <a href="https://hub.docker.com/u/openms/>Dockerhub</a> and <a href="http://biocontainers.pro/">Biocontainers repositories. Depending on what you want to do, images can be pulled via one of the following commands

docker pull biocontainers/openms
docker pull openms/library
docker pull openms/executables
docker pull openms/pyopenms

once you have successfully installed docker (see Docker documentation).

More dockerfiles to build different kinds of images (corresponding to build instructions, e.g. on ArchLinux) can be found on our Github under: https://github.com/OpenMS/dockerfiles