installation-with-conda.md

Conda

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Install via Conda

At this time, we do not provide a conda package for our GUI tools. This means if you want to install e.g., TOPPView or SwathWizard
for use in for example one of our tutorials, please refer to a different installation method below.

You can use conda or mamba to install the OpenMS library and tools without user interface. Depending on the conda channel, you can obtain release versions (bioconda channel) and nightly versions (openms channel).

1. Follow the instructions to install conda or mamba. In the following, every mention of conda may be substituted by mamba for faster environment solving.

2. We recommend to create a new environment with one of the supported python version versions:

    conda create -n openms python=3.10

3. Add some channels to find dependencies:

    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge

   :::{note} You can also add the channels for your current environment only with the --env option. ::: :::{warning} The order of the channels is important! ::: :::{note} conda-forge might already be added if you are using Mambaforge. :::

4. Install any of the following packages related to OpenMS

   :::::{tab-set}

   ::::{tab-item} openms :sync: openms

   openms contains all OpenMS C++ command-line tools. GUI applications like TOPPView currently cannot be installed via conda. ::::

   ::::{tab-item} libopenms :sync: libopenms

   libopenms is the C++ library required for the OpenMS C++ Tools to work. This is also an auto-installed dependency of openms. ::::

   ::::{tab-item} pyopenms :sync: pyopenms

   pyopenms is the python package that allows to use algorithms from libopenms in Python. ::::

   ::::{tab-item} openms-thirdparty :sync: openms-thirdparty

   openms-thirdparty are external tools that are wrapped in OpenMS with adapters. This package is required to use the adapters in the openms package.

   :::{warning} Due to unavailability of a large part of the thirdparty tools for macOS via conda, we are not providing a openms-thirdparty package on macOS either. :::

   ::::

   :::::

   via bioconda for release versions

   ::::{tab-set}

   :::{tab-item} openms :sync: openms

   conda install openms
   

   :::

   :::{tab-item} libopenms :sync: libopenms

   conda install libopenms
   

   :::

   :::{tab-item} pyopenms :sync: pyopenms

   conda install pyopenms
   

   :::

   :::{tab-item} openms-thirdparty :sync: openms-thirdparty

   conda install openms-thirdparty
   

   :::

   ::::

   or our own openms channel for nightly snapshots (which are build based on the same bioconda dependencies)

   ::::{tab-set}

   :::{tab-item} openms :sync: openms

   conda install -c openms openms
   

   :::

   :::{tab-item} libopenms :sync: libopenms

   conda install -c openms libopenms
   

   :::

   :::{tab-item} pyopenms :sync: pyopenms

   conda install -c openms pyopenms
   

   :::

   :::{tab-item} openms-thirdparty :sync: openms-thirdparty

   conda install -c openms  openms-thirdparty
   

   :::

   ::::