diff --git a/conf.py b/conf.py index d69c157b..1fd961a6 100644 --- a/conf.py +++ b/conf.py @@ -30,7 +30,6 @@ 'sphinx_copybutton', 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', - 'sphinx.ext.autosectionlabel', 'myst_parser', 'notfound.extension', 'sphinxcontrib.images', @@ -47,9 +46,6 @@ "linkify_fuzzy_links", ] -# Generate header anchors for cross-linking in markdown until depth n -myst_heading_anchors = 3 - autosummary_generate = True autosummary_imported_members = True diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index 60aac51b..a8d7c3ed 100644 --- a/docs/installations/installation-on-gnu-linux.md +++ b/docs/installations/installation-on-gnu-linux.md @@ -3,17 +3,17 @@ Installation on GNU/Linux ## Install via Conda -You can use conda 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). +Use conda or bioconda to install OpenMS. 1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html). -2. Add channels for dependencies: - ```bash - conda config --add channels defaults - conda config --add channels bioconda - conda config --add channels conda-forge +2. Install OpenMS using conda: + `conda install -c openms openms` +3. Other OpenMS packages can be installed using: + ``` + conda install -c openms pyopenms + conda install -c openms openms-thirdparty + conda install -c openms libopenms ``` -3. Install any of the following packages related to OpenMS ```{tab} openms openms contains OpenMS C++ Tools. @@ -32,57 +32,13 @@ openms-thirdparty are external tools that are wrapped in OpenMS with adapters. T the openms package. ``` -via `bioconda` for release versions - -````{tab} openms -```bash -conda install openms -``` -```` - -````{tab} libopenms -```bash -conda install libopenms -``` -```` - -````{tab} pyopenms -```bash -conda install pyopenms -``` -```` - -````{tab} openms-thirdparty -```bash -conda install openms-thirdparty -``` -```` - -or our own `openms` channel for nightly snapshots (which are build based on the same bioconda dependencies) - -````{tab} openms -```bash -conda install -c openms openms -``` -```` - -````{tab} libopenms -```bash -conda install -c openms libopenms -``` -```` +To install using bioconda: -````{tab} pyopenms -```bash -conda install -c openms pyopenms ``` -```` - -````{tab} openms-thirdparty -```bash -conda install -c openms openms-thirdparty +conda install -c bioconda openms +conda install -c bioconda libopenms +conda install -c bioconda openms-thirdparty ``` -```` ## Install via Debian package @@ -135,60 +91,34 @@ Debian package. Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM. ``` -## Run via a (Bio)Container +## Run via a (Bio)Docker image -Install a containerization software (e.g., [Docker](https://docs.docker.com/engine/install/) or [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps)) +Make sure you have [Docker installed](https://docs.docker.com/engine/install/). -Our container support is constantly updated. Docker images provided by us, -can be obtained via [ghcr.io](https://ghcr.io). +Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io). -1. [openms-executables](https://ghcr.io/openms/openms-executables) -2. [openms-library](https://ghcr.io/openms/openms-library) +1. [openms-executables](https://ghcr.io/openms/openms-executables:latest) +2. [openms-library](https://ghcr.io/openms/openms-library:latest) -Otherwise, the [BioContainers Registries](https://biocontainers.pro/registry) and the associated Galaxy -project provide native containers from our bioconda packages for both Docker and Singularity. +Or via [BioContainers Registeries](https://biocontainers.pro/registry). 1. [BioContainers libopenms](https://biocontainers.pro/tools/libopenms) 2. [BioContainers openms](https://biocontainers.pro/tools/openms) 3. [BioContainers openms-thirdparty](https://biocontainers.pro/tools/openms-thirdparty) 4. [BioContainers pyOpenMS](https://biocontainers.pro/tools/pyopenms) -Images of the containers can be pulled via or one of the following commands: +Docker images can be pulled via or one of the following commands: -````{tab} Docker -```bash -docker pull quay.io/biocontainers/libopenms -docker pull quay.io/biocontainers/openms -docker pull quay.io/biocontainers/pyopenms -docker pull quay.io/biocontainers/openms-thirdparty ``` -```` - -````{tab} Singularity -```bash -docker pull https://depot.galaxyproject.org/singularity/libopenms -docker pull https://depot.galaxyproject.org/singularity/openms -docker pull https://depot.galaxyproject.org/singularity/pyopenms -docker pull https://depot.galaxyproject.org/singularity/openms-thirdparty -``` -```` - -If Singularity images fail to download or run, try to use the Docker images as Singularity will automatically convert them. - -Docker images from our own continuous integration can be installed via the following commands: - -```bash -docker pull ghcr.io/openms/openms-library -docker pull ghcr.io/openms/openms-executables +docker pull biocontainers/openms +docker pull openms/library +docker pull openms/executables +docker pull openms/pyopenms ``` -per default this results in the download of the latest nightly snapshot. Specify a release version to -receive a stable version. - -Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) yourself can be found on -GitHub in our [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository. - ## Build OpenMS from source To build OpenMS from source, follow the build instructions for [Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/install_linux.html). +Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on +GitHub in [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository. diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md index 48b5c61e..4e1769c3 100644 --- a/docs/installations/installation-on-macos.md +++ b/docs/installations/installation-on-macos.md @@ -37,27 +37,9 @@ source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile Make sure `` points to the folder where OpenMS is installed locally (e.g., `/Applications/OpenMS-`) -## Install via Conda with the Bioconda channel +## Install via Conda or Bioconda -Follow the instructions for {ref}`GNU/Linux <./installation-on-gnu-linux.md#install-via-conda>`. Use the Terminal.app or any -terminal of your choice to run the commands. - -```{note} -Due to unavailability of an exact copy of the macOS build machines used in bioconda, we currently cannot offer nightly -builds for macOS on our own conda channel `openms`. -``` - -## Run via (Bio)Container - -Follow the instructions for{ref}`GNU/Linux <./installation-on-gnu-linux.md#run-via-a-bio-container>`. Make sure to -follow specific installation instructions for macOS during the installation of the containerization software. -Use the Terminal.app or any terminal of your choice to run the commands. - -```{note} -Running OpenMS containers (currently built for Linux) on macOS involves -running virtual machines (sometimes hidden from the user, e.g., with Docker). -This comes with disadvantages in runtime and memory consumption. -``` +Follow [these](installation-on-gnu-linux.md#install-via-conda) instructions. ## Build OpenMS from source