From ab7106e25089d3c2b29d2b888901352aea820896 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Fri, 10 Jun 2022 15:27:02 +0200 Subject: [PATCH 1/2] Major fix of installation instructions --- .../installation-on-gnu-linux.md | 105 +++++++++++++----- 1 file changed, 76 insertions(+), 29 deletions(-) diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index f6482b31..ff9b12fb 100644 --- a/docs/installations/installation-on-gnu-linux.md +++ b/docs/installations/installation-on-gnu-linux.md @@ -3,41 +3,68 @@ Installation on GNU/Linux ## Install via Conda -Use conda or bioconda to install OpenMS. +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). 1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html). -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 +2. Add channels for dependencies: ``` + conda config --add channels defaults + conda config --add channels bioconda + conda config --add channels conda-forge +4. Install any of the following packages related to OpenMS -```{tab} openms +```{group-tab} openms openms contains OpenMS C++ Tools. ``` -```{tab} libopenms +```{group-tab} libopenms libopenms is the C++ library required for the OpenMS C++ Tools to work. ``` -```{tab} pyopenms +```{group-tab} pyopenms pyopenms is the python package that allows to use algorithms from libopenms in Python. ``` -```{tab} openms-thirdparty +```{group-tab} openms-thirdparty openms-thirdparty are external tools that are wrapped in OpenMS with adapters. This is required to use the adapters in the openms package. ``` -To install using bioconda: +via `bioconda` for release versions + +```{code-tab} bash openms +conda install openms +``` + +```{code-tab} bash libopenms +conda install libopenms +``` +```{code-tab} bash pyopenms +conda install pyopenms ``` -conda install -c bioconda openms -conda install -c bioconda libopenms -conda install -c bioconda openms-thirdparty + +```{code-tab} bash openms-thirdparty +conda install openms-thirdparty +``` + +or our own `openms` channel for nightly snapshots (which are build based on the same bioconda dependencies) + +```{code-tab} bash openms +conda install -c openms openms +``` + +```{code-tab} bash libopenms +conda install -c openms libopenms +``` + +```{code-tab} bash pyopenms +conda install -c openms pyopenms +``` + +```{code-tab} bash openms-thirdparty +conda install -c openms openms-thirdparty ``` ## Install via Debian package @@ -96,30 +123,50 @@ The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM. ``` -## Run via a (Bio)Docker image +## Run via a (Bio)Container -Make sure you have [Docker installed](https://docs.docker.com/engine/install/). +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)) -Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io). +Our container support is constantly updated. Docker images provided by us, +can be obtained via [ghcr.io](https://ghcr.io). -1. [openms-executables](https://ghcr.io/openms/openms-executables:latest) -2. [openms-library](https://ghcr.io/openms/openms-library:latest) +1. [openms-executables](https://ghcr.io/openms/openms-executables) +2. [openms-library](https://ghcr.io/openms/openms-library) -Or via [BioContainers Registeries](https://biocontainers.pro/registry). +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. 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) -Docker images can be pulled via or one of the following commands: +Images of the containers can be pulled via or one of the following commands: + +```{code-tab} bash Docker +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 +``` +```{code-tab} bash Singularity +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 ``` -docker pull biocontainers/openms -docker pull openms/library -docker pull openms/executables -docker pull openms/pyopenms +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: + ``` +docker pull ghcr.io/openms/openms-library +docker pull ghcr.io/openms/openms-executables +``` + +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) can be found on -GitHub in [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository. +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. From eaf3a63f1dae721a065f13ce33e39db874520209 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Sat, 11 Jun 2022 15:30:30 +0200 Subject: [PATCH 2/2] Fix --- docs/installations/installation-on-gnu-linux.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index ff9b12fb..e85491c8 100644 --- a/docs/installations/installation-on-gnu-linux.md +++ b/docs/installations/installation-on-gnu-linux.md @@ -8,11 +8,12 @@ obtain release versions (`bioconda` channel) and nightly versions (`openms` chan 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 -4. Install any of the following packages related to OpenMS + ``` +3. Install any of the following packages related to OpenMS ```{group-tab} openms openms contains OpenMS C++ Tools. @@ -160,7 +161,7 @@ If Singularity images fail to download or run, try to use the Docker images as S 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 ```