Package Recipe 'openms-meta'

recipe openms-meta

OpenMS is an open-source software C++ library for LC-MS data management and analyses. The openms-meta package should not be installed. Please use one of its outputs libopenms, openms (=tools) or openms-thirdparty.

Homepage:: https://github.com/OpenMS/OpenMS
Documentation:: https://openms.readthedocs.io/en/latest/index.html
License:: BSD / BSD-3-Clause
Recipe:: /openms-meta/meta.yaml
Links:: biotools: openms, usegalaxy-eu: openms_fileconverter, doi: 10.1038/s41592-024-02197-7

package libopenms¶

Versions:

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5,

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5, 3.2.0-4, 3.1.0-4, 3.1.0-3, 3.1.0-2, 3.1.0-1, 3.0.0-1, 3.0.0-0, 2.9.1-4, 2.9.1-1, 2.9.1-0, 2.9.0-0, 2.8.0-4, 2.8.0-3, 2.8.0-2, 2.8.0-1, 2.8.0-0, 2.7.0-1, 2.6.0-0, 2.5.0-6, 2.5.0-5, 2.5.0-4, 2.5.0-3, 2.5.0-2, 2.5.0-1, 2.5.0-0, 2.4.0-3

Depends:

on __glibc >=2.17,<3.0.a0
on _openmp_mutex >=4.5
on bzip2 >=1.0.8,<2.0a0
on coin-or-cbc >=2.10.12,<2.11.0a0
on coin-or-cgl >=0.60,<0.61.0a0
on coin-or-clp >=1.17,<1.18.0a0
on coin-or-utils >=2.11,<2.12.0a0
on libgcc >=13
on libstdcxx >=13
on libsvm >=335,<400
on libzlib >=1.3.1,<2.0a0
on qt6-main >=6.7.3,<6.8.0a0
on xerces-c >=3.2.5,<3.3.0a0
on yaml-cpp >=0.8.0,<0.9.0a0

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install libopenms

to add into an existing workspace instead, run:

pixi add libopenms

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install libopenms

Alternatively, to install into a new environment, run:

conda create -n envname libopenms

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/libopenms:<tag>

(see libopenms/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

package openms¶

Versions:

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5,

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5, 3.2.0-4, 3.1.0-4, 3.1.0-3, 3.1.0-2, 3.1.0-1, 3.0.0-1, 3.0.0-0, 2.9.1-4, 2.9.1-1, 2.9.1-0, 2.9.0-0, 2.8.0-4, 2.8.0-3, 2.8.0-2, 2.8.0-1, 2.8.0-0, 2.7.0-1, 2.6.0-0, 2.5.0-6, 2.5.0-5, 2.5.0-4, 2.5.0-3, 2.5.0-2, 2.5.0-1, 2.5.0-0, 2.4.0-1, 2.4.0-0, 2.3.0-3, 2.3.0-2, 2.3.0-1, 2.3.0-0, 2.2.0-2, 2.2.0-1, 2.2.0-0, 2.1.0-0

Depends:

on eigen >=3.4.0,<3.5.0a0
on libarrow >=21.0.0,<21.1.0a0
on libgcc >=13
on libopenms 3.5.0 hdd6e20e_0
on libparquet >=21.0.0,<21.1.0a0
on libstdcxx >=13
on libsvm >=335,<400
on qt6-main >=6.7.3,<6.8.0a0
on xerces-c >=3.2.5,<3.3.0a0

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install openms

to add into an existing workspace instead, run:

pixi add openms

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install openms

Alternatively, to install into a new environment, run:

conda create -n envname openms

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/openms:<tag>

(see openms/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

package openms-meta¶

Versions:
Additional platforms:: linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install openms-meta

to add into an existing workspace instead, run:

pixi add openms-meta

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install openms-meta

Alternatively, to install into a new environment, run:

conda create -n envname openms-meta

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/openms-meta:<tag>

(see openms-meta/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

package openms-thirdparty¶

Versions:

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5,

3.5.0-0, 3.4.1-1, 3.4.1-0, 3.4.0-1, 3.4.0-0, 3.3.0-8, 3.3.0-6, 3.3.0-5, 3.2.0-5, 3.2.0-4, 3.1.0-4, 3.1.0-3, 3.1.0-2, 3.1.0-1, 3.0.0-1, 3.0.0-0, 2.9.1-4, 2.9.1-1, 2.9.1-0, 2.9.0-0, 2.8.0-4, 2.8.0-3, 2.8.0-2, 2.8.0-1, 2.8.0-0, 2.7.0-1, 2.6.0-0, 2.5.0-6, 2.5.0-5, 2.5.0-4, 2.5.0-3, 2.5.0-2, 2.5.0-1, 2.5.0-0

Depends:

on comet-ms 2024011
on gnuplot
on luciphor2 2020_04_03
on msgf_plus 2024.03.26
on openms 3.5.0 h78fb946_0
on percolator 3.7.1
on r-gplots
on sage-proteomics 0.14.7
on sirius-ms >=6.1.0
on thermorawfileparser 1.4.3

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install openms-thirdparty

to add into an existing workspace instead, run:

pixi add openms-thirdparty

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install openms-thirdparty

Alternatively, to install into a new environment, run:

conda create -n envname openms-thirdparty

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/openms-thirdparty:<tag>

(see openms-thirdparty/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/openms-meta/README.html)