- recipe sirius-csifingerid
SIRIUS (CLI + GUI) LC-MS/MS data analyses framework. Includes: SIRIUS, ZODIAC, CSI:FingerID (with COSMIC) and CANOPUS
- Homepage:
- Documentation:
- Developer docs:
- License:
AGPL-3.0-only AND OTHER
- Recipe:
SIRIUS is a java-based software framework for the analysis of LC-MS/MS data of metabolites and other small molecules of biological interest. SIRIUS integrates a collection of our tools, including CSI:FingerID (with COSMIC), ZODIAC and CANOPUS. In particular, both the graphical user interface and the command line version of SIRIUS seamlessly integrate the CSI:FingerID and CANOPUS web services.
- package sirius-csifingerid¶
- Versions:
5.8.6-0,5.8.5-0,5.8.4-0,5.8.3-0,5.8.2-0,4.9.15-3,4.9.15-2,4.9.15-1,4.9.15-0,5.8.6-0,5.8.5-0,5.8.4-0,5.8.3-0,5.8.2-0,4.9.15-3,4.9.15-2,4.9.15-1,4.9.15-0,4.9.8-2,4.9.8-1,4.9.8-0,4.9.4-0,4.9.3-0,4.0.1-1,4.0.1-0- Depends:
on coin-or-cbc
on openjdk
17.*
- Additional platforms:
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 sirius-csifingerid
to add into an existing workspace instead, run:
pixi add sirius-csifingerid
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 sirius-csifingerid
Alternatively, to install into a new environment, run:
conda create -n envname sirius-csifingerid
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/sirius-csifingerid:<tag>
(see sirius-csifingerid/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:
[](http://bioconda.github.io/recipes/sirius-csifingerid/README.html)
