- recipe easypqp
EasyPQP: Simple library generation for OpenSWATH
- Homepage:
- Developer docs:
- License:
BSD / BSD-3-Clause
- Recipe:
EasyPQP: Simple library generation for OpenSWATH ================================================
EasyPQP is a Python package that provides simplified and fast peptide query parameter generation for OpenSWATH. It can process input from MSFragger or other database search engines in pepXML format. Statistical validation can be conducted either using PyProphet or PeptideProphet/iProphet. Retention times are calibrated using an internal or external standard. In addition to a cumulative library, run-specific libraries are generated for non-linear RT alignment in OpenSWATH.
Installation ============
We strongly advice to install EasyPQP in a Python [*virtualenv*](https://virtualenv.pypa.io/en/stable/). EasyPQP is compatible with Python 3.
Install the development version of *easypqp* from GitHub:
- ````
$ pip install git+https://github.com/grosenberger/easypqp.git@master
````
Running EasyPQP ===============
*EasyPQP* is not only a Python package, but also a command line tool:
- ````
$ easypqp --help
````
or:
- ````
$ easypqp convert --help $ easypqp library --help
````
Docker ======
EasyPQP is also available from Docker (automated builds):
Pull the development version of *easypqp* from DockerHub (synced with GitHub):
- ````
$ docker pull grosenberger/easypqp:latest
````
- package easypqp¶
- Versions:
0.1.58-0,0.1.57-1,0.1.57-0,0.1.56-0,0.1.55-0,0.1.54-0,0.1.53-0,0.1.52-0,0.1.51-0,0.1.58-0,0.1.57-1,0.1.57-0,0.1.56-0,0.1.55-0,0.1.54-0,0.1.53-0,0.1.52-0,0.1.51-0,0.1.50-1,0.1.50-0,0.1.49-0,0.1.48-0,0.1.47-0,0.1.46-0,0.1.45-0,0.1.44-0,0.1.42-0,0.1.41-0,0.1.40-0,0.1.39-0,0.1.37-0,0.1.36-0,0.1.35-0,0.1.34-0,0.1.33-0,0.1.32-0,0.1.30-0,0.1.29-0,0.1.28-0,0.1.27-0,0.1.26-0,0.1.25-0,0.1.24-0,0.1.23-0,0.1.22-0,0.1.21-0,0.1.20-0,0.1.19-0,0.1.18-0,0.1.17-0,0.1.16-0,0.1.15-0,0.1.14-0,0.1.13-0,0.1.12-0,0.1.11-0,0.1.10-0,0.1.9-0,0.1.8-0,0.1.7-0,0.1.6-0,0.1.5-0,0.1.0-0- Depends:
on biopython
on click
on matplotlib-base
on numba
on numpy
on pandas
<3.0on pyopenms
on pyprophet
on python
>=3.9on scikit-learn
on scipy
on seaborn-base
on statsmodels
on tqdm
- 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 easypqp
to add into an existing workspace instead, run:
pixi add easypqp
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 easypqp
Alternatively, to install into a new environment, run:
conda create -n envname easypqp
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/easypqp:<tag>
(see easypqp/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/easypqp/README.html)
