q2-ps-qc¶

Qiime2 Plug-in which allows users to run various quality control tests on files generated using PepSIRF (e.g. correlation measurements).

Installation¶

Dependencies¶

qiime2-2021.11 +
PepSIRF v1.4.0
q2-pepsirf v2021.12
q2-ps-plot v2021.9.15

Qiime2 Installation¶

Visit: https://docs.qiime2.org/2022.2/install/ for installation documentation on Qiime2

PepSIRF Installation:¶

Visit: https://github.com/LadnerLab/PepSIRF for installation documentation on PepSIRF

q2-pepsirf Installation:¶

Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-pepsirf1/ for installation documentation on q2-pepsirf

q2-ps-plot Installation:¶

Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-ps-plot/ for installation documentation on q2-ps-plot

q2-ps-qc Installation:¶

Make sure your Qiime2 conda environment is activated by running the command:

conda activate qiime2-2021.11

You can replace qiime2-2021.11 above with whichever version of QIIME 2 you have currently installed.

Now you are ready to install ps-qc. Run the following commands:

pip install git+https://github.com/LadnerLab/q2-ps-qc.git

Run qiime2 info to check for a successful installation. If installation was successful, you will see q2-ps-qc: version in the list of installed plugins

Updating¶

To update the QC module, run the following command:

pip install -U git+https://github.com/LadnerLab/q2-ps-qc.git