Installation.md

FluViewer-nf

Nextflow pipeline to run the FluViewer tool

Analyses

• Read trimming & QC: fastp
• Sequence analysis with FluViewer

To add in

• ? MultiQC process
• ? cutadapt (or do through fastp)
• Aggregate results in a linelist

Usage

To come

Output

To come

Provencance files

Details to come.

Standard Operating Procedure to Install FluViewer_conda

** Note this is undergoing changes so this is slightly out of date and will be updated shortly **

• This will install Kevin Kuchinski's tool FluViewer and all its necessary dependencies in a conda environment known as FluViewer.

• The dependencies are apparently fragile, so use only the yml file to build the environment.

• Also note, the included Spades version in the yml file does not have a MacOS version available on Conda, so it does not install on a Mac.

• When running FluViewer, the output directory needs to be in the same directory that you are running the script from (no subdirectories)

Install instructions

1. Log-on to Linux server (e.g. Sabin or Almeida)

2. Enter the following on the command line:

git clone https://github.com/JamesZlosnik/FluViewer_installation

3. This will create a directory called: FluViewer_installation.

4. Go into this directory

cd FluViewer_installation

5. Make the conda environment:

conda env create -f FluViewer_conda.yml

6. Once installed then you should be good to go once you activate the environment, e.g.

conda activate FluViewer