artic-software
Table of Contents
artic
artic is a pipeline and set of accompanying tools for working with viral nanopore sequencing data, generated from tiling amplicon schemes.
Information
- Version: 1.2.3
- Added: February, 2023
Usage
See versions which are available:
$ module avail artic
Load one version into your environment and run it:
$ module load artic/1.2.3 $ artic
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ git clone https://github.com/artic-network/fieldbioinformatics -b v1.2.3 $ cd fieldbioinformatics $ module load python/3.8 $ sudo mkdir -p /export/apps/artic/1.2.3 $ sudo chown aorth /export/apps/artic/1.2.3 $ python3 -m venv /export/apps/artic/1.2.3 $ source /export/apps/artic/1.2.3/bin/activate $ pip install biopython==1.79 clint==0.5.1 medaka==1.7.3 multiqc==1.13 pandas==1.4.4 tqdm==4.64.1 $ python setup.py install $ sudo chown -R root:root /export/apps/artic/1.2.3
Run the test datasets:
$ ./test-runner.sh nanopolish $ ./test-runner.sh medaka
artic-software.txt · Last modified: 2023/02/24 03:46 by aorth