ILRI Research Computing

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

====== 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
  * Link: https://github.com/artic-network/fieldbioinformatics

===== Usage =====

See versions which are available:
<code>$ module avail artic</code>

Load one version into your environment and run it:
<code>$ module load artic/1.2.3
$ artic</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

Run the test datasets:

<code>$ ./test-runner.sh nanopolish
$ ./test-runner.sh medaka</code>