====== augur ======
Augur is a bioinformatics toolkit to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. Augur originated as part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data.

===== Information =====

  * Version: 11.2.0
  * Added: March, 2021
  * Link: https://github.com/nextstrain/augur

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load augur/11.2.0
$ augur</code>

To familiarize yourself with the Augur workflow you should try their sample ncov data, for example:

<code>$ interactive -c 4 -w compute05 -J nextstrain-augur
$ git clone https://github.com/nextstrain/ncov.git /var/scratch/aorth-ncov
$ cd /var/scratch/aorth-ncov
$ module load augur/11.2.0
$ gzip -d -c data/example_sequences.fasta.gz > data/example_sequences.fasta
$ snakemake --cores 4 --profile ./my_profiles/getting_started</code>

For more information see the [[https://docs.nextstrain.org/projects/augur/en/stable/|Augur documentation]].

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

<code>$ sudo mkdir -p /export/apps/augur/11.2.0
$ sudo chown aorth:aorth /export/apps/augur/11.2.0
$ module load python/3.7
$ python -m venv /export/apps/augur/11.2.0/.venv
$ source /export/apps/augur/11.2.0/.venv/bin/activate
$ pip install nextstrain-augur==11.2.0
$ pip install nextstrain-cli
$ pip install snakemake
$ module load mafft/7.313 RAxML/8.2.12 fasttree/2.1.11 iqtree/1.6.12 vcftools/0.1.16 nextalign/0.1.7
$ nextstrain setup-check
$ sudo chown -R root:root /export/apps/augur/11.2.0</code>