ILRI Research Computing

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====== panaroo ======

A Bacterial Pangenome Analysis Pipeline. Shares information between genomes to correct errors. Can call large structural variants. Fast and scalable to over 10k bacterial genomes.

===== Information =====

  * Version: 1.3.3
  * Added: August, 2023
  * Link: https://github.com/gtonkinhill/panaroo

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load panaroo/1.3.3
$ panaroo --version</code>

**Note:** Please use the %%''--t''%% option to tell panaroo how many CPU cores it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone https://github.com/gtonkinhill/panaroo -b v1.3.3
$ cd panaroo
$ module load python/3.9
$ sudo mkdir -p /export/apps/panaroo/1.3.3
$ sudo chown aorth:aorth /export/apps/panaroo/1.3.3
$ python3 -m venv /export/apps/panaroo/1.3.3/venv
$ source /export/apps/panaroo/1.3.3/venv/bin/activate
$ pip3 install --upgrade setuptools pip wheel
$ python3 setup.py install
$ sudo chown -R root:root /export/apps/panaroo/1.3.3</code>

See also, the [[https://github.com/bioconda/bioconda-recipes/blob/master/recipes/panaroo/meta.yaml|bioconda recipe for panaroo]].