====== gubbins ======

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

===== Information =====

  * Version: 3.4
  * Added: May, 2025
  * Link: https://github.com/nickjcroucher/gubbins

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load gubbins/3.4</code>

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

<code>$ cd /tmp
$ git clone https://github.com/nickjcroucher/gubbins.git -b v3.4
$ cd gubbins
$ module load python/3.10
$ sudo mkdir -p /export/apps/gubbins/3.4
$ sudo chown aorth /export/apps/gubbins/3.4
$ python -m venv /export/apps/gubbins/3.4/.venv
$ source /export/apps/gubbins/3.4/.venv/bin/activate
$ python -m pip install -U pip setuptools wheel
# Not sure what version gubbins v3.4 supports, but there was note about numpy 2 on master so let's keep this on the last 1.x release
$ python -m pip install numpy==1.26.4
$ python -m pip install biopython dendropy multiprocess scipy
# numba is not listed as a dependency on the gubbins README or setup.py, but it needs it
# Consult version table here: https://numba.readthedocs.io/en/stable/user/installing.html
$ python -m pip install numba==0.61.2
# Only needed for build, can remove after
$ sudo dnf install autoconf-archive.noarch libtool
# See: https://github.com/nickjcroucher/gubbins/issues/379
$ sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py
$ autoreconf -i
$ ./configure --prefix=/export/apps/gubbins/3.4
$ make
$ make install
$ mkdir -p /export/apps/gubbins/3.4/lib/R/x86_64-pc-linux-gnu-library/4.3
$ export R_LIBS_USER=/export/apps/gubbins/3.4/lib/R/x86_64-pc-linux-gnu-library/4.3
$ Rscript -e "install.packages(c('argparser', 'magrittr', 'tidyverse', 'BiocManager', 'aplot', 'patchwork', 'cowplot', 'RColorBrewer'), lib='/export/apps/gubbins/3.4/lib/R/x86_64-pc-linux-gnu-library/4.3', repos = 'https://cloud.r-project.org')"
$ Rscript -e "BiocManager::install(c('treeio', 'ggtree'), lib='/export/apps/gubbins/3.4/lib/R/x86_64-pc-linux-gnu-library/4.3')"
$ sudo chown -R root:root /export/apps/gubbins/3.4</code>