====== squirrel ======

Some QUIck Reconstruction to Resolve Evolutionary Links

===== Information =====

  * Version: 1.1.2
  * Added: May, 2025
  * Link: https://github.com/aineniamh/squirrel

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load squirrel/1.1.2
$ squirrel</code>

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

<code>$ sudo mkdir -p /export/apps/squirrel/1.1.2
$ sudo chown aorth /export/apps/squirrel/1.1.2
$ module load python/3.10
$ python -m venv /export/apps/squirrel/1.1.2/.venv
$ source /export/apps/squirrel/1.1.2/.venv/bin/activate
$ cd /tmp
$ git clone https://github.com/aineniamh/squirrel.git -b 1.1.2
$ cd squirrel
$ python -m pip install -U pip setuptools wheel
# From: https://github.com/aineniamh/squirrel/blob/1.1.2/environment.yml
$ python -m pip install snakemake==7.32
$ python -m pip install pulp==2.7.0 # See: https://github.com/snakemake/snakemake/issues/2607
$ sed -i 's/iqtree  -s/iqtree2  -s/' squirrel/scripts/*.smk # See: https://github.com/aineniamh/squirrel/issues/73
$ python -m pip install .
$ mkdir -p /export/apps/squirrel/1.1.2/lib/R/x86_64-pc-linux-gnu-library/4.3
$ module load R/4.3
$ export R_LIBS_USER=/export/apps/squirrel/1.1.2/lib/R/x86_64-pc-linux-gnu-library/4.3
$ Rscript -e "install.packages(c('tidyverse', 'BiocManager', 'plotly', 'ape'), repos = 'https://cloud.r-project.org')"
$ Rscript -e "BiocManager::install('ggtree')"
$ sudo chown -R root:root /export/apps/squirrel/1.1.2</code>