squirrel-software
Table of Contents
squirrel
Some QUIck Reconstruction to Resolve Evolutionary Links
Information
- Version: 1.1.2
- Added: May, 2025
Usage
See which versions are available:
$ module avail squirrel
Load one version into your environment and run it:
$ module load squirrel/1.1.2 $ squirrel
Installation
Notes from the sysadmin during installation:
$ 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
squirrel-software.txt · Last modified: by aorth