# PartitionFinder with conda on Rackham or Bianca

https://www.robertlanfear.com/partitionfinder/

## Installing the requirements and the tool

1. copy the content in to a file `PartitionFinder.yaml`

# conda env create -f PartitionFinder.yaml
name: PFinder
channels:
  - conda-forge
  - defaults
dependencies:
  - python=2.7
  - numpy
  - pandas
  - pytables
  - pyparsing
  - scipy
  - scikit-learn

2. Run these commands in a terminal on Rackham (or Bianca)

module load conda
source conda_init.sh
export CONDA_ENVS_PATH=/crex/proj/PROJECT/nobackup/CONDA_ENVS
mkdir -p $CONDA_ENVS_PATH

conda env create -f PartitionFinder.yaml

3. Download and extract the tool

cd /crex/proj/PROJECT/some_folder
wget https://github.com/brettc/partitionfinder/archive/refs/tags/v2.1.1.tar.gz
tar xvf v2.1.1.tar.gz

4. Run an example...

module load conda
source conda_init.sh
export CONDA_ENVS_PATH=/crex/proj/PROJECT/nobackup/CONDA_ENVS
conda activate PFinder

(PFinder) cd /crex/proj/PROJECT/some_folder/partitionfinder-2.1.1
(PFinder) python  PartitionFinder.py  examples/nucleotide

INFO     | 2023-06-19 14:25:05,810 | Note: NumExpr detected 16 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO     | 2023-06-19 14:25:05,810 | NumExpr defaulting to 8 threads.
INFO     | 2023-06-19 14:25:05,912 | ------------- PartitionFinder 2.1.1 -----------------
INFO     | 2023-06-19 14:25:05,912 | You have Python version 2.7
INFO     | 2023-06-19 14:25:05,912 | Command-line arguments used: PartitionFinder.py examples/nucleotide/
INFO     | 2023-06-19 14:25:05,912 | ------------- Configuring Parameters -------------
INFO     | 2023-06-19 14:25:05,912 | Setting datatype to 'DNA'
INFO     | 2023-06-19 14:25:05,912 | Setting phylogeny program to 'phyml'

...

INFO     | 2023-06-19 14:25:08,613 |    Your analysis also used PhyML, so please cite:
INFO     | 2023-06-19 14:25:08,613 |    Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology, 59(3), 307-321.
INFO     | 2023-06-19 14:25:08,613 |
INFO     | 2023-06-19 14:25:08,614 | Total processing time: 0:00:03 (h:m:s)
INFO     | 2023-06-19 14:25:08,614 | Processing complete.

## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)


###### tags: `UPPMAX`, `PartitionFinder`, `RT-276058`