Partition Finder 2.1.1

Basic Information

Installation

This entry covers the entire process performed for the installation and configuration of Partition Finder in a Cluster with Conda.

  1. Create a Conda Environment for Partition Finder

conda create -n partitionFinder

  1. Install the following dependencies (numpy, pandas, pytables, pyparsing, scipy, and sklearn).

conda install numpy pandas pytables pyparsing scipy scikit-learn

  1. Download the latest version of Partition Finder and decompress it.

wget https://github.com/brettc/partitionfinder/archive/v2.1.1.tar.gz
tar xfz v2.1.1.tar.gz

  1. Move it to wherever you want to store and give it execution permissions.

mv partitionfinder-2.1.1 /path/to/partition/finder
chmod +x partitionfinder-2.1.1/PartitionFinder.py

Usage

This section describes the method to submit jobs with the resource manager SLURM.

Note

If it is the first time you need Partition Finder or you want to use it locally, you should create and load the environment.

conda env create -f partitionFinder.yml

Partition Finder environment
name: partitionFinder
channels:
- file:///share/apps/intel/ps_xe/2019_update-4/conda_channel
- /share/apps/intel/ps_xe/2019_update-4/conda_channel
- intel
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- atomicwrites=1.3.0=py27_1
- attrs=19.3.0=py_0
- blosc=1.16.3=hd408876_0
- contextlib2=0.6.0.post1=py_0
- hdf5=1.10.4=hb1b8bf9_0
- importlib_metadata=0.23=py27_0
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran-ng=7.3.0=hdf63c60_0
- libstdcxx-ng=9.1.0=hdf63c60_0
- lz4-c=1.8.1.2=h14c3975_0
- lzo=2.10=h49e0be7_2
- mock=1.0.1=py27_0
- more-itertools=5.0.0=py27_0
- packaging=19.2=py_0
- pluggy=0.13.0=py27_0
- py=1.8.0=py_0
- pytables=3.5.2=py27h71ec239_1
- pytest=4.6.2=py27_0
- snappy=1.1.7=hbae5bb6_3
- zipp=0.6.0=py_0
- zstd=1.3.7=h0b5b093_0
- backports=1.0=py27_9
- backports.functools_lru_cache=1.5=py27_2
- bzip2=1.0.6=17
- certifi=2018.1.18=py27_2
- cycler=0.10.0=py27_7
- daal=2019.4=intel_243
- daal4py=2019.4=py27h7b7c402_0
- freetype=2.9=3
- funcsigs=1.0.2=py27_7
- functools32=3.2.3.2=py27_7
- icc_rt=2019.4=intel_243
- impi_rt=2019.4=intel_243
- intel-openmp=2019.4=intel_243
- intelpython=2019.4=0
- kiwisolver=1.0.1=py27_2
- libpng=1.6.36=2
- matplotlib=2.2.4=py27_1
- mkl=2019.4=intel_243
- mkl_fft=1.0.11=py27h7b7c402_2
- mkl_random=1.0.2=py27h7b7c402_4
- numexpr=2.6.8=py27_2
- numpy=1.16.2=py27h7b7c402_0
- numpy-base=1.16.2=py27_0
- openssl=1.0.2r=2
- pandas=0.24.1=py27_3
- pip=10.0.1=py27_0
- pyparsing=2.2.0=py27_2
- python=2.7.16=3
- python-dateutil=2.6.0=py27_12
- pytz=2018.4=py27_3
- scikit-learn=0.20.3=py27h7b7c402_5
- scipy=1.2.1=py27h7b7c402_3
- six=1.11.0=py27_3
- sqlite=3.27.2=4

  1. Run SLURM with the following bash file.

    sbatch partitionFinder.sh
    Partition Finder SLURM
    #!/bin/bash

#SBATCH --job-name=serial_test       # Job name
#SBATCH --mail-type=ALL         # Mail notification
#SBATCH --mail-user=<user>@<domain>  # User Email
#SBATCH --output=mothur-%j.out # Stdout (%j expands to jobId)
#SBATCH --error=mothur-%j.err  # Stderr (%j expands to jobId)
#SBATCH --ntasks=1                   # Number of tasks (processes)
#SBATCH --time=01:00                 # Walltime
#SBATCH --partition=longjobs         # Partition


##### ENVIRONMENT CREATION #####

module load python
source activate partitionFinder

##### JOB COMMANDS ####
/path/to/partition/finder/PartitionFinder.py /path/to/partitionFinder/input/files

Authors