Partition Finder 2.1.1¶
Basic Information¶
- Deploy date: 5 December 2016
- Official Website: http://www.robertlanfear.com/partitionfinder/
- License: GNU General Public License
- Installed on: Apolo II
Installation¶
This entry covers the entire process performed for the installation and configuration of Partition Finder in a Cluster with Conda.
- Create a Conda Environment for Partition Finder
conda create -n partitionFinder
- Install the following dependencies (numpy, pandas, pytables, pyparsing, scipy, and sklearn).
conda install numpy pandas pytables pyparsing scipy scikit-learn
- 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
- 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
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
Run SLURM with the following bash file.
sbatch partitionFinder.sh
#!/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¶
- Manuela Carrasco Pinzón <mcarras1@eafit.edu.co>