Applications/Anaconda
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Contents
Deprecation Notice
IMPORTANT NOTICE: If you're looking to set up a python environment for a particular program (eg. xcube, bwa etc) please use the miniconda virtual environments which are set up here. It is very likely in the future all python environments will be virtual environments using miniconda.
Application Details
There are two types of python provided on Viper, if you looking for the Original Python click here.
- Description: Python is a high-level interpreted programming language for general-purpose programming, supported by a large number of libraries for many tasks
- Versions:
- Python 2.7.11 and 3.5.1
- Anaconda v4.0 Python 2.7 and 3.5
- Anaconda v4.1.1 Python 2.7
- Anaconda v4.6 miniconda python 3.7 (Virtual Enviroments only)
- Module names:
- python/2.7.11 python/3.5.1
- python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 python/anaconda/4.6/miniconda/3.7 (VE)
- License: Free to use
- Python Python Software Foundation License
- Anaconda Python New BSD License
Usage Examples
Interactive
Interactive with command line:
[username@c170 ~]$ module add python/anaconda/4.0/2.7 [username@c170 ~]$ python Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org >>>
Interactive with command line with IPython:
[username@c170 ~]$ ipython Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) Type "copyright", "credits" or "license" for more information. IPython 5.1.0 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. In [1]:
Batch Submission
#!/bin/bash #SBATCH -J PythonTest # Job name, you can change it to whatever you want #SBATCH -N 1 # Number of nodes #SBATCH --ntasks-per-node 1 # Number of cores per node #SBATCH -o %N.%j.out # Standard output will be written here #SBATCH -e %N.%j.err # Standard error will be written here #SBATCH -p compute # Slurm partition, where you want the job to be queued module purge module add python/anaconda/4.0/3.5 python PythonTest.py
This is then submitted as follows:
[username@login01 ~]$ sbatch Pythontest.job Submitted batch job 289522
Python Packages
Common packages such as SciPy and NumPy are available across all Python modules. Other commonly used packages are listed below:
| Python Package | Import Command | Description | Available in |
|---|---|---|---|
| Biopython | import Bio | Collection of Python tools for computational biology and bioinformatics, containing classes to represent biological sequences and sequence annotations, and it is able to read and write to a variety of file formats. Also allows for a programmatic means of accessing online databases of biological information, such as those at NCBI. Separate modules extend Biopython's capabilities to sequence alignment, protein structure, population genetics, phylogenetics, sequence motifs, and machine learning. | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 |
| IPython | import IPython | Enhanced interactive shell for Python, including tools for parallel computing | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
| Keras | import keras | Wrapper for Neural net building library suitable for ML and DL research, see Tensorflow or Theano | python/anaconda/4.0/3.5 |
| Matplotlib | import matplotlib | Plotting library for Python and its numerical mathematics extension NumPy | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
| MPI4Py | import mpi4py | Provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. | python/anaconda/4.0/3.5 |
| OBITools | import obitools | Set of programs developed to simplify the manipulation of sequence files, mainly designed to help analyse Next Generation Sequencer outputs in the context of DNA Metabarcoding | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 |
| Tensorflow | import tensorflow | Neural net building library suitable for ML and DL research | python/anaconda/4.0/3.5 |
| Theano | import theano | Numerical computation library, primarily designed for machine learning | python/anaconda/4.0/3.5 |
| YT | import yt | Package for analysing and visualising volumetric data | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
Further Information