Python - modules

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Python programming language supports extensions in the form of so called 'modules'. To ease the administration of such modules we grouped them into one SW package (module). These packages are dependent on the Python version and used compiler.


Freely available to all MetaCentrum users. Module list:

Module name Included Python modules
python36-modules-gcc alabaster, attrs, audioread, Babel, bioformats, biopython, BUSCO, bz2file, CacheControl, cclib, certifi, cffi, cgeocore, chardet, click, colormath, configparser, contextlib2, cutadapt, cycler, Cython, czifile, decorator, Deepbinner, deepTools, deeptoolsintervals, DendroPy, docutils, fargene, fastcluster, fenics-dijitso, fenics-dolfin, fenics-ffc, fenics-fiat, fenics-ufl, future, futures, gffutils, h5py, HTSeq,iCount, idna, imagesize, intervaltree, ipython, ipython-genutils, jedi, Jinja2, joblib, joypy, jsonschema, jupyter-core, Keras, Keras-Applications, KerasPreprocessing, kiwisolver, librosa, llvmlite, lockfile, lzstring, mappy, Markdown, MarkupSafe, matplotlib, mpmath, msgpack-python, mshr, multiqc, NanoComp, NanoFilt, nanoget, NanoGUI, NanoLyse, nanomath, nanopack, NanoPlot, nanoplotter, NanoStat, natsort, nbformat, networkx, nose, numba, numexpr, numpy, numpydoc, ont_fast5_api, pandas, parso, patsy, pauvre, pexpect, phylo-utils, pickleshare, Pillow, pint, pip, pkgconfig, plotly, progressbar-latest, progressbar2, prompt-toolkit, psutil, psycopg2, ptyprocess, py2bit, pybedtools, pyBigWig, pybloomfiltermmap3, pycparser, pyfaidx, Pygments, pyparsing, pyrsistent, pysam, python-dateutil, python-Levenshtein, python-utils, pytz, PyVCF, pyvips, PyYAML, RaGOO, requests, resampy, retrying, scikit-bio, scikit-learn, scipy, seaborn, setuptools, simplegeneric, simplejson, six, sklearn, snowballstemmer, sortedcontainers, spacy-udpipe, spectra, Sphinx, sphinxcontrib-websupport, statsmodels, stop-words, sympy, tables, tifffile, torch, torchvision, traitlets, tree-distance, treeCl, urllib3, umi-tools, virtualenv, wcwidth, wheel, xopen
python26-modules-gcc backports.ssl-match-hostname, BaseSpacePy, Cython, drmaa, lmdb, matplotlib, mpi4py, nose, numexpr, numpy, pandas, patsy, pip, pyparsing, pysam, python-dateutil, pytz, ruffus, scipy, setuptools, six, statsmodels, tables, tornado
python26-modules-intel backports.ssl-match-hostname, Cython, lmdb, matplotlib, mpi4py, nose, numexpr, numpy, pandas, patsy, pip, pyparsing, pysam, python-ase, python-dateutil, pytz, ruffus, scipy, setuptools, six, statsmodels, tables, tornado
python27-modules-gcc alabaster, amqp, appdirs, argh, astropy, atomicwrites, attrs, audioread, Babel, backports-abc, backports.functools-lru-cache, backports.shutil-get-terminal-size, backports.ssl-match-hostname, beautifulsoup4, BESST, bioformats, biopython, bx, bx-python, bz2file, certifi, cffi, chardet, chromosomer, click, cmake, colormath, configobj,configparser, cycler, Cython, cutadapt, CVXOPT, dask, deap, decorator, DendroPy, dlcpar, docopt, docutils, drmaa, enum34, et-xmlfile, ete2, funcsigs, functools32, future, google, greenlet, h5py, hashlib, HTSeq, idna, imagesize, ipython, ipython-genutils, jdcal, Jinja2, joblib, jsonschema, keras, khmer, kindel, kombu, librosa, llvmlite, lmdb, lxml, lzstring, MACS2, Mako, MAnorm, Markdown, MarkupSafe, mathstats, matplotlib, MCL-Markov-Cluster, more-itertools, mpi4py, mpmath, multiqc, nanoget, nanomath, NanoPlot, nanoplotter, netCDF4, networkx, nose, numba, numexpr, numpy, numpydoc, OBITools, olefile, openpyxl, pandas, Paste, pathlib2, patsy, pexpect, pickleshare, PICOS, Pillow, Pint, pip, pluggy, prompt-toolkit, protobuf, ptyprocess, py, pyaudio, pybedtools, pybind11, PyBrain, pycairo, PyClone, pycparser, pycrypto, pycuda, PyDP, pyfaidx, Pygments, pygpu, pyopencl, pyparsing, pyprotobuf, pyrad, Pyro4, pysam, pytest, python-ase, python-dateutil, python-igraph, python-yaml-logger, pytools, pytz, PyVCF, PyWavelets, PyYAML, pyzmq, RASPA2, repoze.lru, requests, resampy, Routes, rpy2, ruffus, scandir, scikit-image, scikit-learn, scipy, scoop, screed, seaborn, selectors34, serpent, setuptools, simplegeneric, simplejson, simplesam, singledispatch, sisl six, sklearn, snowballstemmer, SomVarIUS, spectra, Sphinx, sphinxcontrib-websupport, SQLAlchemy, statsmodels, subprocess32, sympy, tables, TEPID, Theano, toolz, tornado, tqdm, traitlets, typing, ujson, urllib3, vine, virtualenv, wcwidth, WebHelpers, WebOb, wheel, xopen
python27-modules-intel alabaster, astropy, audioread, Babel, backports.functools-lru-cache, backports.ssl-match-hostname, biopython, bz2file, certifi, chardet, click, colormath, cutadapt, cvxopt, cycler, Cython, deap, decorator, DendroPy, docutils, enum34, funcsigs, functools32, future, greenlet, idna, imagesize, Jinja2, joblib, Keras, librosa, lmdb, lxml, lzstring, MACS2, Mako, Markdown, MarkupSafe, matplotlib, MCL-Markov-Cluster, mock, mpi4py, mpmath, multiqc, networkx, nose, numexpr, numpy, numpydoc, pandas, patsy, PICOS, Pint, pip, protobuf, PyAudio, pybedtools, pycairo, Pygments, pygpu, pyparsing, pyprotobuf, pyrad, pysam, python-ase, python-dateutil, python-igraph, python-yaml-logger, pytz, PyYAML, pyzmq, requests, resampy, ruffus, scikit-learn, scipy, scoop, setuptools, simplejson ,singledispatch, six, snowballstemmer, spectra, Sphinx, sphinxcontrib-websupport, statsmodels, subprocess32, sympy, tables, Theano, tornado, typing, urllib3, virtualenv, xopen
python34-modules-gcc alabaster, argh, audioread, Babel, beautifulsoup4, biopython, bleach, bz2file, certifi, chardet, cycler, Cython, deap, decorator, docutils, elasticsearch, elasticsearch-dsl, fretbursts, future, google, greenlet, h5py, html5lib, idna, imagesize, Jinja2, joblib, Keras, khmer, kindel, librosa, lmfit, MarkupSafe, matplotlib, mpmath, networkx, numexpr, numpy, pandas, pbr, phconvert, pip, protobuf, py, Pygments, pypandoc, pyrad, pyparsing, pyRserve, pysam, PySide, pytest, python-dateutil, pytz, PyYAML, pyzmq, requests, resampy, RNFtools, scikit-learn, scipy, scoop, screed, seaborn, setuptools, simplesam, six, sklearn, SMBL, snakemake, snowballstemmer, Sphinx, sphinx-rtd-theme, sphinxcontrib-napoleon, sphinxcontrib-websupport, sympy, tables, termcolor, Theano, tqdm, typing, urllib3, virtualenv, webencodings, Werkzeug, wheel
python34-modules-intel alabaster, appdirs, ase, audioread, Babel, beautifulsoup4, bleach, click, cutadapt, cycler, Cython, deap, decorator, DendroPy, dnaio, docutils, Flask, google, graphviz, greenlet, h5py, html5lib, imagesize, itsdangerous, Jinja2, joblib, Keras, librosa, lxml, MarkupSafe, matplotlib, networkx, nose, numexpr, numpy, olefile, packaging, pandas, patsy, pbr, Pillow, pip, pockets, protobuf, py, pygame, Pygments, pygraphviz, pypandoc, pyparsing, pyRserve, pysam, pytest, python-dateutil, pytz, PyWavelets, PyYAML, pyzmq, requests, resampy, RNFtools, scikit-image, scikit-learn, scipy, scoop, setuptools, six, SMBL, snakemake, snowballstemmer, sphinx-rtd-theme, sphinxcontrib-napole, statsmodels, tables, termcolor, Theano, virtualenv, webencodings, Werkzeug, wheel, wrapt, xopen
python27-modules-intel15 apptools, backports.functools-lru-cache, backports.weakref, beautifulsoup4, bleach, configobj, cycler, Cython, deap, decorator, envisage, funcsigs, google, googleapis-common-protos, h5py, html5lib, ipython, ipython-genutils, Keras, kiwisolver, lmdb, matplotlib, mayavi, mdtraj, mock, mpi4py, mpmath, networkx, nose, numexpr, numpy, opencv-python, pandas,, pbr, petsc, petsc4py, pexpect, pickleshare, Pillow, Pint, pip, protobuf, pycairo, pyface, Pygments, pyparsing, pysam, python-dateutil, pytz, PyVTK, PyYAML, rmsd, scikit-image, scikit-learn, scipy, setuptools, sfepy, simplegeneric, six, sklearn, subprocess32, sympy, tables, TEToolkit, traitlets, traits, traitsui, webencodings, Werkzeug, wheel
Module notes

For actual list of available modules use command pipX.Y list, e.g.

module add python36-modules-gcc
pip3.6 list
  • To use of python module python-igraph you should also add one of the SW modules igraph-0.7.1-gcc and igraph-0.7.1-intel.
  • To use of python module tables you should also add one of the SW modules hdf5-1.8.12-gcc or hdf5-1.8.12-intel.
  • To use of python module h5py you should also add one of the SW modules hdf5-1.8.14-gcc or hdf5-1.8.14-intel.
  • To use of python module tetoolkit you should also add SW module R-3.2.3-intel.


Differs according to used Python module.


Initialize environment with command:

module add python26-modules-intel

You can also install your own Python module, see SW installation for details.

To get actual list of all installed modules, just run

python -c "help('modules')";

Python modules conflicts

Different modules of Python (and python-modules) are usually impossible to run along. But it is possible to add modules only for calling necessary scripts, not for the whole batch. Like:

 (module add python34-modules-gcc;
      cython ...;
 (module add qiime-1.9.1; ...; ...;


Python modules documentation is available through PyPI installer page.

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