Python - modules

Description

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.

License

Differs according to used Python module.

Availability

Freely available to all MetaCentrum users. Module list:

Module name	Included Python modules
python36-modules-gcc	absl-py, alabaster, antismash, ants, antspyx, appdirs, argcomplete, argh, args, Arpeggio, asgiref, astunparse, atomicwrites, attmap, attrs, audioread, Babel, bagit, bcbio-gff, bioformats, biopython, bleach, blis, blocked-matrix-utils, bmtk, bmtool, bokeh, boltons, boto, BUSCO, bwapy, bz2file, CacheControl, cached-property, cachetools, Cactus, cairocffi, CairoSVG, catalogue, cclib, CCMetagen, certifi, cffi, cgecore, cgen, chardet, chart-studio, clang, click, clint, cloudpickle, cmake, codepy, colorama, coloredlogs, colorlog, colormath, commonmark, ConfigArgParse, configparser, contextlib2, crf-beam, cssselect2, cupy-cuda102, cutadapt, cvxpy, cwl-runner, cwltool, cycler, cymem, Cython, cytocad, czifile, dask, dataclasses, datrie, decorator, Deepbinner, deepTools, deeptoolsintervals, defusedxml, demes, demesdraw, DendroPy, descartes, dill, Django, django-markwhat, dnaio, docopt, docutils, dptools, ecos, edlib, entrypoints, et-xmlfile, ete3, fargene, fast_ctc_decode, fastcluster, fastqsplitter, fastrlock, fenics-dijitso, fenics-dolfin, fenics-ffc, fenics-fiat, fenics-ufl, flatbuffers, funcsigs, future, galaxy-containers, galaxy-tool-util, galaxy-util, gast, genomeworks-cuda-10-2, gevent, gffutils, gitdb, GitPython, google-auth, google-auth-oauthlib, google-pasta, gor4, graphviz, greenlet, GridDataFormats, grpcio, gsd, h5py, helperlibs, hgtector, hmmlearn, horovod, HTSeq, humanfriendly, iCount, idna, imageio, imagesize, importlib-metadata, importlib-resources, iniconfig, instagraal, install, intervaltree, ipykernel, ipyparallel, ipython, ipython-genutils, ipywidgets, isal, isodate, itsdangerous, jdcal, jedi, Jinja2, joblib, joypy, jsonschema, jupyter, jupyter-client, jupyter-console, jupyter-core, kaleido, keras, Keras-Applications, Keras-Preprocessing, keyring, kiwisolver, librosa, llvmlite, lockfile, logmuse, LoProp, lxml, lzstring, Mako, mandrill, MAnorm, mappy, Markdown, markdown2, MarkupSafe, matplotlib, MDAnalysis, mdtraj, MiModD, Minipolish, mistune, mizani, mmtf-python, mock, more-itertools, mpmath, msgpack, msgpack-python, mshr, multiqc, murmurhash, mypy-extensions, NanoComp, NanoFilt, nanoget, NanoGUI, NanoLyse, nanomath, nanopack, NanoPlot, nanoplotter, nanoQC, NanoStat, NanoSV, nanovar, natsort, nbconvert, nbformat, netaddr, networkx, nf-core, nibabel, nose, notebook, numba, numexpr, numpy, numpydoc, oauthlib, ont-bonito, ont-fast5-api, opencv-python, openpyxl, opt-einsum, osqp, oyaml, packaging, pairtools, palettable, pandas, pandocfilters, Paralleltask, parasail, parso, patsy, pauvre, pexpect, phylo-utils, pickleshare, Pillow, Pint, pip, piper, pkgconfig, plac, platformdirs, plotly, plotnine, pluggy, ply, preshed, prettytable, progress, progressbar-latest, progressbar2, progressbar33, prometheus-client, prompt-toolkit, protobuf, prov, psutil, psycopg2, ptyprocess, py, py2bit, pyarrow, pyasn1, pyasn1-modules, pybedtools, pyBigWig, pybind11, pybloomfiltermmap3, pycparser, pycryptodome, pydantic, pydot, pyfaidx, pyfasta, Pygments, pygpu, pymannkendall, pynmodlt, Pyomo, PyOpenGL, pyparsing, PyQt5, PyQt5-Qt5, PyQt5-sip, pyrad, pyrsistent, pysam, pyScss, pyspoa, pysvg-py3, pytabix, pytest, pytest-workflow, python-dateutil, Python-Deprecated, python-igraph, python-Levenshtein, python-utils, pytools, pytz, PyVCF, pyvips, PyWavelets, PyYAML, pyzmq, qdldl, qtconsole, QtPy, questionary, RaGOO, ratelimiter, rdflib, rdflib-jsonld, recentrifuge, refgenconf, refgenie, regex, repoze.lru, requests, requests-cache, requests-oauthlib, resampy, retrying, rich, rich-click, Routes, rsa, ruamel.yaml, ruamel.yaml.clib, Runner, ruptures, schema-salad, scikit-bio, scikit-image, scikit-learn, scikit-misc, scipy, scs, seaborn, Send2Trash, seqdist, setuptools, sewar, shellescape, SICER2, simplegeneric, simplejson, six, sklearn, smmap, snakemake, snowballstemmer, sortedcollections, sortedcontainers, spacy, spacy-udpipe, spectra, spektral, Sphinx, sphinxcontrib-applehelp, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, sqlparse, srsly, statsmodels, stop-words, svgwrite, sympy, tables, tabulate, tagore, tensorboard, tensorboard-data-server, tensorboard-plugin-wit, tensorflow, tensorflow-cpu, tensorflow-estimator, termcolor, terminado, testpath, texttable, textX, Theano, thinc, tifffile, tinycss2, toml, tomli, toposort, torch, tornado, tqdm, traitlets, tree-distance, treeCl, treeswift, Trycycler, tskit, typing-extensions, ubiquerg, ufal.udpipe, umi-tools, url-normalize, urllib3, virtualenv, wasabi, wcwidth, webcolors, webencodings, Werkzeug, whatshap, wheel, widgetsnbextension, wrapt, xgboost, xlrd, XlsxWriter, xmltodict, xopen, yacman, zipp, zipstream-new, zope.event, zope.interface
python26-modules-gcc	backports.ssl-match-hostname, BaseSpacePy, Cython, drmaa, lmdb, matplotlib, mpi4py, nose, numexpr, numpy, pandas, patsy, pip, pyparsing, pysam, python-ase, 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, coloredlogs, colormath, configobj, configparser, cutadapt, cvxopt, cycler, Cython, dask, deap, decorator, DendroPy, dlcpar, docopt, docutils, drmaa, enum34, et-xmlfile, ete2, ete3, fargene, funcsigs, functools32, future, google, greenlet, h5py, hashlib, HTSeq, humanfriendly, 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, monotonic, more-itertools, mpi4py, mpmath, multiqc, nanoget, nanomath, NanoPlot, nanoplotter, netCDF4, networkx, nose, numba, numexpr, numpy, numpydoc, OBITools, olefile, openpyxl, pandas, pandoc, Paste, pathlib2, patsy, pexpect, pickleshare, PICOS, Pillow, Pint, pip, pluggy, ply, prompt-toolkit, protobuf, psutil, 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, repliscan, 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, transposer, 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, ete3, fretbursts, future, google, greenlet, h5py, html5lib, idna, imagesize, ipython-genutils, Jinja2, joblib, Keras, khmer, kindel, kiwisolver, librosa, lmfit, MarkupSafe, matplotlib, mpmath, netaddr, networkx, numexpr, numpy, pandas, pbr, phconvert, pip, pockets, protobuf, py, pyfasta, Pygments, pypandoc, pyparsing, pyrad, pyRserve, pysam, PySide, pytest, python-dateutil, pytz, PyVCF, PyYAML, pyzmq, rabifier, 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, traitlets, 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-napoleon, statsmodels, tables, termcolor, Theano, virtualenv, webencodings, Werkzeug, wheel, wrapt, xopen
python27-modules-intel15	apptools, backports.functools-lru-cache, backports.weakref, beautifulsoup4, biopython, 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, path.py, 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.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of python-modules and load default version of python-modules as

module avail python-modules/ # list available modules
module load python-modules   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail python-modules

and choose explicit version you want to use.

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 (versions) 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;
        alpha_rarefaction.py ...;
        beta_diversity_through_plots.py ...;
 )

Documentation

Python modules documentation is available through PyPI installer page.

Homepage

URL: http://www.python.org/