Python - modules
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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.
Availability
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, 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.
Licence
Differs according to used Python module.
Use
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;
alpha_rarefaction.py ...;
beta_diversity_through_plots.py ...;
)
Documentation
Python modules documentation is available through PyPI installer page.
