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== '''List of modules maintained in our production Python versions''' == | == '''List of modules maintained in our production Python versions''' == | ||
− | The following table provides a list of all supported/maintained Python module versions, per Python version. | + | The following table provides a list of all supported/maintained Python module versions, per Python version. The table concerns the '''biotin{2,3}.hpc.uio.no''' production servers. Please use these production Python versions for your research. If you need to install a module in one of those versions, ask the NCMM IT team to do it for you. |
− | {| class="wikitable" | + | |
+ | '''Note: Python 2.7.x modules will have limited support from Dec 31st 2019, as Python 2.7.x will reach the end of its support life (EOL) as [https://pythonclock.org/ outlined here]. It is therefore important that you start using Python 3 now.''' | ||
+ | {| class="wikitable sortable" | ||
!Library/module | !Library/module | ||
− | !Python 2.7 | + | !Python 2.7.5 |
− | !Python 3.5.1 | + | !Python 3.5.1<syntaxhighlight lang="shell"> |
− | !Python 3.6.3 | + | scl enable rh-python35 bash |
+ | </syntaxhighlight> | ||
+ | !Python 3.6.9<syntaxhighlight lang="shell"> | ||
+ | scl enable rh-python36 bash | ||
+ | </syntaxhighlight> | ||
+ | !Python 3.8.0<syntaxhighlight lang="shell"> | ||
+ | scl enable rh-python38 bash | ||
+ | </syntaxhighlight> | ||
|- | |- | ||
− | |numpy | + | |[https://cython.org/ cython] |
− | | | + | |0.23.4 |
+ | |0.25.2 | ||
+ | |0.29.13 | ||
+ | |0.29.21 | ||
+ | |- | ||
+ | |[https://github.com/keleshev/docopt docopt] | ||
+ | | - | ||
+ | | - | ||
+ | | - | ||
+ | |0.4.0 | ||
+ | |- | ||
+ | |[https://www.numpy.org/ numpy] | ||
+ | |1.14.2 | ||
|1.14.0 | |1.14.0 | ||
|1.17.0 | |1.17.0 | ||
+ | |1.19.2 | ||
|- | |- | ||
− | |scipy | + | |[https://www.scipy.org/ scipy] |
− | | | + | |1.0.1 |
|1.0.0 | |1.0.0 | ||
|1.3.0 | |1.3.0 | ||
+ | |1.5.2 | ||
|- | |- | ||
− | |matplotlib | + | |[https://matplotlib.org/ matplotlib] |
− | | | + | |2.2.2 |
|2.0.2 | |2.0.2 | ||
|3.1.1 | |3.1.1 | ||
+ | |3.3.2 | ||
|- | |- | ||
− | |pandas | + | |[https://pandas.pydata.org/ pandas] |
− | | | + | |0.22.0 |
|0.20.2 | |0.20.2 | ||
|0.25.0 | |0.25.0 | ||
+ | |1.1.2 | ||
|- | |- | ||
− | |biopython | + | |[https://biopython.org/ biopython] |
− | | | + | |1.71 |
− | | | + | |1.69 |
|1.74 | |1.74 | ||
+ | |1.78 | ||
+ | |- | ||
+ | |[https://www.h5py.org/ h5py] | ||
+ | | - | ||
+ | | - | ||
+ | |2.10.0 | ||
+ | |3.0.0 | ||
|- | |- | ||
− | |patsy | + | |[https://intervene.readthedocs.io/en/latest/ intervene] |
− | | | + | |0.6.2 |
− | | | + | |0.6.2 |
+ | |0.6.4 | ||
+ | |<nowiki>-</nowiki> | ||
+ | |- | ||
+ | |[https://joblib.readthedocs.io/en/latest/ joblib] | ||
+ | | - | ||
+ | | - | ||
+ | |0.14.0 | ||
+ | |0.16.0 | ||
+ | |- | ||
+ | |[https://kipoi.org/about/ kipoi] | ||
+ | |<nowiki>-</nowiki> | ||
+ | |0.2.9 | ||
+ | | - | ||
+ | |0.6.29 | ||
+ | |- | ||
+ | |[https://github.com/taoliu/MACS macs2] | ||
+ | |2.1.1 | ||
+ | | - | ||
+ | | - | ||
+ | |2.2.7.1 | ||
+ | |- | ||
+ | |[http://numba.pydata.org/ numba] | ||
+ | | - | ||
+ | | - | ||
+ | |0.48.0 | ||
+ | |0.51.2 | ||
+ | |- | ||
+ | |[https://pypi.org/project/patsy/ patsy] | ||
+ | |0.4.0 | ||
+ | |0.4.1 | ||
+ | |0.5.1 | ||
|0.5.1 | |0.5.1 | ||
|- | |- | ||
− | |python-dateutil | + | |[https://pypi.org/project/python-dateutil/1.4/ python-dateutil] |
− | | | + | |1.11.0 |
− | | | + | |1.11.0 |
|1.11.0 | |1.11.0 | ||
+ | |2.8.1 | ||
|- | |- | ||
− | | | + | |[https://pypi.org/project/pymongo/ pymongo] |
− | | | + | |3.5.1 |
− | | | + | |3.5.0 |
+ | |3.5.1 | ||
+ | |3.11.0 | ||
+ | |- | ||
+ | |[https://pypi.org/project/pyparsing/ pyparsing] | ||
+ | |2.2.0 | ||
|2.4.2 | |2.4.2 | ||
+ | |2.4.2 | ||
+ | |2.4.7 | ||
|- | |- | ||
− | |pybedtools | + | |[https://pypi.org/project/pysam/ pysam] |
− | | | + | |0.8.3 |
− | | | + | |0.12.0 |
+ | |0.15.3 | ||
+ | |0.16.0.1 | ||
+ | |- | ||
+ | |[https://pytorch.org/ pytorch] | ||
+ | | - | ||
+ | | - | ||
+ | |1.2.0 | ||
+ | |1.8.0a0 (as of 2020-10-17) | ||
+ | |- | ||
+ | |[https://pypi.org/project/pybedtools/ pybedtools] | ||
+ | |0.7.9 | ||
+ | |0.7.9 | ||
|0.8.0 | |0.8.0 | ||
+ | |0.8.1 | ||
|- | |- | ||
− | |pybigwig | + | |[https://pypi.org/project/pyBigWig/ pybigwig] |
− | | | + | |<nowiki>-</nowiki> |
− | | | + | |0.3.4 |
+ | |0.3.17 | ||
|0.3.17 | |0.3.17 | ||
|- | |- | ||
− | |snakemake | + | |[https://pypi.org/project/requests/ requests] |
− | | | + | | 2.6.0 |
− | | | + | |2.22.0 |
+ | |2.22.0 | ||
+ | |2.24.0 | ||
+ | |- | ||
+ | |[https://pypi.org/project/rpy2/ rpy2] | ||
+ | |2.7.3 | ||
+ | |3.0.4 | ||
+ | |3.0.5 | ||
+ | |3.3.5 (built with R/4.0.2) | ||
+ | |- | ||
+ | |[https://scikit-learn.org/stable/ scikit-learn] | ||
+ | | 0.17.1 | ||
+ | | - | ||
+ | |0.21.3 | ||
+ | |0.23.2 | ||
+ | |- | ||
+ | |[https://pypi.org/project/snakemake/ snakemake] | ||
+ | |<nowiki>-</nowiki> | ||
+ | |5.5.4 | ||
|5.5.4 | |5.5.4 | ||
+ | |5.25.0 | ||
|- | |- | ||
− | |deepTools | + | |[https://pypi.org/project/deepTools/ deepTools] |
− | | | + | |2.4.0_2 |
− | | | + | |2.5.3_2 |
|3.3.0 | |3.3.0 | ||
+ | |3.5.0 | ||
|- | |- | ||
− | |htseq | + | |[https://pypi.org/project/HTSeq/ htseq] |
− | | | + | |0.6.1 |
− | | | + | |0.8.0 |
|0.11.2 | |0.11.2 | ||
+ | |0.12.4 | ||
|- | |- | ||
− | |seaborn | + | |[https://pypi.org/project/seaborn/ seaborn] |
− | | | + | |0.8.1 |
− | | | + | |0.8.0 |
|0.9.0 | |0.9.0 | ||
+ | |0.11.0 | ||
+ | |- | ||
+ | |[https://pypi.org/project/seqlogo/ seqlogo] | ||
+ | | - | ||
+ | | - | ||
+ | | - | ||
+ | |5.29.8 | ||
|- | |- | ||
− | |statsmodels | + | |[https://pypi.org/project/statsmodels/ statsmodels] |
− | | | + | |0.6.1 |
− | | | + | |0.8.0 |
|0.10.1 | |0.10.1 | ||
+ | |0.12.0 | ||
+ | |- | ||
+ | |[https://xgboost.readthedocs.io/en/latest/python/python_intro.html xgboost] | ||
+ | |0.71 | ||
+ | |0.60 | ||
+ | |0.90 | ||
+ | |1.3.0 SNAPSHOT (as of 2020-10-20) | ||
|- | |- | ||
− | | | + | |[https://pypi.org/project/XlsxWriter/ xlsxwriter] |
− | | | + | | - |
− | | | + | |1.2.7 |
− | | | + | |1.2.7 |
+ | |1.3.7 | ||
|} | |} |
Latest revision as of 13:08, 8 March 2021
List of modules maintained in our production Python versions
The following table provides a list of all supported/maintained Python module versions, per Python version. The table concerns the biotin{2,3}.hpc.uio.no production servers. Please use these production Python versions for your research. If you need to install a module in one of those versions, ask the NCMM IT team to do it for you.
Note: Python 2.7.x modules will have limited support from Dec 31st 2019, as Python 2.7.x will reach the end of its support life (EOL) as outlined here. It is therefore important that you start using Python 3 now.
Library/module | Python 2.7.5 | Python 3.5.1scl enable rh-python35 bash
|
Python 3.6.9scl enable rh-python36 bash
|
Python 3.8.0scl enable rh-python38 bash
|
---|---|---|---|---|
cython | 0.23.4 | 0.25.2 | 0.29.13 | 0.29.21 |
docopt | - | - | - | 0.4.0 |
numpy | 1.14.2 | 1.14.0 | 1.17.0 | 1.19.2 |
scipy | 1.0.1 | 1.0.0 | 1.3.0 | 1.5.2 |
matplotlib | 2.2.2 | 2.0.2 | 3.1.1 | 3.3.2 |
pandas | 0.22.0 | 0.20.2 | 0.25.0 | 1.1.2 |
biopython | 1.71 | 1.69 | 1.74 | 1.78 |
h5py | - | - | 2.10.0 | 3.0.0 |
intervene | 0.6.2 | 0.6.2 | 0.6.4 | - |
joblib | - | - | 0.14.0 | 0.16.0 |
kipoi | - | 0.2.9 | - | 0.6.29 |
macs2 | 2.1.1 | - | - | 2.2.7.1 |
numba | - | - | 0.48.0 | 0.51.2 |
patsy | 0.4.0 | 0.4.1 | 0.5.1 | 0.5.1 |
python-dateutil | 1.11.0 | 1.11.0 | 1.11.0 | 2.8.1 |
pymongo | 3.5.1 | 3.5.0 | 3.5.1 | 3.11.0 |
pyparsing | 2.2.0 | 2.4.2 | 2.4.2 | 2.4.7 |
pysam | 0.8.3 | 0.12.0 | 0.15.3 | 0.16.0.1 |
pytorch | - | - | 1.2.0 | 1.8.0a0 (as of 2020-10-17) |
pybedtools | 0.7.9 | 0.7.9 | 0.8.0 | 0.8.1 |
pybigwig | - | 0.3.4 | 0.3.17 | 0.3.17 |
requests | 2.6.0 | 2.22.0 | 2.22.0 | 2.24.0 |
rpy2 | 2.7.3 | 3.0.4 | 3.0.5 | 3.3.5 (built with R/4.0.2) |
scikit-learn | 0.17.1 | - | 0.21.3 | 0.23.2 |
snakemake | - | 5.5.4 | 5.5.4 | 5.25.0 |
deepTools | 2.4.0_2 | 2.5.3_2 | 3.3.0 | 3.5.0 |
htseq | 0.6.1 | 0.8.0 | 0.11.2 | 0.12.4 |
seaborn | 0.8.1 | 0.8.0 | 0.9.0 | 0.11.0 |
seqlogo | - | - | - | 5.29.8 |
statsmodels | 0.6.1 | 0.8.0 | 0.10.1 | 0.12.0 |
xgboost | 0.71 | 0.60 | 0.90 | 1.3.0 SNAPSHOT (as of 2020-10-20) |
xlsxwriter | - | 1.2.7 | 1.2.7 | 1.3.7 |