Difference between revisions of "This page"

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(Updated info for h5py and numba for Python 3.6.9)
(Edited info on docopt python lib as part of RT 4294814)
 
(22 intermediate revisions by 2 users not shown)
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!Python 3.6.9<syntaxhighlight lang="shell">
 
!Python 3.6.9<syntaxhighlight lang="shell">
 
scl enable rh-python36 bash
 
scl enable rh-python36 bash
 +
</syntaxhighlight>
 +
!Python 3.8.0<syntaxhighlight lang="shell">
 +
scl enable rh-python38 bash
 
</syntaxhighlight>
 
</syntaxhighlight>
 
|-
 
|-
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|0.25.2
 
|0.25.2
 
|0.29.13
 
|0.29.13
 +
|0.29.21
 +
|-
 +
|[https://github.com/keleshev/docopt docopt]
 +
| -
 +
| -
 +
| -
 +
|0.4.0
 
|-
 
|-
 
|[https://www.numpy.org/ numpy]
 
|[https://www.numpy.org/ numpy]
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|1.14.0
 
|1.14.0
 
|1.17.0
 
|1.17.0
 +
|1.19.2
 
|-
 
|-
 
|[https://www.scipy.org/ scipy]
 
|[https://www.scipy.org/ scipy]
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|1.0.0
 
|1.0.0
 
|1.3.0
 
|1.3.0
 +
|1.5.2
 
|-
 
|-
 
|[https://matplotlib.org/ matplotlib]
 
|[https://matplotlib.org/ matplotlib]
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|2.0.2
 
|2.0.2
 
|3.1.1
 
|3.1.1
 +
|3.3.2
 
|-
 
|-
 
|[https://pandas.pydata.org/ pandas]
 
|[https://pandas.pydata.org/ pandas]
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|0.20.2
 
|0.20.2
 
|0.25.0
 
|0.25.0
 +
|1.1.2
 
|-
 
|-
 
|[https://biopython.org/ biopython]
 
|[https://biopython.org/ biopython]
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|1.69
 
|1.69
 
|1.74
 
|1.74
 +
|1.78
 
|-
 
|-
 
|[https://www.h5py.org/ h5py]
 
|[https://www.h5py.org/ h5py]
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| -
 
| -
 
|2.10.0
 
|2.10.0
 +
|3.0.0
 
|-
 
|-
 
|[https://intervene.readthedocs.io/en/latest/ intervene]
 
|[https://intervene.readthedocs.io/en/latest/ intervene]
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|0.6.2
 
|0.6.2
 
|0.6.4
 
|0.6.4
 +
|<nowiki>-</nowiki>
 
|-
 
|-
 
|[https://joblib.readthedocs.io/en/latest/ joblib]
 
|[https://joblib.readthedocs.io/en/latest/ joblib]
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| -
 
| -
 
|0.14.0
 
|0.14.0
 +
|0.16.0
 
|-
 
|-
 
|[https://kipoi.org/about/ kipoi]
 
|[https://kipoi.org/about/ kipoi]
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|0.2.9
 
|0.2.9
 
| -
 
| -
 +
|0.6.29
 
|-
 
|-
 
|[https://github.com/taoliu/MACS macs2]
 
|[https://github.com/taoliu/MACS macs2]
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| -
 
| -
 
| -
 
| -
 +
|2.2.7.1
 
|-
 
|-
 
|[http://numba.pydata.org/ numba]
 
|[http://numba.pydata.org/ numba]
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| -
 
| -
 
|0.48.0
 
|0.48.0
 +
|0.51.2
 
|-
 
|-
 
|[https://pypi.org/project/patsy/ patsy]
 
|[https://pypi.org/project/patsy/ patsy]
 
|0.4.0
 
|0.4.0
 
|0.4.1
 
|0.4.1
 +
|0.5.1
 
|0.5.1
 
|0.5.1
 
|-
 
|-
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|1.11.0
 
|1.11.0
 
|1.11.0
 
|1.11.0
 +
|2.8.1
 
|-
 
|-
 
|[https://pypi.org/project/pymongo/ pymongo]
 
|[https://pypi.org/project/pymongo/ pymongo]
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|3.5.0
 
|3.5.0
 
|3.5.1
 
|3.5.1
 +
|3.11.0
 
|-
 
|-
 
|[https://pypi.org/project/pyparsing/ pyparsing]
 
|[https://pypi.org/project/pyparsing/ pyparsing]
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|2.4.2
 
|2.4.2
 
|2.4.2
 
|2.4.2
 +
|2.4.7
 
|-
 
|-
 
|[https://pypi.org/project/pysam/ pysam]
 
|[https://pypi.org/project/pysam/ pysam]
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|0.12.0
 
|0.12.0
 
|0.15.3
 
|0.15.3
 +
|0.16.0.1
 
|-
 
|-
 
|[https://pytorch.org/ pytorch]
 
|[https://pytorch.org/ pytorch]
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| -
 
| -
 
|1.2.0
 
|1.2.0
 +
|1.8.0a0 (as of 2020-10-17)
 
|-
 
|-
 
|[https://pypi.org/project/pybedtools/ pybedtools]
 
|[https://pypi.org/project/pybedtools/ pybedtools]
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|0.7.9
 
|0.7.9
 
|0.8.0
 
|0.8.0
 +
|0.8.1
 
|-
 
|-
 
|[https://pypi.org/project/pyBigWig/ pybigwig]
 
|[https://pypi.org/project/pyBigWig/ pybigwig]
 
|<nowiki>-</nowiki>
 
|<nowiki>-</nowiki>
 
|0.3.4
 
|0.3.4
 +
|0.3.17
 
|0.3.17
 
|0.3.17
 
|-
 
|-
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|2.22.0
 
|2.22.0
 
|2.22.0
 
|2.22.0
 +
|2.24.0
 
|-
 
|-
 
|[https://pypi.org/project/rpy2/ rpy2]
 
|[https://pypi.org/project/rpy2/ rpy2]
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|3.0.4
 
|3.0.4
 
|3.0.5
 
|3.0.5
 +
|3.3.5 (built with R/4.0.2)
 
|-
 
|-
 
|[https://scikit-learn.org/stable/ scikit-learn]
 
|[https://scikit-learn.org/stable/ scikit-learn]
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| -
 
| -
 
|0.21.3
 
|0.21.3
 +
|0.23.2
 
|-
 
|-
 
|[https://pypi.org/project/snakemake/ snakemake]
 
|[https://pypi.org/project/snakemake/ snakemake]
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|5.5.4
 
|5.5.4
 
|5.5.4
 
|5.5.4
 +
|5.25.0
 
|-
 
|-
 
|[https://pypi.org/project/deepTools/ deepTools]
 
|[https://pypi.org/project/deepTools/ deepTools]
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|2.5.3_2
 
|2.5.3_2
 
|3.3.0
 
|3.3.0
 +
|3.5.0
 
|-
 
|-
 
|[https://pypi.org/project/HTSeq/ htseq]
 
|[https://pypi.org/project/HTSeq/ htseq]
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|0.8.0
 
|0.8.0
 
|0.11.2
 
|0.11.2
 +
|0.12.4
 
|-
 
|-
 
|[https://pypi.org/project/seaborn/ seaborn]
 
|[https://pypi.org/project/seaborn/ seaborn]
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|0.8.0
 
|0.8.0
 
|0.9.0
 
|0.9.0
 +
|0.11.0
 +
|-
 +
|[https://pypi.org/project/seqlogo/ seqlogo]
 +
| -
 +
| -
 +
| -
 +
|5.29.8
 
|-
 
|-
 
|[https://pypi.org/project/statsmodels/ statsmodels]
 
|[https://pypi.org/project/statsmodels/ statsmodels]
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|0.8.0
 
|0.8.0
 
|0.10.1
 
|0.10.1
 +
|0.12.0
 
|-
 
|-
 
|[https://xgboost.readthedocs.io/en/latest/python/python_intro.html xgboost]
 
|[https://xgboost.readthedocs.io/en/latest/python/python_intro.html xgboost]
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|0.60
 
|0.60
 
|0.90
 
|0.90
 +
|1.3.0 SNAPSHOT (as of 2020-10-20)
 
|-
 
|-
 
|[https://pypi.org/project/XlsxWriter/ xlsxwriter]
 
|[https://pypi.org/project/XlsxWriter/ xlsxwriter]
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|1.2.7
 
|1.2.7
 
|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 3.5.1
scl enable rh-python35 bash
Python 3.6.9
scl enable rh-python36 bash
Python 3.8.0
scl 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
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