Difference between revisions of "This page"

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(Inserted info about rh-python38)
(Edited info on docopt python lib as part of RT 4294814)
 
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scl enable rh-python36 bash
 
scl enable rh-python36 bash
 
</syntaxhighlight>
 
</syntaxhighlight>
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!scl enable rh-python38 bash
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!Python 3.8.0<syntaxhighlight lang="shell">
 +
scl enable rh-python38 bash
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</syntaxhighlight>
 
|-
 
|-
 
|[https://cython.org/ cython]
 
|[https://cython.org/ cython]
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|0.29.13
 
|0.29.13
 
|0.29.21
 
|0.29.21
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|-
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|[https://github.com/keleshev/docopt docopt]
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| -
 +
| -
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| -
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|0.4.0
 
|-
 
|-
 
|[https://www.numpy.org/ numpy]
 
|[https://www.numpy.org/ numpy]
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|2.0.2
 
|2.0.2
 
|3.1.1
 
|3.1.1
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|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
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|1.1.2
 
|-
 
|-
 
|[https://biopython.org/ biopython]
 
|[https://biopython.org/ biopython]
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|1.69
 
|1.69
 
|1.74
 
|1.74
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|1.78
 
|-
 
|-
 
|[https://www.h5py.org/ h5py]
 
|[https://www.h5py.org/ h5py]
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| -
 
| -
 
|2.10.0
 
|2.10.0
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|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
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|
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|<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
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|0.16.0
 
|-
 
|-
 
|[https://kipoi.org/about/ kipoi]
 
|[https://kipoi.org/about/ kipoi]
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|0.2.9
 
|0.2.9
 
| -
 
| -
−
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|0.6.29
 
|-
 
|-
 
|[https://github.com/taoliu/MACS macs2]
 
|[https://github.com/taoliu/MACS macs2]
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| -
 
| -
 
| -
 
| -
−
|
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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
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|0.51.2
 
|-
 
|-
 
|[https://pypi.org/project/patsy/ patsy]
 
|[https://pypi.org/project/patsy/ patsy]
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|0.4.1
 
|0.4.1
 
|0.5.1
 
|0.5.1
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|0.5.1
 
|-
 
|-
 
|[https://pypi.org/project/python-dateutil/1.4/ python-dateutil]
 
|[https://pypi.org/project/python-dateutil/1.4/ python-dateutil]
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|1.11.0
 
|1.11.0
 
|1.11.0
 
|1.11.0
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|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
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|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
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|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
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|0.16.0.1
 
|-
 
|-
 
|[https://pytorch.org/ pytorch]
 
|[https://pytorch.org/ pytorch]
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| -
 
| -
 
|1.2.0
 
|1.2.0
−
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|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]
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|0.3.4
 
|0.3.4
 
|0.3.17
 
|0.3.17
−
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|0.3.17
 
|-
 
|-
 
|[https://pypi.org/project/requests/ requests]
 
|[https://pypi.org/project/requests/ requests]
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|2.22.0
 
|2.22.0
 
|2.22.0
 
|2.22.0
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|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
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|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
−
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|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
−
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|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
−
|
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|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
−
|
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|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
−
|
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|0.11.0
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|-
 +
|[https://pypi.org/project/seqlogo/ seqlogo]
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| -
 +
| -
 +
| -
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|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
−
|
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|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
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|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
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|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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