Difference between revisions of "This page"
From medicin.ncmm.IT
(Added notes for PyTorch, XGBoost, XlsxWriter, all for rh-python38) |
(List installed versions of h5py, kipoi, macs2, numba, pymongo, requests in rh-python38 SCL) |
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|[https://intervene.readthedocs.io/en/latest/ intervene] | |[https://intervene.readthedocs.io/en/latest/ intervene] | ||
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|0.2.9 | |0.2.9 | ||
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|[https://github.com/taoliu/MACS macs2] | |[https://github.com/taoliu/MACS macs2] | ||
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|[http://numba.pydata.org/ numba] | |[http://numba.pydata.org/ numba] | ||
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|0.48.0 | |0.48.0 | ||
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|[https://pypi.org/project/patsy/ patsy] | |[https://pypi.org/project/patsy/ patsy] | ||
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|[https://pypi.org/project/pyparsing/ pyparsing] | |[https://pypi.org/project/pyparsing/ pyparsing] | ||
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|2.22.0 | |2.22.0 | ||
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|[https://pypi.org/project/rpy2/ rpy2] | |[https://pypi.org/project/rpy2/ rpy2] | ||
Revision as of 12:44, 10 November 2020
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 |
| 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 |
