Difference between revisions of "This page"

From medicin.ncmm.IT
Jump to: navigation, search
(List of modules maintained in our production Python versions)
(Edited info on docopt python lib as part of RT 4294814)
 
(2 intermediate revisions by one other user not shown)
Line 23: Line 23:
 
|0.29.13
 
|0.29.13
 
|0.29.21
 
|0.29.21
 +
|-
 +
|[https://github.com/keleshev/docopt docopt]
 +
| -
 +
| -
 +
| -
 +
|0.4.0
 
|-
 
|-
 
|[https://www.numpy.org/ numpy]
 
|[https://www.numpy.org/ numpy]
Line 58: Line 64:
 
| -
 
| -
 
|2.10.0
 
|2.10.0
|
+
|3.0.0
 
|-
 
|-
 
|[https://intervene.readthedocs.io/en/latest/ intervene]
 
|[https://intervene.readthedocs.io/en/latest/ intervene]
Line 76: Line 82:
 
|0.2.9
 
|0.2.9
 
| -
 
| -
|
+
|0.6.29
 
|-
 
|-
 
|[https://github.com/taoliu/MACS macs2]
 
|[https://github.com/taoliu/MACS macs2]
Line 82: Line 88:
 
| -
 
| -
 
| -
 
| -
|
+
|2.2.7.1
 
|-
 
|-
 
|[http://numba.pydata.org/ numba]
 
|[http://numba.pydata.org/ numba]
Line 88: Line 94:
 
| -
 
| -
 
|0.48.0
 
|0.48.0
|
+
|0.51.2
 
|-
 
|-
 
|[https://pypi.org/project/patsy/ patsy]
 
|[https://pypi.org/project/patsy/ patsy]
Line 106: Line 112:
 
|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]
Line 124: Line 130:
 
| -
 
| -
 
|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]
Line 142: Line 148:
 
|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]
Line 196: Line 202:
 
|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]
Line 202: Line 208:
 
|1.2.7
 
|1.2.7
 
|1.2.7
 
|1.2.7
|
+
|1.3.7
 
|}
 
|}

Latest revision as of 12:08, 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