python3.sif container runs Python packaged by Conda-forge, and has many useful python modules already installed,
including pandas, numpy, scipy, matplotlib, jupyter and few others (see here for full details).
Basic usage is very simple:
>singularity exec --contain --home $PWD:/home python3.sif python
Python 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:35:26) [GCC 10.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
You may also use jupyter notebook like this:
singularity exec --contain --home $PWD:/home $SIF/python3.sif jupyter notebook --no-browser --port 8890
The port is optional, but you may want to specify it if you'd like to run jupyter on a remote server - in which case you need to enable port forwarding as described here. This also works if you connect from Windows using Putty as described here.
python3.sif container has few additional tools installed:
-
/tools/ukb/ukb_helper.py- https://github.com/precimed/ukb/ -
/tools/python_convert- https://github.com/precimed/python_convert -
ldpred- https://github.com/bvilhjal/ldpred is installed via pip, simply run 'ldpred --help' to get started
List of software in the container:
| OS/tool | version | license |
|---|---|---|
| ubuntu | 20.04 (LTS) | Creative Commons CC-BY-SA version 3.0 UK licence |
| LDpred1 | 1.0.11 | MIT |
| plink2 | v1.90b6.18 64-bit (16 Jun 2020) | GPLv3 |
| python33 | python 3.10.6 + numpy, pandas, etc. | PSF |
| python_convert4 | git SHA bcde562 | GPLv3 |
Footnotes
-
Bjarni J. Vilhjálmsson, et al. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores, The American Journal of Human Genetics Volume 97, Issue 4, 2015, Pages 576-592, https://doi.org/10.1016/j.ajhg.2015.09.001. ↩
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Christopher C Chang, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee, Second-generation PLINK: rising to the challenge of larger and richer datasets, GigaScience, Volume 4, Issue 1, December 2015, s13742–015–0047–8, https://doi.org/10.1186/s13742-015-0047-8 ↩
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Van Rossum, G., & Drake, F. L. (2009). Python 3 Reference Manual. Scotts Valley, CA: CreateSpace. ↩