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r.sif container

Description

The r.sif container has multiple genetics tools based or relying on R, with a full R environment and Rstudio-server, based on the Rocker Project rocker/verse image. Please refer to the Software table below for details. In addition, several standard R packages are also included (e.g. data.table, ggplot2, rmarkdown, etc.)

Please report an issue if you encounter errors that have not been reported.

For GSMR, the example data (http://cnsgenomics.com/software/gsmr/static/test_data.zip) is available in $COMORMENT/containers/reference/example/gsmr folder. You may start the container like this:

cd $COMORMENT/containers/reference/examples/gsmr
singularity shell --home $PWD:/home $SIF/r.sif

and then follow the official tutorial https://cnsgenomics.com/software/gsmr/ . Note that gcta64 tool is also included in r.sif container, as the tutorial depends on it.

Invoking Rstudio-server

The r.sif container includes Rstudio-server, which can be accessed in a browser running on the host machine by

  1. Start Rstudio-server on the local or remote machine as:
cd <working/dir>
mkdir -p run var-lib-rstudio-server
printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf
singularity exec --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf <path/to/r.sif /usr/lib/rstudio-server/bin/rserver --www-address=127.0.0.1

where <working/dir> is the directory where you want to start Rstudio-server, and <path/to/r.sif> is the path to the r.sif container.

  1. (Optional) Create SSH tunnel using port 8787 from the local host to the remote machine
ssh -N -f -L "localhost:8787:localhost:8787" <remote/machine/address>  # replace <remote/machine/address> as necessary
  1. Then, open 0.0.0.0:8787 in a web browser on the host.

Please refer to the Rocker Project documentation for more details.

Software

Genetic analysis software

List of main software in the container:

OS/tool version license
ubuntu 20.04 Creative Commons CC-BY-SA version 3.0 UK licence
R1 4.0.5 (2021-03-31) + data.table, ggplot, etc. misc
gcta642 1.94.1 GPLv3
GenomicSEM3 GenomicSEM/GenomicSEM@bcbbaff GPLv3
GSMR4 v1.0.9 GPL>=v2
rareGWAMA5 dajiangliu/rareGWAMA@72e962d -
seqminer6 zhanxw/seqminer@142204d GPL
PRSice_linux7 2.3.5 GPLv3
TwoSampleMR8 MRCIEU/TwoSampleMR@c174107 unknown/MIT
snpStats8 v1.40.0 GPLv3

R packages

In addition to the rocker/verse image and the above genomics tools listed above there are a host of additional R packages and dependencies installed in the container. See the installer scripts for CRAN, Bioconductor, GitHub, and source packages for details.

Footnotes

  1. https://www.r-project.org ↩

  2. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011 Jan 7;88(1):76-82. doi: 10.1016/j.ajhg.2010.11.011. Epub 2010 Dec 17. ↩

  3. Grotzinger, A.D., Rhemtulla, M., de Vlaming, R. et al. Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits. Nat Hum Behav 3, 513–525 (2019). https://doi.org/10.1038/s41562-019-0566-x ↩

  4. Zhu, Z., Zheng, Z., Zhang, F. et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nat Commun 9, 224 (2018). https://doi.org/10.1038/s41467-017-02317-2 ↩

  5. Liu, D., Peloso, G., Zhan, X. et al. Meta-analysis of gene-level tests for rare variant association. Nat Genet 46, 200–204 (2014). https://doi.org/10.1038/ng.2852 ↩

  6. Lina Yang, Shuang Jiang, Bibo Jiang, Dajiang J Liu, Xiaowei Zhan, Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset, Bioinformatics, Volume 36, Issue 19, October 2020, Pages 4951–4954, https://doi.org/10.1093/bioinformatics/btaa628 ↩

  7. Shing Wan Choi, Paul F O'Reilly, PRSice-2: Polygenic Risk Score software for biobank-scale data, GigaScience, Volume 8, Issue 7, July 2019, giz082, https://doi.org/10.1093/gigascience/giz082 ↩

  8. Hemani, G., Haycock, P., Zheng, J., Gaunt, T., Elsworth, B., & Palmer, T. (2024). TwoSampleMR R package (v0.5.10). Zenodo. https://doi.org/10.5281/zenodo.10684540 ↩ ↩2