Containers

gwas.sif container

Description

The gwas.sif container file has multiple tools related to imputation and GWAS analysis, as summarized in the Sofware table below.

Note that some specific tools (e.g. bolt) are added to the path directly from their /tools folder (e.g. /tools/bolt) due to hard-linked dependencies. Either way, all tools can be invoked by their name, as listed above. For example:

>apptainer exec gwas.sif regenie
              |=============================|
              |      REGENIE v2.0.2.gz      |
              |=============================|

Copyright (c) 2020 Joelle Mbatchou and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.

ERROR: You must provide an output prefix using '--out'
For more information, use option '--help' or visit the website: https://rgcgithub.github.io/regenie/

Software

List of software included in the container:

OS/tool	version	license
ubuntu	24.04LTS	Creative Commons CC-BY-SA version 3.0 UK licence
bcftools[1]	1.19	MIT/Expat/GPLv3
bedtools[2]	2.31.1	MIT
beagle[3] [4]	22Jul22.46e	GPLv3
bgenix[5]	1.1.7	Boost
bolt[6]	v2.4.1	GPLv3
cat-bgen[7]	same version as bgenix	Boost
duohmm[8]	95bd395	MIT
eagle[9]	v2.4.1	GPLv3
edit-bgen[10]	same version as bgenix	Boost
flashpca_x86-64[11]	2.0	GPLv3
gcta64[12]	1.94.1	GPLv3
gctb[13]	2.04.3	MIT
GWAMA[14]	2.2.2	BSD-3-Clause
HTSlib[15]	1.19.1	MIT/Expat/Modified-BSD
king[16]	2.3.2	permissive
ldak[17]	6	GPLv3
liftOver[18]	latest	permissive
metal[19]	2020-05-05	-
minimac4[20]	v4.1.6	GPLv3
OPERA[21]	v1.18	-
plink[22]	v1.9.0-b.7.11 64-bit (19 Aug 2025)	GPLv3
plink2[23]	v2.0.0-a.6.23LM 64-bit Intel (24 Aug 2025)	GPLv3
plink2_avx2[23]	v2.0.0-a.6.23LM AVX2 Intel (24 Aug 2025)	GPLv3
PRSice_linux[24]	2.3.5	GPLv3
(qctool[25])	2.2.2, revision e5723df2c0c85959	Boost
regenie[26]	v4.1.2	MIT/Boost
samtools[1]	v1.19.2	MIT/ExpatD
shapeit4.2[27]	v4.2.2	MIT
simu_linux[28]	v0.9.4	GPLv3
SMR[29]	v1.3.2	GPLv2
snptest[30]	v2.5.6	permissive
switchError[31]	6e688b1	MIT
vcftools[32]	0.1.17 (git SHA: d511f469e)	GPLv3

python3.sif container

Description

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:

>apptainer 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:

apptainer 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

Software

List of software in the container:

OS/tool	version	license
ubuntu	24.04 (LTS)	Creative Commons CC-BY-SA version 3.0 UK licence
LDpred[33]	1.0.11	MIT
plink[22]	v1.9.0-b.7.11 64-bit (19 Aug 2025)	GPLv3
Miniforge	25.3.1-0	BSD-3-Clause
python3[34]	python 3.10.6 + numpy, pandas, etc.	PSF
python_convert[35]	git SHA bcde562	GPLv3

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
apptainer 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
apptainer exec --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf --home=$PWD <path/to>/r.sif /usr/lib/rstudio-server/bin/rserver --www-address=127.0.0.1 --www-port=8787 --server-user $USER

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.

If you want to mount additional directories, you can append the --bind argument to the apptainer call (attaching /ess and /cluster as examples):

--bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf,/ess:/ess,/cluster:/cluster

If you get messages like “address already in use”, try and replace the port number 8787 with another port number (e.g., 8888, etc.) everywhere in the steps above and below.

2. (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

3. Then, open address 0.0.0.0:8787 or 127.0.0.1:8787 in a web browser like Firefox 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	24.04LTS	Creative Commons CC-BY-SA version 3.0 UK licence
R[36]	4.5.1 (2025-06-13) + data.table, ggplot, etc.	misc
gcta64[12]	1.94.1	GPLv3
GenomicSEM[37]	GenomicSEM/GenomicSEM@8e0ef5	GPLv3
GSMR[38]	v1.0.9	GPL>=v2
rareGWAMA[39]	dajiangliu/rareGWAMA@72e962d	-
seqminer[40]	zhanxw/seqminer@142204d	GPL
PRSice_linux[24]	2.3.5	GPLv3
TwoSampleMR[41]	MRCIEU/TwoSampleMR@c174107	unknown/MIT
snpStats[41]	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.

ldsc.sif container

LD score regression. For details, see github.com/comorment/ldsc.

HDL.sif container

High-Definition Likelihood. For details, see github.com/comorment/HDL.

MAGMA.sif container

MAGMA, LAVA, and LAVA-partitioning tools. For details, see github.com/comorment/MAGMA.

MiXeR.sif container

Causal Mixed Effect Models for Cross-Trait and Cross-Ancestry Analysis. For details, see github.com/comorment/MiXeR.

MTAG.sif container

Multi-Trait Analysis of GWAS. For details, see github.com/comorment/mtag_container.

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