Singularity

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:

>singularity 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	20.04	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]	5.2	GPLv3
liftOver[18]	latest	permissive
metal[19]	2020-05-05	-
minimac4[20]	v4.1.6	GPLv3
plink[21]	v1.90b7.2 64-bit (11 Dec 2023)	GPLv3
plink2[22]	v2.00a5.10LM 64-bit Intel (5 Jan 2024)	GPLv3
plink2_avx2[22]	v2.00a5.10LM AVX2 Intel (5 Jan 2024)	GPLv3
PRSice_linux[23]	2.3.5	GPLv3
qctool[24]	2.2.2, revision e5723df2c0c85959	Boost
regenie[25]	v3.4	MIT/Boost
samtools[1]	v1.19.2	MIT/ExpatD
shapeit4.2[26]	v4.2.2	MIT
shapeit5[27] phase_rare	v5.1.1	MIT
shapeit5[27] phase_common	v5.1.1	MIT
shapeit5[27] ligate	v5.1.1	MIT
shapeit5[27] switch	v5.1.1	MIT
shapeit5[27] xcftools	v5.1.1	MIT
simu_linux[28]	v0.9.4	GPLv3
snptest[29]	v2.5.6	permissive
switchError[30]	6e688b1	MIT
vcftools[31]	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:

>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

Software

List of software in the container:

OS/tool	version	license
ubuntu	20.04 (LTS)	Creative Commons CC-BY-SA version 3.0 UK licence
LDpred[32]	1.0.11	MIT
plink[21]	v1.90b6.18 64-bit (16 Jun 2020)	GPLv3
python3[33]	python 3.10.6 + numpy, pandas, etc.	PSF
python_convert[34]	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
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.

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 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
R[35]	4.0.5 (2021-03-31) + data.table, ggplot, etc.	misc
gcta64[12]	1.94.1	GPLv3
GenomicSEM[36]	GenomicSEM/GenomicSEM@bcbbaff	GPLv3
GSMR[37]	v1.0.9	GPL>=v2
rareGWAMA[38]	dajiangliu/rareGWAMA@72e962d	-
seqminer[39]	zhanxw/seqminer@142204d	GPL
PRSice_linux[23]	2.3.5	GPLv3
TwoSampleMR[40]	MRCIEU/TwoSampleMR@c174107	unknown/MIT
snpStats[40]	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.

References

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