Imputation set up
The software we use for imputation, impute5
, has a restrictive license. You
will need to accept this license, download the
software, and configure snpQT
to use it.
Singularity
To set up imputation with Singularity, firstly copy impute5 v1.1.4
to the
environments/impute5
directory:
$ cd environments/impute5/
$ cp ~/Downloads/impute5_v1.1.4.zip .
Then build a Singularity .sif
file:
$ sudo singularity build impute5.sif impute5.def
Singularity containers can run by normal users, but building Singularity images
requires root access. If you want to impute on a computer where you don't have
root access, you can transfer the impute5.sif
to environments/impute5/
.
If you don't have root access on any computers, you could try Singularity's remote builder service. Or maybe use a virtual machine!
Modules
If you are using -profile modules
on a cluster, the easiest thing to do is to
run module avail
and search for impute5
. On our cluster, impute5
is
installed as impute/5_1.1.4
. If your cluster is different, you will need to
edit conf/modules.config
:
// imputation with environment modules
// http://modules.sourceforge.net
// https://www.nextflow.io/docs/latest/process.html#module
// module names won't be consistent across systems :(
withName: 'convert_imp5|impute5' {
module = 'impute/5_1.1.4'
}
And change impute/5_1.1.4
to whatever is listed in module avail
. -profile
modules
also requires Anaconda to be installed.
Docker
Docker requires root access to build and run containers, so isn't an option for many people. However, it's simple to build a docker image from the Dockerfile:
$ cd environments/impute5/
$ cp ~/Downloads/impute5_v1.1.4.zip .
$ sudo docker build -t impute5 .