Running Leafcutter and Leafviz on Windows

[Laurenz...@ugent.be]

Dear Leafcutter and Leafviz developers,

In the documentation you mentioned that there would be a macOS and/or windows package if there was demand for them. We are using LeafCutter in our lab as part of a RNA-Seq processing pipeline.

However, we have Linux, macOS and windows users in our lab. On mac both packages work for me, however, I was wondering whether or not there was also support for windows users?

Kind regards,

Laurenz De Cock

[countja...@gmail.com]

Dear Laurenz,

as far as I'm aware there are no plans to support Windows for the main Leafcutter package.

However, for Leafviz this should be more tractable now that we have a standalone leafviz R package: https://github.com/jackhump/leafviz 

I don't have a Windows machine to hand, so let me know if it's possible to run standalone Leafviz on a Windows machine. If not I'm sure we can work out how to accomplish it.

best,

Jack

[Bruce Southey]

Hi,

At least Leafviz can be installed and run under Windows 10 with some workarounds without trying to change code.

I what I did with a fresh install of R Windows 10 version 4.0.4 (2021-02-15) but no guarantees. Files are on the E: drive so ensure correct location and specification for Windows (no single backslash).

Installation:

1) Download and unzip the leafviz package from github.

2) Within R 

> install.packages("remotes")

> remotes::install_local("E:/leafviz-master")

> install.packages("shinyjs")

Installing from github or zip archive fails:

"Error : (converted from warning) unable to re-encode 'utils.R' line 17"

This is due to 'improper' encoding of a greek symbol under my Windows install.

The shinyjs requirement appears to be missing somewhere in the setup.

Running:

This fails for me because of the error:

"Error in if (getOption("browser") == "") { : argument is of length zero"

As per manual, this is due to the correct return being NULL not an empty string!

"For getOption, the current value set for option x, or default (which defaults to NULL) if the option is unset."

Thus

> getOption("browser")

NULL

This is trivial to overcome within R with an appropriate RData file:

> infile="E:/example.RData"

> load(infile, envir = .GlobalEnv)

> shiny::runApp(launch.browser = TRUE, appDir = system.file("application", package = "leafviz"))

Bruce

[Bruce Southey]

Also,

Leafcutter does install under Windows but don't know if it actually works. Leafcutter scripts have special options and do extra processing from the input that would need to be written as a set of functions that can be called within R.

Bruce