[Bioc-devel] MAGMA executable

[Brian Schilder]

Hi everyone, 

I’m a developer for the R package MAGMA.Celltyping <https://github.com/neurogenomics/MAGMA_Celltyping/tree/bschilder_dev> (on the bschilder_dev branch). It’s currently only distributed via GitHub but I’m trying to get it on Bioc if possible. The dilemma is, it relies on MAGMA <https://ctg.cncr.nl/software/magma>, which is only available as a CLI program.

I have everything passing CRAN/Bioc checks on my local machine, but the final hurdle is installing MAGMA <https://ctg.cncr.nl/software/magma> on other machines (e.g. via GitHub Actions checks) such that it can be called from within R.

Here’s the steps I’ve taken:
Upon .onLoad <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/zzz.R> of MAGMA.Celltyping, magma_installed_version() <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_installed_version.R> will check whether MAGMA is installed. If not, it proceeds to try and install it via magma_install() <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_install.R> .
magma_install() finds the latest version of MAGMA in their archives <https://ctg.cncr.nl/software/MAGMA/prog/>, installs it wherever the user has permissions (from a list of possible installation locations <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/find_install_dir.R>), and sets up the symlink.
Checks that MAGMA is indeed installed and callable from within R using functions like system(“magma ….”).
This all seems to work fine locally, but when I launch to GitHub actions, MAGMA.Celltyping can’t seems to install/find MAGMA. it doesn’t seem to be able to find it.  

Does anyone know of any solutions to this that are Bioc (or at least CRAN) -compatible?

Many thanks in advance,
Brian
___________
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
Profile | bit.ly/imperial_profile <https://bit.ly/imperial_profile>
LinkedIn | linkedin.com/in/brian-schilder <https://www.linkedin.com/in/brian-schilder/>
Twitter | twitter.com/BMSchilder <http://www.twitter.com/BMSchilder>
Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/>
UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/>
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