[Bioc-devel] MAGMA executable

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Thu Dec 9 14:29:31 CET 2021

I didn't find an obvious licensing statement at the magma site.  I did see

note that standard copyright applies; the MAGMA binaries and source code
may not be distributed or modified)

the licensing situation would affect my advice on this process, but others
may have other more
specific advice

On Thu, Dec 9, 2021 at 7:37 AM Brian Schilder <
brian_schilder using alumni.brown.edu> wrote:

> 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/>
>         [[alternative HTML version deleted]]
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