[Bioc-devel] MAGMA executable

[Brian Schilder]

Thank you both for the helpful feedback. I’ll follow up with the developers of MAGMA for clarification on license.

Regarding installation, I agree Kasper, this is not an ideal solution. Installing MAGMA at the R package installation time would be ideal, but I’ve been unable to come up with a way to do this. 

I’ve been look to Rsamtools <https://github.com/Bioconductor/Rsamtools> for some sources of inspiration, since it relies on multiple CLI tools (rsamtools, tabix). I’m unfamiliar with getting bash scripts to run while installing R packages, but looking into this now.

Best, 
Brian

> On 13 Dec 2021, at 13:59, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
> 
> Ignoring the license issues (which may be significant), I strongly dislike this installation strategy. It (IMO) unreasonable that you potentially write in system locations on package load. You're looking in 
>   /usr/local/bin
>   R.home/bin <- this makes not sense, this is the R home location, why should anything else but R be here?
>   $HOME
>   working directory
> 
> In my opinion, if you want to do something like this, you need to do it at installation time and you should install MAGMA in the package location.
> 
> 
> 
> On Thu, Dec 9, 2021 at 8:30 AM Vincent Carey <stvjc using channing.harvard.edu <mailto:stvjc using channing.harvard.edu>> wrote:
> 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 <mailto: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 <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 <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 <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 <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 <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 <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/ <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 <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 <http://bit.ly/imperial_profile> <https://bit.ly/imperial_profile <https://bit.ly/imperial_profile>>
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> > https://www.linkedin.com/in/brian-schilder/ <https://www.linkedin.com/in/brian-schilder/>>
> > Twitter | twitter.com/BMSchilder <http://twitter.com/BMSchilder> <http://www.twitter.com/BMSchilder <http://www.twitter.com/BMSchilder>>
> > Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/> <http://neurogenomics.co.uk/ <http://neurogenomics.co.uk/>>
> > UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/> <http://www.ukdri.ac.uk/ <http://www.ukdri.ac.uk/>>
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