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 at alumni.brown.edu> wrote:
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
from within R.
Here?s the steps I?ve taken:
Upon .onLoad <
of MAGMA.Celltyping, magma_installed_version() <
will check whether MAGMA is installed. If not, it proceeds to try and
install it via magma_install() <
.
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 <
),
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