Please consider packaging as R package

[JEFworks]

Dependencies such as monocle-docker currently source files from this repo as seen here:

library(monocle)
source("/home/traj-converters/src/R/monocle_convert.r")
...

This requires users to maintain a folder explicitly in their home directory, which may not be possible when using shared resources for example.

It would be much easier for users and for Dockerizing if these trajectory converters can simply be loaded as a library:

library(monocle)
library(traj-converters)
...

The Dockerfile will then also be also be modified to add:

RUN R -e 'install.packages(c("devtools"))
devtools::install_github('Stuartlab-UCSC/traj-converters')

Many resources including Hadley's guide for making R packages are available to help you make these conversion functions available as a part of a traj-converters package.

[mrJeppard]

Thank you, yes that is a future goal.

Please note that the usage of source does not require users to maintain a folder explicitly in their home directory. You may clone traj-converters to any/directory and then source("any/directory/traj-converters/src/R/monocle_convert.r") from R. In the case of monocle-docker /home is where the traj-converters directory is copied inside the container.

[JEFworks]

Hi Duncan,

Excellent.

I see. I was testing the scripts outside of Docker as it was taking awhile to build. The scripts work fine in the context of the Docker image.

Best,
Jean