User-defined config files not recognized anymore in TM

[etournay]

Although the command tm "export TM_CONFIG=/movies/my_config.R; env" shows that the TM_CONFIG environment is set properly, TM doesn't take it into account.

This bug will be corrected in the next release.

In the meantime, the workaround is to set another tm alias in the .bashrc file:
alias tm2='docker run --rm -ti -v $(dirname $PWD)/my_config.R:/tissue_miner/config/default_config.R -v $(dirname $PWD):/movies -w /movies/$(base name $PWD) -u rstudio etournay/tissue_miner'

where the user-defined configuration file my_config.R is located in the movie folder.
Then running
tm2 sm shear_calculate topo_countt1 polygon_class tri_categorize; analyze_movie.R . output_analysis
would take the user-defined configuration into account.