DESeq2 Plots Incorrectly Displayed

The MA and PCA plots produced by DESeq2 lack any text labels. These labels are replaced by empty rectangles. The same issue occurs with JPEG and SVG files (only included JPEG because GitHub prevents SVG uploads).

The issue occurs whether I’m using the deseq2.yaml environment provided in this repo or an updated environment using newer versions of the software packages.

[tjbencomo]

I posted about this issue on StackOverflow and adding mscorefonts to the conda environment fixes the issue and creates plots with normal text.

I’ve added mscorefonts to deseq2.yaml on my local machine and the updated conda environment builds without any issues. @johanneskoester would you be interested if I created a pull request with an updated deseq2.yaml that includes mscorefonts?

[tjbencomo]

When you run the pipeline are you using both conda and singularity? After running some tests, it seems the error occurs when I run the pipeline with conda and singularity together (--use-conda --use-singularity) but not when I run the pipeline only with conda environments enabled (--use-conda).

This leads me to suspect that the singularity container may be missing a library needed to draw text. I’ve created a self contained repo here that reproduces the graph issue on a different dataset. The repo uses the same deseq2.yaml conda environment as this pipeline and the same singularity container. When I run the pipeline with --use-conda --use-singularity the graph shows the same issue but when run with only --use-conda the graph is formatted properly.

Do you know if it’s possible to check the plots produced by the Travis CI tests using --use-conda --use-singularity to see if the issue occurs there as well?