Control-FREEC *.png output files don't show text

[mauro-saporita]

Description of the bug

CONTROLFREEC_MAKEGRAPH generates tree *.png files as expected but those plots don't contain text instead there are some white little boxes (see image attached).

Biocontainer used: quay.io/biocontainers/control-freec:11.6--h1b792b2_1

Command used and terminal output

No response

Relevant files

No response

System information

Sarek version 3.1.2
Biocontainer used: quay.io/biocontainers/control-freec:11.6--h1b792b2_1

[maxulysse]

Hi @mauro-saporita thanks for reporting this issue, we will investigate

[maxulysse]

Results from the AWS megatests: https://nf-co.re/sarek/results#sarek/results-c87f4eb694a7183e4f99c70fca0f1d4e91750b33/somatic_test/variant_calling/controlfreec/HCC1395T_vs_HCC1395N/HCC1395T_vs_HCC1395N_BAF.png

So definitively we can reproduce.
Thanks @apeltzer

[FriederikeHanssen]

We just looked into this trying to figure out which font may be missing, however it is non-obvious from the makeGraph.R script. Probably some more research is needed to figure out what exactly the container needs.

[nschcolnicov]

Hi @FriederikeHanssen! I have been looking into this issue, since I was struggling with it too. In my case I couldn't reproduce it using the Biocontainer "quay.io/biocontainers/control-freec:11.6--h1b792b2_1" image. This image seems to be working fine in regards of the plot's text.
Instead I saw that I had this issue only when using the image: 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1'

I looked into the containers, and comparing the one from biocontainer and the one from galaxyproject, if I run the command "fc-list" I don't get any results in the latter one, while I do get the full list of fonts in the biocontainer one

@mauro-saporita is it possible that the image that was selected when running the module was the one from galaxyproject instead of the biocontainer one? Do you by any chance still have the log or the command used?

PROPOSED SOLUTION
R looks for the fonts in the following paths: /usr/share/fonts, /usr/local/share/fonts, ~/.fonts, ~/.local/share/fonts, and their subdirectories.
link to document

In order to fix this issue, the image in galaxyproject should be updated to include the font files in the path /usr/local/fonts, which is the same one that is used in the biocontainer image. I'm attaching the full list of fonts included in the working biocontainer image, in case it might help:
fontList.txt

[FriederikeHanssen]

Hey! Thanks a lot for investigating. Coincidentally, i just updated the container in the modules repo today (nf-core/modules#3843) and it seems it was fixed with the latest release. This is an image generated with singularity on 11.6b

In the PR you can also see two images one generated with Docker and one with conda

[nschcolnicov]

@FriederikeHanssen Thank you! Running it with the new container fixed the issue for me