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GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.
https://gregoryschwartz.github.io/too-many-cells/
GNU General Public License v3.0
105 stars 19 forks source link

Font missing in docker container #3

Closed grst closed 5 years ago

grst commented 5 years ago

Sorry for bothering you again... In the "Painting tree" step the docker container fails because of a font missing: 

> sudo docker run -it -v /storage/scratch/toomanycells:/scratch gregoryschwartz/too-many-cells:0.1.1.0 make-tree -m /scratch/harmony_toomanycells.csv --no-filter --normalization NoneNorm  --dense
Painting sketches [===================================>..............]  70%
Clumpiness requires labels for cells, skipping...
Painting tree [===========================================>..........]  80%
too-many-cells: /opt/build/.stack-work/install/x86_64-linux/lts-12.0/8.4.3/share/x86_64-linux-ghc-8.4.3/SVGFonts-1.6.0.3/fonts/LinLibertine.svg: openFile: does not exist (No such file or directory)
GregorySchwartz commented 5 years ago

Wow, nice catch! I usually use labels so I never get to see this issue which only appears in the docker without a labels file. I fixed it, confirmed working on my end. I needed to copy the font svg over and change the locale of the docker image. I updated the docker image version 0.1.1.0, so pull that. Let me know if everything goes well! Fixed in https://github.com/GregorySchwartz/too-many-cells/commit/e1abd8cf846f082d4e2799e615636db09588631e.

GregorySchwartz commented 5 years ago

By the way, you have not mounted an output in your example, so it will write to the docker container, not your filesystem. So be sure to specify the output if you use docker! For example: -v /path/to/output:/output ... -o /output.

grst commented 5 years ago

Works like a charm now, thanks!