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s-andrews / compter

An application to graphically summarise kmer enrichment in a set of sequences
GNU General Public License v3.0
5 stars 3 forks source link

Problem generating heatmaps on Ubuntu #6

Closed StevenWingett closed 4 years ago

StevenWingett commented 4 years ago

I tried to quickly put together a GitHub Actions workflow for Compter. However, it seems that the code below does not work on Ubuntu (I've also tried this on a Virtual Box running Ubuntu).

I could re-write the code to write out an R script and then run with an "Rscript" system command. (This would mean running Rscript rather than R). What do you think?

Thanks, Steven

Run $GITHUB_WORKSPACE/compter --background mouse --outfile testing.txt $GITHUB_WORKSPACE/test/high_seqs.fa $GITHUB_WORKSPACE/test/low_seqs.fa Reading background from /home/runner/work/compter/compter/backgrounds/mouse.cmp Processing /home/runner/work/compter/compter/test/high_seqs.fa ... Processing /home/runner/work/compter/compter/test/low_seqs.fa .. Drawing heatmap Can't write to 'R' pipe - do you need to set an rpath? at /home/runner/work/compter/compter/compter line 201.

[error]Process completed with exit code 1.

s-andrews commented 4 years ago

It's probbaly just that pheatmap isn't installed in the R environment.

StevenWingett commented 4 years ago

This was the problem and has now been fixed.