Using conda-forge to install dependencies for Circos

[Ryan Morin]

I thought it might be useful to share this as I have had my fair share of frustration installing Circos on various systems. I recently realized that the bioconda and conda-forge communities have solved a lot of the dependency issues that plague Circos. Assuming you already have an anaconda installation on your system, which is not difficult to do, here is how I got Circos' dependencies installed. Essentially I iterated over the running of circos, install bioconda/forge package until I stopped receiving errors. 

. activate root #this would install everything into your root anaconda. If you prefer, you may want to create your own environment for circos first

conda install -c conda-forge libgd=2.2.4

conda install -c bioconda perl-gd=2.56 #this one probably makes the former command unnecessary, actually

conda install -c bioconda perl-list-moreutils

conda install -c bioconda perl-params-validate

conda install -c bioconda perl-clone

That's it! 
If anyone is ambitious enough to make a bioconda recipe for biopython then this could all be replaced, theoretically with a command like:

conda install circos=0.69

Best,
Ryan

[Martin Krzywinski]

Thanks Ryan!

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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