Missing graphviz dependency

cgat-developers / cgat-flow

cgat-flow repository

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Missing graphviz dependency #40

Closed IanSudbery closed 6 years ago

IanSudbery commented 6 years ago

Graphviz is no longer installed as part of the conda envs, and it is needed for ruffus to plot the pipeline, which, in turn is part of report building, even in reports where there is no longer a CGATReport.

sebastian-luna-valero commented 6 years ago

Hi,

graphviz is added with cgat-apps here: https://github.com/cgat-developers/cgat-apps/blob/master/conda/environments/apps-extra.yml#L13

It should be installed with the cgat-flow installer in this statement: https://github.com/cgat-developers/cgat-flow/blob/master/install-CGAT-tools.sh#L418

I recently installed the code and I do have graphviz with it.

Can you please paste:

conda env list
conda list graphviz

Best regards, Sebastian

IanSudbery commented 6 years ago

I just installed it manually, so its going to be there now. I guess found it wasn't installed in my env and so checked the *-devel.yml's and didn't see it there, especially when I saw this int he log:

commit df754e911b6e36f8d72a96a30c5e06ea440482d1
Author: Sebastian Luna Valero <sebastian.luna.valero@gmail.com>
Date:   Wed Mar 21 17:31:11 2018 +0000

     replace graphviz with sphinx deps