Alright, the snakemake pipeline now proceeds all the way through global epistasis fits for the binding and expression phenotypes.
Getting the .Rmd files to render from snakemake/the command line (as opposed to "knitting" within RStudio) was a bit of a pain, as dealing with placement of files in subdirectories during the render apparently causes many people lots of headaches -- so as you'll see in the Snakefile, I settled on just doing everything in the base directory and then moving the .md and images to results/summary after rendering.
I have partially interpreted the binding global epistasis models, but I haven't annotated the md text in the expression global epistasis models as much yet -- but I wanted to just get this stage PR in since a lot was happening.
Also, I am committing my environment.yml file. I did rebuild my conda env from environment_unpinned.yml several times when trying out different R builds, though in the end I ended up reverting to the original environment_unpinned.yml -- but my environment.yml file appears to remain different from what was on master previously so I have kept that in the PR.
Also not sure what conflict arose with master commits which is preventing automatic merging of this PR, but I will also look through the change log here...
Alright, the
snakemake
pipeline now proceeds all the way through global epistasis fits for the binding and expression phenotypes.Getting the
.Rmd
files to render fromsnakemake
/the command line (as opposed to "knitting" within RStudio) was a bit of a pain, as dealing with placement of files in subdirectories during the render apparently causes many people lots of headaches -- so as you'll see in theSnakefile
, I settled on just doing everything in the base directory and then moving the.md
and images toresults/summary
after rendering.I have partially interpreted the binding global epistasis models, but I haven't annotated the md text in the expression global epistasis models as much yet -- but I wanted to just get this stage PR in since a lot was happening.
Also, I am committing my
environment.yml
file. I did rebuild my conda env fromenvironment_unpinned.yml
several times when trying out different R builds, though in the end I ended up reverting to the originalenvironment_unpinned.yml
-- but myenvironment.yml
file appears to remain different from what was onmaster
previously so I have kept that in the PR.Also not sure what conflict arose with
master
commits which is preventing automatic merging of this PR, but I will also look through the change log here...