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kyleam / snakemake-mode

[MIRROR] Emacs support for Snakemake
https://git.kyleam.com/snakemake-mode/about/
GNU General Public License v3.0
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Graph and show workflow in emacs. #9

Closed endrebak closed 8 years ago

endrebak commented 8 years ago

I messed up my git repo, so here I try again. Thanks for the patience. Since emacs and snakemake is all I use, you will probably have to brace yourself for more PRs.

Hmm, but this is limited to creating the graph for the first rule ofthe Snakefile, right?

Yes, I do not think it is possible to create a graph for anything but the all rule. But if it is, I have never done it and do not know how to do it. I do not yet understand the compile-code either.

I'd prefer to have this as a customizable variable, as is done with snakemake-program.

I have made snakemake-graph-program a defcustom. But I do not know of other pieces of software that can do the same thing though.

kyleam commented 8 years ago

I messed up my git repo, so here I try again.

OK, thanks. You can also force push the topic branch rather than opening up a new PR.

Since emacs and snakemake is all I use, you will probably have to brace yourself for more PRs.

Great, thanks for the PRs and suggestions so far. And it's nice to know someone else is using snakemake{,-mode}.el.

Hmm, but this is limited to creating the graph for the first rule ofthe Snakefile, right?

Yes, I do not think it is possible to create a graph for anything but the all rule. But if it is, I have never done it and do not know how to do it.

It's specified by the targets passed to Snakemake, in the same way that you build targets other than the top-most rule.

I'd prefer to have this as a customizable variable, as is done with snakemake-program.

I have made snakemake-graph-program a defcustom. But I do not know of other pieces of software that can do the same thing though.

Graphviz contains a few other options (see "man dot"). I suppose any program that understands the dot format as input would work. But a defcustom also allows the user to specify a program that isn't in their PATH.

I've tried a slightly different approach in the km/graph branch (aa756b6). Thoughts?

endrebak commented 8 years ago

Looks good, reading all your snakemake-mode code now to get better aquainted with it.

Going to start writing yasnippets for snakemake, do you have any you'd like to share?

kyleam commented 8 years ago

Going to start writing yasnippets for snakemake, do you have any you'd like to share?

That'd be great.

I only have these two snippets. I'm not sure if the second one is generally useful, or even the best way to accomplish that (running a script from it's directory) in Snakemake.