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* What is the snakemake popup actions supposed to do/how are they supposed to work? (#11)
@ 2016-04-18  6:36 Endre Bakken Stovner
  2016-04-18 17:53 ` Endre Bakken Stovner
                   ` (3 more replies)
  0 siblings, 4 replies; 5+ messages in thread
From: Endre Bakken Stovner @ 2016-04-18  6:36 UTC (permalink / raw)
  To: kyleam/snakemake-mode

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Whenever I am in a snakefile and try one of the actions I get "no snakefile found for <dirname>`.

I do not really want to run the workflows within emacs, so this does not bother me but I suspect it is undesired behavior.

My file is called `"/Users/labsenter/havpryd/code/programmable_epigenetics/snakefiles/csaw/graph_filter_parameters.snakefile"` if that might matter.

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* Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11)
  2016-04-18  6:36 What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Endre Bakken Stovner
@ 2016-04-18 17:53 ` Endre Bakken Stovner
  2016-04-18 18:09 ` Endre Bakken Stovner
                   ` (2 subsequent siblings)
  3 siblings, 0 replies; 5+ messages in thread
From: Endre Bakken Stovner @ 2016-04-18 17:53 UTC (permalink / raw)
  To: kyleam/snakemake-mode; +Cc: Kyle Meyer

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I have folders upon folders of snakefiles for each of my projects. 

I am usually in the base folder of my current project calling snakefiles in subfolders.

Example of my last invocation:

`endrebak@havpryd ~/c/programmable_epigenetics> snakemake --snakefile snakefiles/csaw/graph_filter_parameters.snakefile -j 4`.

Will read the docs of the functions you mentioned.

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* Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11)
  2016-04-18  6:36 What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Endre Bakken Stovner
  2016-04-18 17:53 ` Endre Bakken Stovner
@ 2016-04-18 18:09 ` Endre Bakken Stovner
  2016-04-19  4:19 ` Endre Bakken Stovner
  2020-04-17  0:05 ` Kyle Meyer
  3 siblings, 0 replies; 5+ messages in thread
From: Endre Bakken Stovner @ 2016-04-18 18:09 UTC (permalink / raw)
  To: kyleam/snakemake-mode; +Cc: Kyle Meyer

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It seems your function only finds files called `Snakefile`, right? So no matter what I set the dir functions to it would not work in my case.

My original graph functions just took the absolute path of the file visited by the buffer, which is what I would want in 100% of cases. Perhaps you (or I) could add some similar capability with an interactive function (`snakemake-create-dag(/rulegraph)-for-this-file`)?

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* Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11)
  2016-04-18  6:36 What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Endre Bakken Stovner
  2016-04-18 17:53 ` Endre Bakken Stovner
  2016-04-18 18:09 ` Endre Bakken Stovner
@ 2016-04-19  4:19 ` Endre Bakken Stovner
  2020-04-17  0:05 ` Kyle Meyer
  3 siblings, 0 replies; 5+ messages in thread
From: Endre Bakken Stovner @ 2016-04-19  4:19 UTC (permalink / raw)
  To: kyleam/snakemake-mode; +Cc: Kyle Meyer

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I am working on my PhD which requires plenty of different analyses. I collect the related analyses into different snakefiles in the same folders. My main reason for not having them in the same file is to keep the files small and easier to edit, understand and reason about. 

Perhaps your setup would work if I created new folders for each snakefile, so that `a/b.snakefile` becomes `a/b/Snakefile`.

I guess you could ping https://github.com/johanneskoester and ask about his opinion.

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* Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11)
  2016-04-18  6:36 What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Endre Bakken Stovner
                   ` (2 preceding siblings ...)
  2016-04-19  4:19 ` Endre Bakken Stovner
@ 2020-04-17  0:05 ` Kyle Meyer
  3 siblings, 0 replies; 5+ messages in thread
From: Kyle Meyer @ 2020-04-17  0:05 UTC (permalink / raw)
  To: snakemake-mode

Some replies are missing, as described at

  https://inbox.kyleam.com/snakemake-mode/874ktmyh4u.fsf@kyleam.com/

Please visit the link in the parent message to see the full discussion.

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2016-04-18  6:36 What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Endre Bakken Stovner
2016-04-18 17:53 ` Endre Bakken Stovner
2016-04-18 18:09 ` Endre Bakken Stovner
2016-04-19  4:19 ` Endre Bakken Stovner
2020-04-17  0:05 ` Kyle Meyer

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