From mboxrd@z Thu Jan 1 00:00:00 1970 Date: Sun, 17 Apr 2016 23:36:52 -0700 From: Endre Bakken Stovner Reply-To: kyleam/snakemake-mode Message-ID: Subject: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="--==_mimepart_571480849bd27_119b3fe78ef872c0228039d"; charset=UTF-8 Content-Transfer-Encoding: 7bit List-ID: kyleam/snakemake-mode List-Archive: https://github.com/kyleam/snakemake-mode List-Post: List-Unsubscribe: , To: kyleam/snakemake-mode ----==_mimepart_571480849bd27_119b3fe78ef872c0228039d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Whenever I am in a snakefile and try one of the actions I get "no snakefile found for `. 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. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/kyleam/snakemake-mode/issues/11 ----==_mimepart_571480849bd27_119b3fe78ef872c0228039d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

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

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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----==_mimepart_571480849bd27_119b3fe78ef872c0228039d-- From mboxrd@z Thu Jan 1 00:00:00 1970 Date: Mon, 18 Apr 2016 10:53:04 -0700 From: Endre Bakken Stovner Reply-To: kyleam/snakemake-mode Message-ID: In-Reply-To: References: Subject: Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="--==_mimepart_57151f00d7e82_74193fcb1142b2bc18345d"; charset=UTF-8 Content-Transfer-Encoding: 7bit List-ID: kyleam/snakemake-mode List-Archive: https://github.com/kyleam/snakemake-mode List-Post: List-Unsubscribe: , To: kyleam/snakemake-mode Cc: Kyle Meyer ----==_mimepart_57151f00d7e82_74193fcb1142b2bc18345d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit 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. --- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/kyleam/snakemake-mode/issues/11#issuecomment-211501029 ----==_mimepart_57151f00d7e82_74193fcb1142b2bc18345d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

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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----==_mimepart_57151f00d7e82_74193fcb1142b2bc18345d-- From mboxrd@z Thu Jan 1 00:00:00 1970 Date: Mon, 18 Apr 2016 11:09:36 -0700 From: Endre Bakken Stovner Reply-To: kyleam/snakemake-mode Message-ID: In-Reply-To: References: Subject: Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="--==_mimepart_571522e0f2e08_701e3fd1ecaeb2a080045"; charset=UTF-8 Content-Transfer-Encoding: 7bit List-ID: kyleam/snakemake-mode List-Archive: https://github.com/kyleam/snakemake-mode List-Post: List-Unsubscribe: , To: kyleam/snakemake-mode Cc: Kyle Meyer ----==_mimepart_571522e0f2e08_701e3fd1ecaeb2a080045 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit 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`)? --- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/kyleam/snakemake-mode/issues/11#issuecomment-211507107 ----==_mimepart_571522e0f2e08_701e3fd1ecaeb2a080045 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

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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----==_mimepart_571522e0f2e08_701e3fd1ecaeb2a080045-- From mboxrd@z Thu Jan 1 00:00:00 1970 Date: Mon, 18 Apr 2016 21:19:46 -0700 From: Endre Bakken Stovner Reply-To: kyleam/snakemake-mode Message-ID: In-Reply-To: References: Subject: Re: What is the snakemake popup actions supposed to do/how are they supposed to work? (#11) Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="--==_mimepart_5715b1e2cdfff_75313f8b673752bc27052"; charset=UTF-8 Content-Transfer-Encoding: 7bit List-ID: kyleam/snakemake-mode List-Archive: https://github.com/kyleam/snakemake-mode List-Post: List-Unsubscribe: , To: kyleam/snakemake-mode Cc: Kyle Meyer ----==_mimepart_5715b1e2cdfff_75313f8b673752bc27052 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit 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. --- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/kyleam/snakemake-mode/issues/11#issuecomment-211723035 ----==_mimepart_5715b1e2cdfff_75313f8b673752bc27052 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

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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