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benjaminhgood / LTEE-metagenomic

Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli
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Generating `annotate_pvalues ` + code license #3

Open wrshoemaker opened 6 years ago

wrshoemaker commented 6 years ago

Dr. Good,

I really enjoyed the paper that this code was written for and I'm looking to apply your pipeline to some sequence data from a long-term evolution experiment that our lab is conducting. I have two questions I'd like to ask.

First, I'm working on running process_cluster_output.py and I'm at the step where the script calls ./annotate_pvalues. I have no experience with C++ and am having trouble finding a straight answer from stackoverflow. How do you generate ./annotate_pvalues from makefile?

Second, have you considered adding a license to this repo? I'd like to use your code for inferring mutation trajectories for an upcoming publication, but there are potential legal issues for using code from a repo that doesn't have an appropriate license. Our lab uses a GNU General Public License v3.0, when possible. Just something to keep in mind since your recent publication on the LTEE was a statistically rigorous attempt at analyzing this type of data, so others besides myself may want to safely use and cite your code.

Aside from these points, I greatly enjoyed the series of theoretical papers that you wrote with Michael Desai for your dissertation. As well as your popgen_notes repo. I'm looking to incorporate more evolutionary theory into my experimental work and both of these resources have been a great help.

Best, Will Shoemaker

benjaminhgood commented 6 years ago

Hi Will,

Thanks for the kind words about our papers (new and old). I'm happy to help you set up the pipeline -- unfortunately things have been very busy on my end during the past year, so I have not had time to make a very user friendly installation script.

Re: make, the way it's supposed to work is that you run "make all" on the command line when you're in the directory with the C++ code, and it will produce an "annotate_pvalue" program in that directory, which you'll have to move to the base directory. There are two complications in this case:

(1) I just noticed a typo in the makefile on the repository (a tab got replaced by 4 spaces in my editor), which prevented the makefile from running correctly. I fixed this in the repository now. (2) This particular makefile will only work with the LLVM compiler, since the compiler name is hardcoded in. If you're using gcc instead, try replacing clang++ with g++. (3) In this particular case, the makefile is sort of overkill -- you can just run the "clang++ ..." command directly on the command line in the directory that contains the code.

I've also updated the README.md file to include some license info (GPLv2) -- thanks for pointing this out.

Let me know if there's anything else I can do to help.

Best, Ben

On Tue, Jan 16, 2018 at 4:51 PM, Will Shoemaker notifications@github.com wrote:

Dr. Good,

I really enjoyed the paper that this code was written for and I'm looking to apply your pipeline to some sequence data from a long-term evolution experiment that our lab is conducting. I have two questions I'd like to ask.

First, I'm working on running process_cluster_output.py and I'm at the step where the script calls ./annotate_pvalues. I have no experience with C++ and am having trouble finding a straight answer from stackoverflow. How do you generate ./annotate_pvalues from makefile?

Second, have you considered adding a license to this repo? I'd like to use your code for inferring mutation trajectories for an upcoming publication, but there are potential legal issues for using code from a repo that doesn't have an appropriate license. Our lab uses a GNU General Public License v3.0 https://github.com/LennonLab/Micrococcus/blob/master/LICENSE, when possible. Just something to keep in mind since your recent publication on the LTEE was a statistically rigorous attempt at analyzing this type of data, so others besides myself may want to safely use and cite your code.

Aside from these points, I greatly enjoyed the series of theoretical papers that you wrote with Michael Desai for your dissertation. As well as your popgen_notes repo. I'm looking to incorporate more evolutionary theory into my experimental work and both of these resources have been a great help.

Best, Will Shoemaker

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