Structure README.md file(s)

comorment / gwas

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Structure README.md file(s) #5

Closed ofrei closed 3 years ago

ofrei commented 4 years ago

I suggest to split README.md file into several files, for example:

into.md with general info about docker, singularity, interactive / passive modes, mounting data to containers, etc. Basically, everything users need to know about docker and singularity that is not specific to your containers.
One file per each tool. For now I suggest we pick one tool, i.e. plink, and finalize it's readme file - and then proceed to other tools.
root-level README.md file, serving as list of contents - and containing links to all other README files.

The readme file for each tool may have

usage example
version of the tool
link to it's original help
overview of demo data included (and it's location)

bayramakdeniz commented 4 years ago

The structure of the readme file has been changed as suggested (just for plink for now)

ofrei commented 3 years ago

I've messed docs folder - could you take a look there, and also at the README file in the root? Also, I think we need to provide usage examples for other tools now included in gwas container, namely gcta, gctb, qctools, king, metal, vcftools, bcftools. If they require additional data we also need to include it here https://github.com/norment/comorment_data

bayramakdeniz commented 3 years ago

Thanks, I will have a look. By the way, there are some examples of other tools here: https://github.com/comorment/gwas/blob/main/docs/others.md

I may clean and organize them if you like.

ofrei commented 3 years ago

Ah, right - this is very useful! Let's change these instructions to use singularity. Is it possible to use existing bfile in /hapgen/chr21 (the 10K subjects, 150K SNPs dataset)? If not, all new data needed to runs these tools should be added to reference dataset (here: https://github.com/norment/comorment_data ). Please use GIT LFS when commit large files: https://docs.github.com/en/free-pro-team@latest/github/managing-large-files/configuring-git-large-file-storage

I've removed this code - do we need to re-add it into reference data?

RUN wget https://5c2d08d4-17d1-4dd8-bb49-f9593683e642.filesusr.com/archives/e7bc47_f74626b357ed453584e9e775713fe9ac.zip?dn=data_chapter10.zip && \
unzip -j  e7bc47_f74626b357ed453584e9e775713fe9ac.zip?dn=data_chapter10.zip  && \
rm -rf   e7bc47_f74626b357ed453584e9e775713fe9ac.zip?dn=data_chapter10.zip

ofrei commented 3 years ago

README files are getting a lot better :)