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in-house Added tpm_table.py script Nov 11, 2016
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README.rst

Metagenomics Workshop

This repository holds the code for the website of the metagenomics workshop held in Uppsala 25-26 November 2014. The website is written using Sphinx. The webpage can be found at:

http://metagenomics-workshop.readthedocs.org/

How does it work?

In short, we use a python package called Sphinx to convert a bunch of text files written in reStructuredText (reST) to HTML pages. Instead of editing the HTML directly you change text files in the reST format. Those are the *.rst files in the source directory. That's all you need to know to start Contributing.

Contributing

We follow the Fork & pull model. It's not necessary to do anything on the command line. All you have to is click on fork in the GitHub interface. Then you can edit the *.rst files directly through the GitHub interface if you want. Only the Sphinx specific commands will not work, such as the table of contents command toctree. You can also add new files by clicking on the plus symbol next to a directory. After you are satisfied with you changes you click on the pull request button. Do note that changing the *.rst files does not change the actual webpage, maybe somebody else (.e.g me) can do that for you. If you want to learn how to compile the *.rst files to *.html, please read on.

Compile the reST files to HTML locally

The only thing that is a bit more tricky is actually compiling the *.rst files to *.html files. This is not necessary to contribute since you can see the results in Github (GitHub shows *.rst files as they would look like in HTML by default). If you want to compile the files locally you would do:

pip install sphinx  # install sphinx
git clone https://github.com/envgen/metagenomics-workshop
make html

The resulting HTML pages are in the folder build/. You can open the files in your browser by typing e.g. file:///home/inodb/path/to/build/html/index.html in the address bar. If you want to make changes you should:

  1. fork this repo
  2. clone your forked repo
  3. Make the changes to the *.rst files
  4. run make html
  5. look at the results
  6. add the changes with git add files that you changed
  7. commit the changes with git commit
  8. push the changes to your own repo with git push
  9. do a pull request by clicking on the pull request button on the GitHub page of your repo

This only changes the *.rst files in the master branch, not the actual webpage, which is in the gh-pages branch. How that is set up is explained in the section.

Updating the HTML to GitHub Pages

The website is hosted on GitHub Pages. It works by having a branch called gh-pages on this repository, which has all the HTML. I used brantfaircloth's sphinx_to_github.sh script to set it up. Basically it sets up a gh-pages branch in the build/html folder of the repository, so everytime you run make html it changes the files in that branch. You then cd build/html, commit the new HTML files and push them to the gh-pages branch. After that the result can be viewed at:

http://yourusername.github.io/reponame/

I'll update the branch gh-pages myself after your pull request with the changed *.rst files on the master branch was accepted.

The file structure

The result files:

├── assembly
│   ├── gut_out_31
│   ├── gut.pair.fastq
│   ├── interleaved_reads
│   ├── out_10M_31
│   ├── skin_out_31
│   └── teeth_out_31
├── functional_annotation
│   ├── krona
│   ├── minpath
│   └── prokka
├── mapping
│   └── bowtie2
├── phylogeny
│   ├── 16S
│   └── phylosift
└── quality_check
    └── fastqc

The Data files:

├── gut
│   ├── contigs
│   ├── README
│   └── reads
├── skin
│   ├── contigs
│   ├── README
│   └── reads
└── teeth
    ├── contigs
    ├── README
    └── reads
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