Develop built-in help manuals for existing packages

[alyeffy]

Currently, learning about the features of bioSyntax and what they translate to involves looking through the manual on our site. If we could package this together with the installation, I think users would be a lot more willing to learn it, especially if we could create custom help text within the editor. e.g. with vim we could possibly incorporate the manual into the vim help doc and make it easy to search the doc using help tags like :h bS.

If it is not possible to do something like this for a specific editor, create a pdf infographic to be packaged with the files that's easily available once you install bioSyntax.

OR ALTERNATELY: create a text file version of the manual, and in the installation script, create an alias e.g. bS-help that prints out the file in the terminal.

[ababaian]

I've made a PDF draft of the manual based on the website jekyll-markdown file (found here). It's not complete by any means but a starting place.

Development files are found in bioSyntax/dev/man here. PDF generated with pandoc.

Also an idea I've had kicking around is to make a sam file "cheat-sheet" in the spirit of the R cheat sheets. Beside my desk I have sticky notes that I've kept up for years with the PHRED scales, CIGAR definitions, a decoding of the SAM flags. Essentially there is a whole lot of information in the headers and ways to read the files; if that can be condensed down to a 1 page sheet with colors matching bioSyntax I think that would a great 'documentation' as well.

[alyeffy]

Yeah, including information on the general structure of each of the file types would be helpful too, so it's a one-stop resource and people don't have to look up the structures of the files to use bioSyntax as well. See #2 Task 6