How to edit docs?

[jamesbraza]

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Looking at https://github.com/BenLangmead/bowtie2/commit/99eba20a9ac1a199aba8971fb06b42982b8cec8a#diff-fee45415ce1a1c290e697917da2b716532bcff66dbe1d9ae5caea30144bb0cc3, it's unclear what was the original docs file edited, and which are autogenerated:

• MANUAL
• MANUAL.markdown
• doc/manual.html

Which file does one edit, and which make commands does one then run?

[jamesbraza]

Cc @ch4rr0 and @BenLangmead. I am trying to upstream some info from https://github.com/BenLangmead/bowtie2/issues/410 to the docs, so it can be closed.

[ch4rr0]

Hello, you can submit a pull request that modifies MANUAL.markdown. MANUAL and manual.html are generated from the markdown file using pandoc (make doc). Once done I will then push updated documentation to the website.