Cookbook has disappeared

[cthoyt]

The cookbook is currently missing... The only way to look up tutorials is through google searches and cached pages

[andreasprlic]

unfortunately we had to do an emergency migration of the old website. In the process of this the cookbook got moved here: http://biojava.org/wiki.html . However it is not well structured and many links don't work. As such @rmoszczynski is working on moving it to a GitHub wiki. See #10

[ghost]

@cthoyt here is a direct link to the fork I'm working on: https://github.com/rmoszczynski/biojava/wiki

[ghost]

@cthoyt you can tell me what information you are looking for so I can prioritize it first.

[cthoyt]

It would be really nice to have a recipe for retrieving FASTA files by Uniprot and HGNC identifiers, and working with the sequence alignment packages

[ghost]

Ok, thank you. I will do it first.

[ghost]

Here is what you are looking for: http://biojava.org/wiki/BioJava%3ACookbook%3ASeqIO%3AGBtoFasta

I have not migrated the recipe to the wiki because we want to put the cookbook recipes not to the wiki but to a separate repo https://github.com/biojava/biojava-cookbook. I'm working on the technical concept of the cookbook and will start to migrate probably after New Year.

[andreasprlic]

actually that's an entry for BioJava 1 ...

[sbliven]

We should at least make http://biojava.org/wiki/BioJava:CookBook4.0 give a reasonable page, for backwards compatibility. This currently seems to have two problems:

• The : needs to be escaped to %3A to get Jekyll to find it
• The .0 is recognized by Jekyll as an extension and delivered with content-type application/octet-stream

[sbliven]

Adding / to the end of the permlink seems to fix both problems.