biojava/biojava.github.io

Cookbook has disappeared

Closed this issue · 9 comments

cthoyt commented

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

andreasprlic commented

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

Deleted user commented

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

Deleted user commented

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

cthoyt commented

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

Deleted user commented

Ok, thank you. I will do it first.

Deleted user commented

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 commented

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

sbliven commented

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 commented

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