PolyMarker

This is a server to facilitate the use of PolyMarker.

System dependencies

This server is developed with ruby 2.4 on rails 5.1. Other versions may work, but it is not tested. PolyMarker is tested in MacOS X and Linux (Ubuntu). PolyMarker is queued using sidekiq which also depends in redis.

You need to have installed ncbi-blast.

Setting up the server.

The first thing to do is to load the different references

rake reference:add[references.yml]

The file is formated as yaml. It can contain several references with the following fields:

• name. The name that is going to be displayed in the server
• path. The full path to the uncompressed fasta file with the reference. The fai and blast indeces will be generated on that path.
• genome_count. The number of genomes in the reference: 1 for tetraplods, 2 for tetraploids, etc.
• arm_description The algorithm used in polymarker to parse

-reference:
  name : RefSeq v1.0
  path: /home/USER/References/161010_Chinese_Spring_v1.0_pseudomolecules.fasta
  genome_count: 3
  arm_selection: nrgene
  description: >
    Reference sequence available in [website](http://tada/)
    The reference contains the chromosomes assembled as pseudomolecules,
    hence it is possible to distinguish duplications in the same chromosome.

Important Note

On some machines due to version differences (either ruby/rails/os etc.), webpacker/webpack can malfunction and an error could occur such as:

• the following error

[Webpacker] Compilation failed:
  /usr/lib/ruby/vendor_ruby/bundler/rubygems_integration.rb:458:in `block in replace_bin_path': can't find executable webpack for gem webpacker (Gem::Exception)
	from /usr/lib/ruby/vendor_ruby/bundler/rubygems_integration.rb:489:in `block in replace_bin_path

In this case do the following:

• gem install webpacker
  • yes to all except:
    • app/javascript/packs/application.js
    • config/webpack/environment.js
  • Modify config/webpack/environment.js
    • environment.plugins.provide --> environment.plugins.prepend
    • module.exports = environment.toWebpackConfig() --> module.exports = environment