This is a server to facilitate the use of PolyMarker.
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
.
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.
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
- yes to all except: