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Scripts to manage website and database

• Data Loading
  1. Loading GBS genotype experiment
  2. Loading genome assembly from Ensembl
  3. Loading genome annotation from Ensembl
  4. Loading pathway information from plantreactome.gramene.org
  5. Loading metabolite reference
  6. Loading metabolite profile
• Loading GBS genotype data
• Creating BLAST Database
• Creating Physical Map from genome assembly
• JBrowse
  1. Adding track
  2. Creating new JBrowse Genome
• Analysis
  1. Run GWAS analysis (rrBLUP)
  2. Load QTL results (qtl_anotations)
  3. Run Variant Effect Predictor (ensemblVEP)
  4. Load VEP results (vep_annotations)
  5. Marker Synonym Report
• Browse
  1. Genes
  2. Pathways
• Database caches
  1. Content Status
  2. allele_cache
  3. allele-byline
  4. allele-bymarker
  5. allele_bymarker_exp
     • allele_bymarker_exp_101
     • allele_bymarker_exp_ACTG
     • allele_bymarker_expidx
  6. allele_byline_exp
     • allele_byline_exp_ACTG
     • allele_byline_expidx