The [DOI release] of the GOMAP pipeline contains code, software, and data files to run the pipeline. Although, there are some basic requirements which need to be installed. The requirements that have to be installed are listed below.

What are the requirements that need to be installed to run GOMAP?

  • Hardware
    • Storage
      • minimum: 250GB
      • recommended: \(\geq\)300GB
    • Memory
      • minimum: 16 GB
      • recommended: \(\geq\)32 GB
  • Software
    • OS
      • linux
    • Programming Languages
      • R v3.4
      • Python v2
      • Java v1.8
      • Perl
    • Software
      • MATLAB \(\geq\)v2016a
      • MySQL/MariaDB
    • Python Packages
      • biopython
      • numpy
      • scipy
      • MySQL-python
    • R packages
      • ontologyIndex
      • data.table
      • ggplot2
      • futile.logger
      • jsonlite

What are the software tools needed to run specific annotation methods?

  • Sequence-similarity
    • BLASTP
  • Domain-presence
    • InterProScan5
  • Mixed-method Pipelines
    • FANN-GO
      • MATLAB\(^\dagger\)
      • BLASTP
      • MySQL/MariaDB\(^\dagger\)
      • BLASTP
    • Argot2
      • Hmmer
      • BLASTP
      • Web browser\(^{\dagger\ddagger}\)
\(^\dagger\)Part of requirements installed as mentioned in this section
\(^\ddagger\)To submit jobs to batch processing
The pipeline file downloaded from CyVerse contains the data files and software tools to run the process on a given protein sequence fasta file. The disk space required for the pipeline is large (~160GB) and when it runs it will require close to 300GB of disk space.