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Technical Details

At the core, aNtiLoPe consists of various independent Nextflow pipeline scripts (the *.nf scripts). These pipeline scripts provide the logic to connect a number of inter-dependent processes and determines the data flow between them. Within these processes, any language may be use to define the scripts that performs the tasks (bash/python/perl/etc...). Typically, a process script invokes a single external tool.

The underlying tools that are invoked are not provided by aNtiLoPe itself, but installation and distribution thereof is delegated to LaMachine, upon which aNtiLoPe depends.

The exception to the above are some scripts (shell/perl/python/etc) that are not otherwise distributed nor can be considered proper reusable tools out of the scope of aNtiLoPe. These are distributed as part of aNtiLoPe in in scripts/. This is a fall-back solution that be preferably be kept to a minimum.

For linguistic annotation, the pivot format in aNtiLoPe is FoLiA.

Contributor Guidelines

  • The aNtiLoPe codebase is maintained in git at https://github.com/proycon/aNtiLoPe
    • Never do any development outside of version control!!!
    • Pull requests welcome!! (direct push access for main project contributors)
    • the master branch corresponds to the latest development version and should serve as the basis for all development
      • do not use this branch for production, always use the latest release (LaMachine takes care of this for you automatically)
      • keep the master branch in a workable state, use separate git branches for intensive development cycles.
  • For development of workflows, consult the Nextflow Documentation. The Nextflow scripting language is an extension of the Groovy programming language (runs on the Java VM) whose syntax has been specialized to ease the writing of computational pipelines in a declarative manner.
    • The process scripts within Nextflow pipeline scripts should typically invoke only a single external tool, or at least perform a single well-defined task (if you want to invoke a series of tools, use separate processes)
  • To make additional tools available for use in aNtiLoPe, consult the documentation on adding new software to LaMachine, installing tools should never be the responsibility of the end-user and rarely that of aNtiLoPe itself.
  • Report all bugs and feature requests pertaining to pipelines and webservice (or in case you simply don't know) to https://github.com/proycon/aNtiLoPe/issues
  • Integration tests are defined in test.sh and will automatically be run on our continuous integration platform at https://travis-ci.com/proycon/aNtiLoPe after each git push.
    • If you add a feature, we strongly recommend you to add a test.
    • The coverage of the tests is currently seriously sub-optimal!!
    • Tests should be limited in scope so they can be performed quickly, often and with limited resources (no OCRing of whole books!!)
    • Tests on a lower (unit) level are the responsibility of the underlying tools, rather than aNtiLoPe

Setting up a Development Environment

  • Install the development version of LaMachine, in any flavour, and enable aNtiLoPe in the installation manifest during the bootstrap procedure (or just run lamachine-add antilope after the fact)
  • The aNtiLoPe git repository will be cloned in $LM_SOURCEPATH/aNtiLoPe. If you do not have direct push access to the aNtiLoPe repository, we recommend you fork https://github.com/proycon/aNtiLoPe and add do a git remote add to track your own branch there.
  • You can always upgrade your LaMachine environment with lamachine-update, but make sure you don't have uncommitted changes (they will be stashed away automatically)!!