💌 Files from Debian 🐞

In the awesome YAMLs from Debian - despite of the highly appreciated perfectionism - we found a couple of 🐞🐛. @smoe if/when you'll have a bit of time for hacking the "yamlDump" again, it'd be super lovely if you could test the following records/phenomena with the edam.sh and edamJson2biotools.py? e^6 thanks!! 🚀🙏🏽

• beast looks like a cluttered record from beast-mcmc and beast-mcmc2 deb src packages, resulting in invalid YAML

description: >
  BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
  sequences. It is entirely orientated towards rooted, time-measured
  phylogenies inferred using strict or relaxed molecular clock models. It
  can be used as a method of reconstructing phylogenies but is also a
  framework for testing evolutionary hypotheses without conditioning on a
  single tree topology. BEAST uses MCMC to average over tree space, so that
  each tree is weighted proportional to its posterior probability. Included
  is a simple to use user-interface program for setting up standard
  analyses and a suit of programs for analysing the results.
version: 1.10.4
no new upstream version of beast-mcmc (1.x) but rather a rewritten
  version.
version: 2.6.0

• The same problem for soapdenovo, deb src pkgs soapdenovo and soapdenovo2

Note 1: In these 2 cases, there is probably a reason to maintain both major versions in Debian (or isn't it?), and therefore we should consider that in bio.tools too: consider whether they should have different descriptions, and maybe also EDAM annotation (if not, keep just 1 record), plus credits, pubs, ...

• Are there any more pairs of src pkgs that point to the same bio.tools record? What should be the general solution, or options, here? Any additional ideas on this issue @hmenager @bgruening ? (e.g. having 2 debian.yaml files in 1 bio-tools/content directory for the start? )

• dnacopy: some YAML validators are happy, but some dislike the colon+space in R package: DNA copy number data analysis

• bowtie: funny "punctuation" of function Genome indexing (Burrow-Wheeler). Ok in bowtie2. It looks like the only occurence of this phenomenon.

Note 2: Btw., @hmenager @bgruening @OlegZharkov have the best experiences with using the ruamel.yaml python lib for creating pretty YAML files.

Start with the listed beast, soapdenovo, dnacopy, and bowtie Debian YAML files, then run edam.sh and edamJson2biotools.py against the reported cases. Check how duplicate Debian source packages and the YAML validator differences are handled. Done means the reported records are valid and the general handling for duplicate packages is decided.