bioconda-recipes: Updating PacBio FALCON - dealing with package version naming problem

Currently the recipe https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pacbio_falcon/meta.yaml for https://anaconda.org/bioconda/pacbio_falcon uses:

{% set name = "pacbio_falcon" %}
{% set version = "052016" %}

package:
  name: {{ name }}
  version: {{ version }}

about:
  home: 'https://github.com/PacificBiosciences/FALCON'
  license: "Standard PacBio Open Source License"
  summary: "A set of tools for fast aligning long reads for consensus and assembly"

source:
  fn: funzip_052016.tar.gz
  url: https://github.com/PacificBiosciences/FALCON/archive/funzip_052016.tar.gz
  md5: be4a225262ee4bd9729b6b7e81a83615

...

The https://github.com/PacificBiosciences/FALCON/ repository only currently has tags for v0.1, v0.2 and funzip_052016 which seems to be the latest tag:

https://github.com/PacificBiosciences/FALCON/tree/funzip_052016

That was presumably how things stood when the recipe was first written (@bebatut Jan 2017):

https://github.com/bioconda/bioconda-recipes/commit/fd53551df5042f2d554504c752216fcb0cf390a1#diff-9cd1477e255f1bcb7b1f395abbdf2d30

The README is outdated https://github.com/PacificBiosciences/FALCON/issues/637 but if I understand correctly releases since have been via https://github.com/PacificBiosciences/FALCON-integrate which includes tags for 0.2.2, 0.3.0, …, 2.1.1, 2.1.2, 2.1.4 which appears to be the latest.

It would appear that the tag funzip_052016 (i.e. May 2016, sadly not year month order for sorting) was never intended to be regarded as a version number, and instead the major.minor.revision pattern is being used.

Unfortunately, we now have a BioConda package with version 052016 - how will this behave if we try to package FALCON v2.1.4 using 2.1.4 as the version?

Can we delete or tag the current package in some way as not to be used? Thus far https://anaconda.org/bioconda/pacbio_falcon reports only 416 downloads.

About this issue

  • Original URL
  • State: open
  • Created 6 years ago
  • Comments: 15 (14 by maintainers)

Most upvoted comments

Moving the recipe to bioconda-legacy sounds legitimate