The question about `vg` version of pggb

[zwh82]

According to the PGGB Dockerfile, I believe PGGB should be compatible with the latest version of vg. However, PGGB on Bioconda still uses vg 1.40. I have a tool that needs to be uploaded to Bioconda, and it requires PGGB and vg version 1.52 or later. This creates a version conflict with vg. Is it possible to update the vg version of PGGB on Bioconda? https://github.com/pangenome/pggb/blob/e8dd3fd3adffc3efcfc4f8ac0efc79cf0d54771b/Dockerfile#L103

https://github.com/bioconda/bioconda-recipes/blob/77e90150442fa23bfd227b88696ffc982be7abc0/recipes/pggb/meta.yaml#L31

requirements:
  run:
    - bc
    - tabix
    - gfaffix ==0.1.5b
    - gsl 2.7.0 
    - multiqc ==1.19
    - odgi ==0.8.6
    - pigz
    - bcftools
    - seqwish ==0.7.10
    - smoothxg ==0.7.4
    - time
    - vg 1.40.0
    - wfmash ==0.13.0
    - python-igraph ==0.10.4

[AndreaGuarracino]

That's right! Unfortunately, updating things on bioconda is often a pain, which is why we're slower there. I've just triggered the update of vg to v 1.59.0. After accepted and merged, it will take a bit before becoming available via bioconda.

[bgruening]

Why is updating Bioconda painful? :)

[AndreaGuarracino]

Every now and then, automatic updates (new GitHub releases that trigger Bioconda recipe updates) stop working, and it's not always easy to understand why. Then I start spying on other recipes to figure out what to fix. :/

[AndreaGuarracino]

@zwh82, pggb's recipe has vg 1.59.0, I hope everything will be fine now!

[zwh82]

Thanks. Everything is all right.