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Update pggb to 0.7.0 #51436

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merged 6 commits into from
Oct 16, 2024
Merged

Update pggb to 0.7.0 #51436

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6bd984c
Update pggb to 0.7.0
BiocondaBot Oct 16, 2024
7aacf25
update pggb components, and add vcfbub and vcflib
AndreaGuarracino Oct 16, 2024
3835015
skip osx
AndreaGuarracino Oct 16, 2024
52ddad5
remove noarch
AndreaGuarracino Oct 16, 2024
313c4b6
noarch after skip true
AndreaGuarracino Oct 16, 2024
dd278ad
add skip-lints
AndreaGuarracino Oct 16, 2024
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30 changes: 17 additions & 13 deletions recipes/pggb/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,36 +1,38 @@
{% set name = "pggb" %}
{% set version = "0.6.0" %}
{% set version = "0.7.0" %}

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

source:
url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
sha256: e201410e5b7ca7c598267797a7fa30b065a1b2b76ee5c309341a93fc489704f3
sha256: 1ea167eadd66db7665c8135a629aea046d79491f57227a4a332a376b92caf911

build:
noarch: generic
number: 0
skip: true # [osx]
run_exports:
- {{ pin_subpackage(name, max_pin='x.x') }}
number: 1

requirements:
run:
- wfmash ==0.14.0
- seqwish ==0.7.11
- smoothxg ==0.8.0
- odgi ==0.9.0
- gfaffix ==0.1.5b
- vg ==1.59.0
- vcfbub ==0.1.1
- vcflib ==1.0.10
- multiqc ==1.22
- python-igraph ==0.11.5
Comment on lines +20 to +29
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💡 Codebase verification

Missing meta.yaml File in Tag v0.7.0.

The meta.yaml file was not found in the pggb repository at tag v0.7.0. This may indicate that the file has been moved, renamed, or removed in this version.

Please verify the location of the dependencies file or update the review comment to reflect the current structure of the repository.

🔗 Analysis chain

Significant changes in dependencies.

The requirements section has undergone substantial changes:

  1. New dependencies added: wfmash, seqwish, smoothxg, odgi, gfaffix, vg, vcfbub, vcflib, multiqc, and python-igraph.
  2. Some existing dependencies have been updated or removed.

These changes are likely necessary for the new version of pggb. However, please ensure that:

  1. All these dependencies are indeed required for version 0.7.0.
  2. The specified versions are compatible with each other and with pggb 0.7.0.
  3. There are no missing dependencies that pggb 0.7.0 might need.

To verify the dependencies, you can run the following script:

- 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 1.59.0
- wfmash ==0.13.0
- python-igraph ==0.10.4

test:
commands:
Expand All @@ -40,8 +42,10 @@ about:
home: https://github.com/pangenome/pggb
license: MIT
license_file: LICENSE
summary: This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model).
summary: PanGenome Graph Building pipeline renders
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⚠️ Potential issue

Incomplete package summary

The updated summary appears to be truncated and doesn't provide a clear description of the package's functionality. Please revise the summary to accurately and completely describe the purpose of the pggb package.

Consider reverting to the previous summary or providing a more comprehensive description:

summary: This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model).


extra:
recipe-maintainers:
- AndreaGuarracino
skip-lints:
- should_be_noarch_generic
Comment on lines +50 to +51
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⚠️ Potential issue

Clarify architecture requirements

The addition of should_be_noarch_generic to skip-lints suggests that the package should be architecture-independent. However, this conflicts with the earlier addition of skip: true # [osx], which implies the package is not compatible with macOS.

Please clarify:

  1. Is the package truly architecture-dependent? If so, remove the should_be_noarch_generic skip-lint.
  2. If the package is architecture-independent, remove the skip: true # [osx] condition and keep the skip-lint.