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Add bubblegun recipe #51903

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merged 5 commits into from
Nov 5, 2024
Merged

Add bubblegun recipe #51903

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d40401e
adding bubblegun recipe
fawaz-dabbaghieh Nov 4, 2024
114ac12
Merge branch 'master' into bubblegun
fawaz-dabbaghieh Nov 4, 2024
90a0e29
adding some fixes to what coderabbit suggested
fawaz-dabbaghieh Nov 4, 2024
40696b8
adding back the run_export that coderabbitair specifically suggested …
fawaz-dabbaghieh Nov 4, 2024
6394cbb
Update meta.yaml
mencian Nov 5, 2024
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39 changes: 39 additions & 0 deletions recipes/bubblegun/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
{% set name = "BubbleGun" %}
{% set version = "1.1.9" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: "https://github.com/fawaz-dabbaghieh/bubble_gun/archive/refs/tags/v1.1.9.tar.gz"
sha256: 005d61a1e5774dfec810e612c1b4c5ce6c8d15f80d131237590ef71f62704c94


build:
number: 0
noarch: python
script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
run_exports:
- {{ pin_compatible('BubbleGun', max_pin="x") }}

requirements:
host:
- python >=3.6
- pip
- setuptools
run:
- python >=3.6

test:
commands:
- BubbleGun -h

about:
home: "https://github.com/fawaz-dabbaghieh/bubble_gun"
license: MIT
license_family: MIT
license_file: LICENSE
summary: 'BubbleGun is a tool for detecting bubbles and superbubbles in GFA graphs, and reports them and their nested structures'
doc_url: "https://github.com/fawaz-dabbaghieh/bubble_gun/blob/master/README.md"
dev_url: "https://github.com/fawaz-dabbaghieh"
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💡 Codebase verification

Package name needs to be lowercase to avoid conflicts

The package name should be lowercase to follow Bioconda naming conventions and avoid potential conflicts. Currently, there are similar packages in the ecosystem:

  • bioconductor-bubbletree
  • scbubbletree
  • bubbletree

Please modify the package name in the recipe to use bubblegun (lowercase) consistently:

  • Change {% set name = "BubbleGun" %} to {% set name = "bubblegun" %}
  • Update the run_exports section to use lowercase: {{ pin_compatible('bubblegun', max_pin="x") }}
🔗 Analysis chain

Verify package name in bioconda-utils.

Since this is a Bioconda package, let's verify the package name doesn't conflict with existing packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if package name exists in bioconda
rg -l "name:\s*bubblegun" --type yaml

Length of output: 39

Script:

#!/bin/bash
# Let's try a case-insensitive search and also check for the exact package name
rg -il "name:.*bubblegun" --type yaml
rg -il "name:.*BubbleGun" --type yaml

# Also check if there are any other recipes with similar names
fd -t f "meta.yaml" | xargs cat | grep -i "name.*bubble"

Length of output: 261

🧰 Tools
🪛 yamllint

[error] 19-19: trailing spaces

(trailing-spaces)

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

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