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Add bam2plot #51975

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merged 5 commits into from
Nov 7, 2024
Merged

Add bam2plot #51975

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b44604d
Add bam2plot
druvus Nov 6, 2024
60c398f
Fix typo
druvus Nov 6, 2024
aea705b
Fixes
druvus Nov 6, 2024
e1d9361
Add mosdepth
druvus Nov 6, 2024
4029b48
Fix help section
druvus Nov 6, 2024
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48 changes: 48 additions & 0 deletions recipes/bam2plot/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
{% set name = "bam2plot" %}
{% set version = "0.3.6" %}

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

source:
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz
sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541
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💡 Codebase verification

SHA256 checksum mismatch detected

The SHA256 checksum in the recipe (7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541) does not match the official PyPI package checksum (19e6c72cd31318c43f511c926090136b748923151ff0c37a9da782ea4dc1359e).

  • Update the sha256 value in meta.yaml to: 19e6c72cd31318c43f511c926090136b748923151ff0c37a9da782ea4dc1359e
🔗 Analysis chain

Verify the source package integrity.

The URL and checksum format are correct, but let's verify the SHA256 checksum matches the PyPI package.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the SHA256 checksum of the PyPI package
# Expected: The checksum should match "7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541"

curl -sL "https://pypi.org/packages/source/b/bam2plot/bam2plot-0.3.6.tar.gz" | sha256sum

Length of output: 165

Script:

#!/bin/bash
# Let's try a different approach using Python's pip to get package info
curl -sL "https://pypi.org/pypi/bam2plot/json" | jq -r '.releases."0.3.6"[0].digests.sha256'

Length of output: 157


build:
entry_points:
- bam2plot=bam2plot.main:cli
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
run_exports:
- {{ pin_subpackage('bam2plot', max_pin="x.x") }}
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🛠️ Refactor suggestion

Remove unnecessary run_exports section.

The run_exports section is not needed for Python packages as they don't have ABI compatibility concerns like C/C++ packages do.

-  run_exports:
-    - {{ pin_subpackage('bam2plot', max_pin="x.x") }}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
run_exports:
- {{ pin_subpackage('bam2plot', max_pin="x.x") }}


requirements:
host:
- python >=3.10
- pip
- setuptools
run:
- python >=3.10
- pysam >=0.22.0
- seaborn >=0.13.2
- polars >=0.20.15
- mappy >=2.28
- pyfastx
- pyarrow
- mosdepth

test:
imports:
- bam2plot
commands:
- bam2plot from_bam --help
- bam2plot from_reads --help
- bam2plot guci --help

about:
home: https://github.com/willros/bam2plot
summary: Plot of coverage from bam file
license: GPL-3.0-only
license_file: LICENSE
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