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Add new package kestrel in version 1.0.3 #51810

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merged 6 commits into from
Nov 16, 2024
Merged

Add new package kestrel in version 1.0.3 #51810

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7fbf331
New recipe for kestrel v1.0.3
Oct 30, 2024
eec963b
fix test
Oct 31, 2024
77ec8c2
Apply suggestions from code review
holtgrewe Oct 31, 2024
dfd53c7
Update build.sh
holtgrewe Oct 31, 2024
f81fe62
use SPDX license id
martin-g Nov 1, 2024
ef51e5f
Merge branch 'master' into new-recipe-kestrel-1.0.3
richard-burhans Nov 15, 2024
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9 changes: 9 additions & 0 deletions recipes/kestrel/build.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
#!/bin/bash

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kestrel=$PREFIX/opt/$PKG_NAME-$PKG_VERSION
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mkdir -p $kestrel
cp -r ./* $kestrel
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chmod +x $kestrel/kestrel
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mkdir -p $PREFIX/bin
ln -s $kestrel/kestrel $PREFIX/bin/kestrel
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💡 Codebase verification

Version inconsistency confirmed: meta.yaml shows 1.0.3 while PR targets 1.0.5

The meta.yaml file explicitly sets the version to 1.0.3:

{% set version = "1.0.3" %}

This needs to be updated to match the intended version 1.0.5 mentioned in the PR objectives.

🔗 Analysis chain

Verify package version consistency.

The AI summary mentions version 1.0.3, but the PR objectives state version 1.0.5.

Let's verify the version in meta.yaml:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check package version in meta.yaml
grep "version:" recipes/kestrel/meta.yaml

Length of output: 66

Script:

#!/bin/bash
# Let's check the package version from multiple sources
cat recipes/kestrel/meta.yaml

Length of output: 1023

37 changes: 37 additions & 0 deletions recipes/kestrel/meta.yaml
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{% set name = "kestrel" %}
{% set version = "1.0.3" %}
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package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://github.com/paudano/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}-linux.tar.gz
sha256: 992c579fc52dce7b9d80e6232914da02663a2480d28b672277d80fdfcdda33e3

build:
noarch: generic
detect_binary_files_with_prefix: true
number: 0
run_exports:
- {{ pin_subpackage('kestrel', max_pin="x") }}

requirements:
run:
# Enforce a version requirement on openjdk to ensure
# it comes from the conda-forge channel and not default.
# Many yaks were shaved to bring us this information.
# Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906
- openjdk >=8.0.144

test:
commands:
- fastqc
- fastqc -h
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⚠️ Potential issue

Incorrect test commands.

The test commands are checking for fastqc which is a different tool. The tests should verify the kestrel executable instead.

Replace with appropriate test commands:

test:
  commands:
-    - fastqc
-    - fastqc -h 
+    - kestrel --version
+    - kestrel --help
📝 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
test:
commands:
- fastqc
- fastqc -h
test:
commands:
- kestrel --version
- kestrel --help


about:
home: 'https://github.com/paudano/kestrel'
license: GPL 3
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license_file: COPYING
summary: 'Mapping-free variant caller for short-read Illumina data'

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