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Update hmftools CHORD and CUPPA #52175

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merged 9 commits into from
Nov 19, 2024
Merged

Update hmftools CHORD and CUPPA #52175

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b473b1f
Update hmftools-chord to v2.1.0_beta.2
luan-n-nguyen Nov 19, 2024
0259b87
Update hmftools-cuppa to v2.3_beta.1
luan-n-nguyen Nov 19, 2024
fbfe1fa
Update cuppa jar shasum
luan-n-nguyen Nov 19, 2024
791d442
Fix cuppa jar URL pattern
luan-n-nguyen Nov 19, 2024
f274a18
Unzip and install pycuppa
luan-n-nguyen Nov 19, 2024
b5a96a6
Remove docker RUN command
luan-n-nguyen Nov 19, 2024
622f116
Add unzip dependency
luan-n-nguyen Nov 19, 2024
32c5163
Make unzip a host dependency
luan-n-nguyen Nov 19, 2024
4193eb2
Fix wrong path to cuppa jar
luan-n-nguyen Nov 19, 2024
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6 changes: 3 additions & 3 deletions recipes/hmftools-chord/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set version = "2.1.0_beta" %}
{% set beta_suffix = ".1" %}
{% set sha256 = "25a4dfd8a0ab436e0f23d94e77cebb59a0830a052a90c823844b798bd409bfc3" %}
{% set beta_suffix = ".2" %}
{% set sha256 = "847e0239b7440b70d67957d38afb3ab42bd3acecb931afc49ab8aef4c248a1da" %}

package:
name: hmftools-chord
Expand All @@ -12,7 +12,7 @@ source:

build:
noarch: generic
number: 2
number: 3
run_exports:
- {{ pin_subpackage("hmftools-chord", max_pin="x.x") }}

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14 changes: 5 additions & 9 deletions recipes/hmftools-cuppa/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,22 +1,18 @@
{% set version = "2.3.0_beta" %}
{% set sha256_jar = "69f94a54f232a2a22927dce165120d1f166d4931bfb8f299515edaa577607c7c" %}
{% set sha256_src = "65a2070e78243fed975b8738d2ce79dfead1a5702c2bc91e26488c806e25d158" %}
{% set beta_suffix = ".1" %}
{% set sha256 = "ae3a3d9bc31e45cba52943df01b6f8f190beff904dff392e6413c1396d7db36d" %}

package:
name: hmftools-cuppa
version: '{{ version }}'

source:
- folder: jar
url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa-{{ version|replace(".0", "") }}.jar
sha256: '{{ sha256_jar }}'
- folder: src
url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/cuppa-v{{ version }}.tar.gz
sha256: '{{ sha256_src }}'
url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa-{{ version|replace(".0", "") }}{{ beta_suffix }}.jar
sha256: '{{ sha256 }}'
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💡 Codebase verification

URL pattern in meta.yaml needs correction

The current URL pattern in meta.yaml is incorrect. The actual asset names in the release follow a different pattern:

  • Current pattern: cuppa-2.3_beta.1.jar
  • Actual pattern: cuppa_v2.3_beta.1.jar

The differences are:

  • Uses underscore (_) instead of hyphen (-) after "cuppa"
  • Includes "v" in the version part
🔗 Analysis chain

Verify the GitHub release URL accessibility.

The URL construction involves multiple string manipulations. Let's verify that the release artifact is accessible.

Let me verify the correct URL pattern by checking the repository's releases.

Let me check specifically for CUPPA releases to understand their naming pattern.

Let me check the actual assets in the specific CUPPA release we're interested in.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the GitHub release artifact exists
# Extract version and construct URL
VERSION="2.3.0_beta"
BETA_SUFFIX=".1"
URL="https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v${VERSION}/cuppa-${VERSION/.0/}${BETA_SUFFIX}.jar"

# Check if the URL is accessible
curl -sI "$URL" | head -n 1

Length of output: 278

Script:

#!/bin/bash
# Check recent releases and their asset patterns
gh release list --repo hartwigmedical/hmftools --limit 5

Length of output: 459

Script:

#!/bin/bash
# Search for CUPPA releases
gh release list --repo hartwigmedical/hmftools | grep -i cuppa

Length of output: 865

Script:

#!/bin/bash
# Check assets for CUPPA v2.3 beta release
gh release view cuppa-v2.3.0_beta --repo hartwigmedical/hmftools

Length of output: 478


build:
noarch: generic
number: 0
number: 1
run_exports:
- {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }}

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