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bug fixes for CAMPneu #51527

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bug fixes for CAMPneu #51527

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b92acf5
edit email for CAMPneu
mmkadam Oct 21, 2024
eb76457
Merge branch 'master' into update_my_recipe
mmkadam Oct 21, 2024
b261d18
Update recipes/CAMPneu/build.sh
mmkadam Oct 21, 2024
3095db1
Update meta.yaml
mmkadam Oct 23, 2024
6ba35df
Merge branch 'master' into update_my_recipe
mmkadam Oct 25, 2024
a061dd4
Delete recipes/CAMPneu/build.sh
mmkadam Oct 25, 2024
6df1112
change package name to lowercase
mmkadam Oct 29, 2024
98a5027
Merge branch 'master' into update_my_recipe
mmkadam Oct 30, 2024
4b2bf1f
Merge branch 'master' into update_my_recipe
mmkadam Nov 12, 2024
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9 changes: 9 additions & 0 deletions recipes/CAMPneu/build.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
#!/bin/bash

# $PYTHON -m pip install . -vv

mkdir -p $PREFIX/bin/

cp $RECIPE_DIR/../CAMPneu.nf $RECIPE_DIR/../nextflow.config $PREFIX/bin/
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💡 Codebase verification

Source files CAMPneu.nf and nextflow.config are missing from the repository.

The build.sh script attempts to copy CAMPneu.nf and nextflow.config from the parent directory of the recipe, but these files were not found in any location within the repository. This will cause the copy operation to fail.

  • Ensure that CAMPneu.nf and nextflow.config are present in the repository.
  • If necessary, relocate these files to the recipe directory and update the copy command accordingly.
🔗 Analysis chain

Verify the correct location of source files.

The command copies files from $RECIPE_DIR/.., which is the parent directory of the recipe. This is unusual, as typically, files are copied from within the recipe directory. Ensure that CAMPneu.nf and nextflow.config are indeed located in the parent directory of the recipe.

Consider moving these files into the recipe directory for better organization and to follow conventional practices.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if the files exist in the expected location
if [ -f "$RECIPE_DIR/../CAMPneu.nf" ] && [ -f "$RECIPE_DIR/../nextflow.config" ]; then
  echo "Files found in the parent directory of the recipe."
else
  echo "Files not found in the expected location. Please verify their placement."
fi

# Check if the files exist in the recipe directory
if [ -f "$RECIPE_DIR/CAMPneu.nf" ] && [ -f "$RECIPE_DIR/nextflow.config" ]; then
  echo "Files already exist in the recipe directory. Update the copy command accordingly."
fi

Length of output: 405

Script:

#!/bin/bash
# Locate CAMPneu.nf and nextflow.config in the repository
fd "CAMPneu.nf" . --type f
fd "nextflow.config" . --type f

# Check if 'file' command is available
if command -v file >/dev/null 2>&1; then
  echo "'file' command is available."
else
  echo "'file' command is not available. Please ensure it is installed."
fi

Length of output: 219


chmod +x $PREFIX/bin/CAMPneu.nf $PREFIX/bin/nextflow.config
48 changes: 48 additions & 0 deletions recipes/CAMPneu/meta.yaml
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{% set name = "CAMPneu" %}
{% set version = "1.1.0" %}
{% set hash = "1f2bc9dbb9fa71fce9876852ba0dedad997cca800734b81a6a43fff8e5e20ac3" %}
{% set user = "appliedbinf" %}

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

source:
url: https://github.com/{{ user }}/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
sha256: {{ hash }}

build:
number: 0
noarch: generic
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missing run_exports


requirements:
build:
- python
- setuptools
- skip: True # [win]
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This should be part of root > build, not root > requirements > build

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Please do not resolve conversations if you haven't addressed the issue.


host:
- python
- pip

run:
- nextflow
- python <3.11
- minimap2==2.28
- samtools
- fastp
- fastANI
- bcftools
- kraken2
- unicycler
- freebayes
- jq

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test:
commands:
- CAMPneu.nf --help
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about:
home: "https://github.com/{{ user }}/{{ name }}"
license: MIT
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summary: "Comprehensive Analysis of Mycoplasma Pneumoniae"
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🛠️ Refactor suggestion

Enhance the about section with more details.

The about section provides essential information, but it could be more comprehensive:

  1. The use of Jinja2 variables for the home URL is consistent and good.
  2. The license information (MIT) is correctly specified.
  3. The summary is very brief and could be more informative.

Consider expanding the about section with more details:

about:
  home: "https://github.com/{{ user }}/{{ name }}"
  license: MIT
  license_file: LICENSE  # Add this if a LICENSE file exists in the source
  summary: "Comprehensive Analysis of Mycoplasma Pneumoniae"
  description: |
    CAMPneu is a bioinformatics pipeline for the comprehensive analysis of Mycoplasma pneumoniae.
    It integrates various tools for tasks such as genome assembly, variant calling, and annotation.
  dev_url: "https://github.com/{{ user }}/{{ name }}"
  doc_url: "https://github.com/{{ user }}/{{ name }}#readme"

Would you like help in drafting a more detailed description based on the CAMPneu documentation?

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