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Add recipe for stxtyper v1.0.25 #51792

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Oct 29, 2024
Merged

Add recipe for stxtyper v1.0.25 #51792

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a868214
Add recipe for stxtyper v1.0.25
mencian Oct 29, 2024
8f655ef
add sha256
mencian Oct 29, 2024
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11 changes: 11 additions & 0 deletions recipes/stxtyper/build.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash

export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3"
export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
Comment on lines +3 to +7
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🛠️ Refactor suggestion

Consider more robust compiler flag handling.

While the environment setup is generally correct, there are a few suggestions for improvement:

  1. The -O3 optimization level might be too aggressive and could cause issues on some platforms
  2. Consider using DESTDIR for staged installations

Here's a more robust approach:

-export INCLUDES="-I${PREFIX}/include"
-export LIBPATH="-L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -O3"
-export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+# Use -O2 for better stability
+export CXXFLAGS="${CXXFLAGS} -O2"
+export CPPFLAGS="${CPPFLAGS} -O2 -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
📝 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
export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3"
export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
# Use -O2 for better stability
export CXXFLAGS="${CXXFLAGS} -O2"
export CPPFLAGS="${CPPFLAGS} -O2 -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"


make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"

make install PREFIX="${PREFIX}"
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⚠️ Potential issue

Add error checking and ensure proper installation.

The build and install commands should include error checking and use DESTDIR for staged installations.

Apply these improvements:

-make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"
+# Ensure CPU_COUNT is set
+export CPU_COUNT=${CPU_COUNT:-1}
+
+# Build with error checking
+if ! make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"; then
+    echo "Build failed"
+    exit 1
+fi
 
-make install PREFIX="${PREFIX}"
+# Install with DESTDIR for proper staging
+if ! make install DESTDIR="${PREFIX}" PREFIX=""; then
+    echo "Installation failed"
+    exit 1
+fi
📝 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
make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"
make install PREFIX="${PREFIX}"
# Ensure CPU_COUNT is set
export CPU_COUNT=${CPU_COUNT:-1}
# Build with error checking
if ! make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"; then
echo "Build failed"
exit 1
fi
# Install with DESTDIR for proper staging
if ! make install DESTDIR="${PREFIX}" PREFIX=""; then
echo "Installation failed"
exit 1
fi

36 changes: 36 additions & 0 deletions recipes/stxtyper/meta.yaml
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{% set name = "stxtyper" %}
{% set version = "1.0.25" %}
{% set sha256 = "adc734340c6a10f1bfc34ca637197e93e1515d0231bd023b33ce4c07aab9578e" %}

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

source:
url: https://github.com/ncbi/stxtyper/archive/refs/tags/v{{ version }}.tar.gz
sha256: {{ sha256 }}

build:
number: 0
run_exports:
- {{ pin_subpackage('stxtyper', max_pin='x') }}

requirements:
build:
- make
- {{ compiler('cxx') }}
host:
- zlib
run:
- blast

test:
commands:
- "stxtyper -h"

about:
home: https://github.com/ncbi/stxtyper
license: Public Domain
license_file: LICENSE
summary: 'Accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.'
dev_url: https://github.com/ncbi/stxtyper
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