Create FC-Virus #51579
There are no files selected for viewing
| Original file line number | Diff line number | Diff line change | ||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,14 @@ | ||||||||||||||||||||||||||||||||||
| #!/bin/bash | ||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||
| export LDFLAGS="$LDFLAGS -L$PREFIX/lib" | ||||||||||||||||||||||||||||||||||
| export CPATH=${PREFIX}/include | ||||||||||||||||||||||||||||||||||
| export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib | ||||||||||||||||||||||||||||||||||
| export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include | ||||||||||||||||||||||||||||||||||
| #export PATH=$BUILD_PREFIX/bin:$PATH | ||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||
| make \ | ||||||||||||||||||||||||||||||||||
| CXX="${CXX}" \ | ||||||||||||||||||||||||||||||||||
| CFLAGS="${CFLAGS} " | ||||||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||||||
| install -d "${PREFIX}/bin" | ||||||||||||||||||||||||||||||||||
| install ./bin/fc-virus "${PREFIX}/bin/" | ||||||||||||||||||||||||||||||||||
|
There was a problem hiding this comment. Improve installation process with error handling and verification. The installation commands need error handling and post-install verification. Apply these improvements: -install -d "${PREFIX}/bin"
-install ./bin/fc-virus "${PREFIX}/bin/"
+# Create installation directory
+install -d "${PREFIX}/bin" || { echo "Failed to create bin directory"; exit 1; }
+
+# Install binary
+install ./bin/fc-virus "${PREFIX}/bin/" || { echo "Failed to install fc-virus"; exit 1; }
+
+# Verify installation
+if [ ! -x "${PREFIX}/bin/fc-virus" ]; then
+ echo "Installation verification failed"
+ exit 1
+fi
+
+# Clean up
+rm -rf ./bin📝 Committable suggestion
Suggested change
|
||||||||||||||||||||||||||||||||||
| Original file line number | Diff line number | Diff line change | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,38 @@ | ||||||||||||||
| {% set version = "1.0.1" %} | ||||||||||||||
| package: | ||||||||||||||
| name: fc-virus | ||||||||||||||
| version: {{ version }} | ||||||||||||||
|
|
||||||||||||||
| source: | ||||||||||||||
| url: https://github.com/qdu-bioinfo/fc-virus/archive/v{{ version }}.tar.gz | ||||||||||||||
| sha256: d78288864a0db981b5d29edc14e715939372641f58c587777e4cd9359c34562b | ||||||||||||||
|
|
||||||||||||||
| build: | ||||||||||||||
| number: 0 | ||||||||||||||
| run_exports: | ||||||||||||||
| - {{ pin_subpackage("fc-virus", max_pin="x") }} | ||||||||||||||
|
|
||||||||||||||
| requirements: | ||||||||||||||
| build: | ||||||||||||||
| - {{ compiler("c") }} | ||||||||||||||
| - {{ compiler("cxx") }} | ||||||||||||||
| - make | ||||||||||||||
| host: | ||||||||||||||
| - make | ||||||||||||||
qdu-bioinfo marked this conversation as resolved.
Show resolved
Hide resolved
|
||||||||||||||
| - boost | ||||||||||||||
| - zlib | ||||||||||||||
| - htslib | ||||||||||||||
|
Comment on lines
+23
to
+25
There was a problem hiding this comment. 🛠️ Refactor suggestion Add version constraints for core dependencies For better reproducibility, consider adding version constraints for core dependencies: - - boost
- - zlib
- - htslib
+ - boost >=1.74.0
+ - zlib >=1.2.11
+ - htslib >=1.15📝 Committable suggestion
Suggested change
|
||||||||||||||
|
|
||||||||||||||
qdu-bioinfo marked this conversation as resolved.
Show resolved
Hide resolved
|
||||||||||||||
| about: | ||||||||||||||
| home: https://github.com/qdu-bioinfo/fc-virus | ||||||||||||||
| license: MIT | ||||||||||||||
| license_file: LICENSE | ||||||||||||||
| summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" | ||||||||||||||
| dev_url: https://github.com/qdu-bioinfo/fc-virus | ||||||||||||||
|
|
||||||||||||||
| test: | ||||||||||||||
| commands: | ||||||||||||||
| - ./bin/fc-virus --help | ||||||||||||||
|
There was a problem hiding this comment. 🛠️ Refactor suggestion Enhance test coverage and fix binary path.
Apply this diff: test:
commands:
- - ./bin/fc-virus --help
+ - $PREFIX/bin/fc-virus --help
+ - $PREFIX/bin/fc-virus --version
+ # Add a basic functionality test if possible
|
||||||||||||||
| extra: | ||||||||||||||
| additional-platforms: | ||||||||||||||
| - linux-aarch64 | ||||||||||||||
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Enhance build command with error handling and optimization flags.
The current build command lacks error handling and important compiler flags.
Apply this diff to improve the build command:
📝 Committable suggestion