Add fc-virus recipe #51809
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| MIT License | ||
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| Copyright (c) [2022] [Runpeng Luo] | ||
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| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
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| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
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| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
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| #!/bin/bash | ||||||||||||||||||
| set -xe | ||||||||||||||||||
| make CXX="${CXX}" INCLUDES="-I$PREFIX/include" CFLAGS+="-g -Wall -O2 -L$PREFIX/lib" | ||||||||||||||||||
| #chmod +x ./bin/fc-virus | ||||||||||||||||||
| chmod 777 ./bin/fc-virus | ||||||||||||||||||
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There was a problem hiding this comment. Security: Fix overly permissive file permissions Using chmod 777 grants read/write/execute permissions to all users, which is a security risk. The executable only needs to be executable by users (755). -#chmod +x ./bin/fc-virus
-chmod 777 ./bin/fc-virus
+chmod 755 ./bin/fc-virus📝 Committable suggestion
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| mkdir -p ${PREFIX}/bin | ||||||||||||||||||
| cp -f ./bin/fc-virus ${PREFIX}/bin | ||||||||||||||||||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Add error handling for installation steps The installation commands should:
-mkdir -p ${PREFIX}/bin
-cp -f ./bin/fc-virus ${PREFIX}/bin
+if [ ! -f ./bin/fc-virus ]; then
+ echo "Error: fc-virus binary not found" >&2
+ exit 1
+fi
+mkdir -p "${PREFIX}/bin" || exit 1
+install -v -m 755 ./bin/fc-virus "${PREFIX}/bin/" || exit 1📝 Committable suggestion
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| {% set name = "fc-virus" %} | ||||||||||||||||||||||||||||||||
| {% set version = "1.0.1" %} | ||||||||||||||||||||||||||||||||
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| package: | ||||||||||||||||||||||||||||||||
| name: "fc" | ||||||||||||||||||||||||||||||||
| version: {{ version }} | ||||||||||||||||||||||||||||||||
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| source: | ||||||||||||||||||||||||||||||||
| url: "https://github.com/qdu-bioinfo/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" | ||||||||||||||||||||||||||||||||
| sha256: "6545124184e7ac743ff8149e97a0972230dad4f458248d2cad088e329e91b836" | ||||||||||||||||||||||||||||||||
| build: | ||||||||||||||||||||||||||||||||
| number: 0 | ||||||||||||||||||||||||||||||||
| skip: true | ||||||||||||||||||||||||||||||||
| run_exports: | ||||||||||||||||||||||||||||||||
| - {{ pin_subpackage("fc", max_pin="x") }} | ||||||||||||||||||||||||||||||||
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There was a problem hiding this comment. Remove redundant skip directive The build:
number: 0
- skip: true
run_exports:
- {{ pin_subpackage("fc", max_pin="x") }}📝 Committable suggestion
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| requirements: | ||||||||||||||||||||||||||||||||
| build: | ||||||||||||||||||||||||||||||||
| - make | ||||||||||||||||||||||||||||||||
| - {{ compiler('c') }} | ||||||||||||||||||||||||||||||||
| host: | ||||||||||||||||||||||||||||||||
| - zlib | ||||||||||||||||||||||||||||||||
| - boost | ||||||||||||||||||||||||||||||||
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There was a problem hiding this comment. Add C++ compiler requirement Since the package depends on boost, which is a C++ library, you should add the C++ compiler to the build requirements. build:
- make
- {{ compiler('c') }}
+ - {{ compiler('cxx') }}📝 Committable suggestion
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| test: | ||||||||||||||||||||||||||||||||
| commands: | ||||||||||||||||||||||||||||||||
| - ./bin/fc-virus --help | ||||||||||||||||||||||||||||||||
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There was a problem hiding this comment. Fix test command path. The current test command uses a relative path Apply this fix: test:
commands:
- - ./bin/fc-virus --help
+ - fc-virus --help📝 Committable suggestion
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| about: | ||||||||||||||||||||||||||||||||
| home: "https://github.com/qdu-bioinfo/fc-virus" | ||||||||||||||||||||||||||||||||
| license: MIT | ||||||||||||||||||||||||||||||||
| license_family: MIT | ||||||||||||||||||||||||||||||||
| license_file: LICENSE | ||||||||||||||||||||||||||||||||
| summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" | ||||||||||||||||||||||||||||||||
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| skip: | ||||||||||||||||||||||||||||||||
| - osx-64 | ||||||||||||||||||||||||||||||||
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There was a problem hiding this comment. Move skip configuration to build section The skip configuration should be under the build section, not at the root level. build:
number: 0
run_exports:
- {{ pin_subpackage("fc", max_pin="x") }}
+ skip:
+ - osx-64
-skip:
- - osx-64📝 Committable suggestion
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Fix shebang line position
The shebang must be on the first line of the script. Remove the blank line 1.
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[error] 2-2: The shebang must be on the first line. Delete blanks and move comments.
(SC1128)