adding RDEVAL #52070
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| #!/usr/bin/env bash | ||
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| set -o errexit | ||
| set -o nounset | ||
| set -o xtrace | ||
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| cd "$SRC_DIR" | ||
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| export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" | ||
| export LDFLAGS="$LDFLAGS -L$PREFIX/lib" | ||
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| make | ||
| install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" |
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| Original file line number | Diff line number | Diff line change |
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| {% set name = "rdeval" %} | ||
| {% set version = "0.0.2" %} | ||
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| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
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| source: | ||
| url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip | ||
| sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d | ||
| patches: | ||
| - quote.patch | ||
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| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - make | ||
| - zlib | ||
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| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name|lower, max_pin="x.x") }} | ||
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| test: | ||
| commands: | ||
| - ${PREFIX}/bin/rdeval --help | ||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Enhance test coverage The current test only verifies that the help command works. Consider adding more comprehensive tests:
Would you like assistance in generating additional test commands based on the tool's functionality? |
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| about: | ||
| home: https://github.com/vgl-hub/{{ name }} | ||
| summary: A general purpose, multithreaded read analysis and manipulation tool. | ||
| license: MIT | ||
| license_file: LICENSE | ||
| license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE | ||
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There was a problem hiding this comment. 💡 Codebase verification LICENSE file verified and README requires a detailed Description section
🔗 Analysis chainVerify license file and update summary
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Verify license file existence and content
gh api repos/vgl-hub/rdeval/contents/LICENSE --jq '.content' | base64 -d
# Check if there's a more detailed description in README
gh api repos/vgl-hub/rdeval/contents/README.md --jq '.content' | base64 -d | grep -A 5 "^#.*Description"
Length of output: 298 Script: #!/bin/bash
# Verify license file existence and content without using base64
gh api repos/vgl-hub/rdeval/contents/LICENSE --raw
# Check if there's a more detailed description in README
gh api repos/vgl-hub/rdeval/contents/README.md --raw | grep -A 5 "^#.*Description"
Length of output: 2865 Script: #!/bin/bash
# Verify license file existence and content using jq to decode base64
gh api repos/vgl-hub/rdeval/contents/LICENSE --jq '.content | @base64d'
# Check if there's a more detailed description in README using jq to decode and grep for keywords
gh api repos/vgl-hub/rdeval/contents/README.md --jq '.content | @base64d' | grep -A 5 "^#.*Description"
Length of output: 1244 |
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| Original file line number | Diff line number | Diff line change | ||||||||
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| @@ -0,0 +1,25 @@ | ||||||||||
| diff --git a/Makefile b/Makefile | ||||||||||
| index 5823f28..7e1295c 100644 | ||||||||||
| --- a/Makefile | ||||||||||
| +++ b/Makefile | ||||||||||
| @@ -14,6 +14,7 @@ BINDIR := $(BUILD)/.o | ||||||||||
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| LDFLAGS := -pthread | ||||||||||
| LIBS = -lz | ||||||||||
| +-L/usr/lib/x86_64-linux-gnu -lz | ||||||||||
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There was a problem hiding this comment. Remove hard-coded library path and fix duplicate linker flags The current changes introduce two issues:
Apply this fix to maintain portability and clean up duplicates: LDFLAGS := -pthread
-LIBS = -lz
--L/usr/lib/x86_64-linux-gnu -lz
+LIBS = -lzInstead of hard-coding the library path, rely on Conda's build environment variables and the proper dependency specification in meta.yaml. 📝 Committable suggestion
Suggested change
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| OBJS := main input reads | ||||||||||
| BINS := $(addprefix $(BINDIR)/, $(OBJS)) | ||||||||||
| diff --git a/src/reads.cpp b/src/reads.cpp | ||||||||||
| index 866f49b..ac714cf 100644 | ||||||||||
| --- a/src/reads.cpp | ||||||||||
| +++ b/src/reads.cpp | ||||||||||
| @@ -14,7 +14,7 @@ | ||||||||||
| #include "functions.h" // global functions | ||||||||||
| #include "stream-obj.h" | ||||||||||
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| -#include "zlib.h" | ||||||||||
| +#include <zlib.h> | ||||||||||
| #include "zstream/zstream_common.hpp" | ||||||||||
| #include "zstream/ozstream.hpp" | ||||||||||
| #include "zstream/ozstream_impl.hpp" | ||||||||||
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Add runtime dependencies section
The recipe is missing a
runsection underrequirements. Since you're usingzlibduring build, it's likely needed at runtime too.Add the following section:
requirements: build: - {{ compiler('cxx') }} - make - zlib + host: + - zlib + run: + - zlib📝 Committable suggestion