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add files for equirep #51972

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merged 20 commits into from
Dec 10, 2024
Merged

add files for equirep #51972

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c575d95
add files for equirep
shaogroup Nov 6, 2024
caf4a10
update package name
shaogroup Nov 6, 2024
6f1f654
rename folder
shaogroup Nov 6, 2024
c085598
update meta.yaml
shaogroup Nov 6, 2024
562d361
add back run-exports
shaogroup Nov 6, 2024
e8b5fb7
update
shaogroup Nov 13, 2024
f4588db
update tarball
shaogroup Dec 4, 2024
672db31
Merge branch 'bioconda:master' into EquiRep
shaomingfu Dec 4, 2024
d1b41ff
update
shaogroup Dec 9, 2024
e83ccde
Merge branch 'EquiRep' of github.com:shaomingfu/bioconda-recipes into…
shaogroup Dec 9, 2024
d857303
Merge branch 'bioconda:master' into EquiRep
shaomingfu Dec 9, 2024
294233c
update
shaogroup Dec 10, 2024
f20bd99
Merge branch 'EquiRep' of github.com:shaomingfu/bioconda-recipes into…
shaogroup Dec 10, 2024
2419bec
Merge branch 'bioconda:master' into EquiRep
shaomingfu Dec 10, 2024
b3b777d
update
shaogroup Dec 10, 2024
dc6d6be
Merge branch 'EquiRep' of github.com:shaomingfu/bioconda-recipes into…
shaogroup Dec 10, 2024
6a1bc82
update
shaogroup Dec 10, 2024
1b0d9bc
update
shaogroup Dec 10, 2024
8183907
update
shaogroup Dec 10, 2024
51fa254
update
shaogroup Dec 10, 2024
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6 changes: 6 additions & 0 deletions recipes/equirep/build.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
#!/bin/bash

set -xe
Comment on lines +1 to +3
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⚠️ Potential issue

Add required Conda build environment setup.

The build script needs to incorporate Conda-specific environment variables and error handling:

Apply these changes:

 #!/bin/bash
 
-set -xe
+set -euo pipefail
+
+# Conda build environment setup
+export CFLAGS="${CFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CPATH="${PREFIX}/include"
+export LIBRARY_PATH="${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
#!/bin/bash
set -xe
#!/bin/bash
set -euo pipefail
# Conda build environment setup
export CFLAGS="${CFLAGS} -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CPATH="${PREFIX}/include"
export LIBRARY_PATH="${PREFIX}/lib"


./configure
make
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⚠️ Potential issue

Complete the build and installation process.

The current build commands are insufficient for proper Conda package creation:

  1. Configure needs to specify installation prefix
  2. Make should utilize parallel builds
  3. Missing installation step

Apply these changes:

-./configure
-make 
+./configure --prefix="${PREFIX}"
+make -j${CPU_COUNT}
+make install
📝 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
./configure
make
./configure --prefix="${PREFIX}"
make -j${CPU_COUNT}
make install

38 changes: 38 additions & 0 deletions recipes/equirep/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
{% set name = "equirep" %}
{% set version = "1.0.0" %}

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

source:
url: "https://github.com/Shao-Group/EquiRep/releases/download/v{{ version }}/EquiRep-{{ version }}.tar.gz"
sha256: "2cb4bad860eade6bf59a3153ed4aa25094b519740e421d628d1470b03115730b"

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

requirements:
build:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}

test:
commands:
- EquiRep
Comment on lines +23 to +25
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🛠️ Refactor suggestion

Enhance test coverage

The current test only verifies that the executable runs. Consider adding:

  • Version check command (EquiRep --version)
  • Help command test (EquiRep --help)
  • Test with example data if available
test:
  commands:
    - EquiRep
+   - EquiRep --version
+   - EquiRep --help

Committable suggestion skipped: line range outside the PR's diff.


about:
home: "https://github.com/Shao-Group/EquiRep"
license: BSD-3-Clause
license_file: LICENSE
summary: "EquiRep is tool to identify tandem repeats."

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
recipe-maintainers:
- shaomingfu
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