Add Reseek

[apcamargo]

This PR adds reseek.

---

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If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 60fbea9 and f4ba7a7.

📒 Files selected for processing (2)

• recipes/reseek/build.sh (1 hunks)
• recipes/reseek/meta.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/reseek/build.sh

🧰 Additional context used

🪛 yamllint

recipes/reseek/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)

recipes/reseek/meta.yaml (3)

19-24: ⚠️ Potential issue

Add OpenMP runtime dependencies.

The package requires OpenMP support, but the runtime dependencies are missing. This was previously flagged in earlier reviews and needs to be addressed.

Apply this diff:

 requirements:
   build:
     - {{ compiler("cxx") }}
     - {{ compiler("c") }}
     - make
+    - llvm-openmp  # [osx]
+  run:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]

---

32-32: ⚠️ Potential issue

Add maintainer and platform information.

The recipe is missing the extra section with maintainer information and additional platform support, which is required for Bioconda packages.

Add after the about section:

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

---

20-22: ⚠️ Potential issue

Configure GCC compiler for builds.

As mentioned in previous reviews, reseek requires GCC for compilation. The compiler configuration needs to be explicitly set.

Create a new file conda_build_config.yaml with:

c_compiler_version:         # [osx]
  - 12                     # [osx]
cxx_compiler_version:      # [osx]
  - 12                     # [osx]
c_compiler:                # [osx]
  - gcc                    # [osx]
cxx_compiler:              # [osx]
  - gxx                    # [osx]

[apcamargo]

@BiocondaBot please add label

[bgruening]

where is this coming from? Maybe add a comment here, that this file needs to be kept in sync?

[apcamargo]

This is the author's own script. In his repository he downloads it at build time, but I decided to have it within the recipe to have more control over it. I'll add a comment.

[apcamargo]

Thanks, @bgruening
@bioconda/osx This build is failing for macOS with the error below:

 07:53:49 BIOCONDA INFO (ERR) parasail.cpp:56:11: error: reference to unresolved using declaration
07:53:49 BIOCONDA INFO (ERR)    56 |     ptr = aligned_alloc(alignment, size);
07:53:49 BIOCONDA INFO (ERR)       |           ^
07:53:49 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/reseek_1730620228398/_build_env/bin/../include/c++/v1/cstdlib:150:1: note: using declaration annotated with 'using_if_exists' here
07:53:49 BIOCONDA INFO (ERR)   150 | using ::aligned_alloc _LIBCPP_USING_IF_EXISTS;
07:53:49 BIOCONDA INFO (ERR)       | ^
07:53:49 BIOCONDA INFO (ERR) parasail.cpp:56:11: error: excess elements in scalar initializer
07:53:49 BIOCONDA INFO (ERR)    56 |     ptr = aligned_alloc(alignment, size);
07:53:49 BIOCONDA INFO (ERR)       |           ^                      ~~~~~~
07:53:49 BIOCONDA INFO (ERR) 2 errors generated.
07:53:49 BIOCONDA INFO (ERR) make: *** [Makefile:270: o/parasail.o] Error 1

I tried several approaches to use a newer version of Clang, but they failed. The author of the package compiles it for macOS using GCC, but this is not an option for us (as far as I know). Is there a solution that I'm missing?