Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add SuSiEx with a patch to make its Makefile portable to Apple Clang. #44131

Open
wants to merge 13 commits into
base: master
Choose a base branch
from

Conversation

pettyalex
Copy link
Contributor

This adds SuSiEx, https://github.com/getian107/SuSiEx, a fine-mapping tool.

I could use a hand understanding if this recipe needs openMP libraries in the host and run section, it seems like other recipes don't have that but the binaries that this produces are dynamically linked against libomp.dylib on Mac and libgomp on Linux.


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
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.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

@bgruening
Copy link
Member

Hi @pettyalex! Please have a look at the KB from our conda-forge friends regarding your OpenMP question: https://conda-forge.org/docs/maintainer/knowledge_base.html#openmp

recipes/susiex/meta.yaml Outdated Show resolved Hide resolved
recipes/susiex/build.sh Outdated Show resolved Hide resolved
@pettyalex
Copy link
Contributor Author

Whoops, I lost track of this one.

I'd love to get it in.

@pettyalex
Copy link
Contributor Author

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jan 26, 2024
@pettyalex
Copy link
Contributor Author

@BiocondaBot please update

mkdir -p $PREFIX/bin

pushd src
make
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
make
make -j ${CPU_COUNT}

+ CXXFLAGS+=-fopenmp
+ LDLIBS+=-fopenmp
+else
+ CXXFLAGS=-fopenmp
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why this overwrites CXXFLAGS ? The earlier set -O3 -Wall -Wextra will be lost

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
please review & merge set to ask for merge
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

5 participants