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Add seq2squiggle recipe #53053

Merged
merged 11 commits into from
Jan 7, 2025
Merged

Add seq2squiggle recipe #53053

merged 11 commits into from
Jan 7, 2025

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denisbeslic
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This PR adds seq2squiggle.


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.

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@BiocondaBot please add label Add the please review & merge label.
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@martin-g martin-g enabled auto-merge (squash) January 6, 2025 16:09
auto-merge was automatically disabled January 7, 2025 09:10

Head branch was pushed to by a user without write access

@denisbeslic
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Hi @bioconda/core @martin-g

Is there a way to include a dependency from a channel outside of conda-forge and bioconda? Specifically, I'm trying to add POD5 (v0.3.23) as a dependency, but it's currently only available on the nanoporetech channel. Without this, my package cannot be installed due to the missing dependency.

Would appreciate any guidance on how to handle this scenario or suggestions for potential workarounds.

Thanks in advance!

@BiocondaBot
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Reposting for @denisbeslic to enable pings (courtesy of the BiocondaBot):

Hi @bioconda/core @martin-g

Is there a way to include a dependency from a channel outside of conda-forge and bioconda? Specifically, I'm trying to add POD5 (v0.3.23) as a dependency, but it's currently only available on the nanoporetech channel. Without this, my package cannot be installed due to the missing dependency.

Would appreciate any guidance on how to handle this scenario or suggestions for potential workarounds.

Thanks in advance!

@aliciaaevans
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Reposting for @denisbeslic to enable pings (courtesy of the BiocondaBot):

Hi @bioconda/core @martin-g

Is there a way to include a dependency from a channel outside of conda-forge and bioconda? Specifically, I'm trying to add POD5 (v0.3.23) as a dependency, but it's currently only available on the nanoporetech channel. Without this, my package cannot be installed due to the missing dependency.

Would appreciate any guidance on how to handle this scenario or suggestions for potential workarounds.

Thanks in advance!

Only conda-forge and bioconda channels are supported. If you can add to bioconda (in another PR), that would work, assuming that pod5 doesn't have dependencies in unsupported channels (and the license allows it).

@denisbeslic
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Thanks! I was able to find an older version of pod5 on bioconda!

@denisbeslic
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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jan 7, 2025
@martin-g martin-g merged commit 90f538b into bioconda:master Jan 7, 2025
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4 participants