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Merge in updated master #11

Merged
merged 4,104 commits into from
Jul 1, 2024
Merged

Merge in updated master #11

merged 4,104 commits into from
Jul 1, 2024

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poshul
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@poshul poshul commented Jul 1, 2024

Describe your pull request here


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BiocondaBot and others added 30 commits June 18, 2024 09:45
* Update biobloomtools - rebuild after bulk failure

* Update CXXFLAGS
* rebuild selene-sdk

* bump build number
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
* Add r-circrnafull

* Add "extra" section

* Add run dependencies

* Add missing dependencies
* pgscatalog-utils initial commit

* drop LICENSE

* bump version

---------

Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: mencian <[email protected]>
* fraggenescan: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Use Clang 15 for osx

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
* phyml: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Use sse2neon.h to translate Intel SSE to ARM NEON for linux-aarch64

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
* remove build failures

* change meta to get a build
* Update DeepMicroClass recipe

* Update DeepMicroClass recipe
* add usearch

* fix lint

* fix dash in version

* fix typo
* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Add bracken as a dependency

* Update meta.yaml

* Update meta.yaml
* bump iqtree

* re-add circleci limit

* Make use of the JOBS variable

* try building with large machine

---------

Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
* alignlib_lite: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Try with Cython 0.x

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* The license_file is not included in the sources tarball

* Disable the test for Linux ARM64 to be able to test/debug locally

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
* Bump to v0.0.13

* Debugging

* Bugfix

* Update patch

* Update version

* Update URL and sha256
* Update pyclone-vi to 0.1.4

* add run_exports

* fix typo

---------

Co-authored-by: mencian <[email protected]>
BiocondaBot and others added 29 commits June 29, 2024 08:48
* add recipe argo

* fix sha

* Update recipes/argo/meta.yaml

Co-authored-by: Martin Grigorov <[email protected]>

---------

Co-authored-by: Martin Grigorov <[email protected]>
* Update tides-ml to 1.3.0

* Pin Python to <=3.11.7

Suggested by the following error:
ERROR: Package 'tides-ml' requires a different Python: 3.11.9 not in '<=3.11.7'

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
* clermontyping

* clermontyping

* adding .sh

* additional changes from review

* additional changes from review

* additional changes from review

* Copy clermonTyping.sh to $PREFIX/bin

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Co-authored-by: Martin Tzvetanov Grigorov <[email protected]>
* Update Auspice to 2.56.0

See the changelog on the [Auspice releases page](https://github.com/nextstrain/auspice/releases/) for more details

* Reset the build number

---------

Co-authored-by: Martin Grigorov <[email protected]>
* Update deeplc to 2.2.37

* Update deeplc to 2.2.38
* Updated dependencies and restored tests

* Added FluMutDB, required by FluMut

* Update recipes/flumutdb/meta.yaml

Co-authored-by: Martin Grigorov <[email protected]>

* Fixed sha256

---------

Co-authored-by: Martin Grigorov <[email protected]>
* Update meta.yaml for piscem v0.9.0

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Create build_rs.patch

* Update meta.yaml
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
* extract_fullseq: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Build bmtagger the same way as in bmtool and bmfilter

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@poshul poshul merged commit 834157c into nightly Jul 1, 2024
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