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bigdatagenomics / mango

A scalable genome browser. Apache 2 licensed.
Apache License 2.0
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[MANGO-546] Update ADAM dependency version to 0.30.0 #547

Closed heuermh closed 4 years ago

heuermh commented 4 years ago

Fixes #546

Work in progress, will require bumping ADAM python library version when it has been released.

coveralls commented 4 years ago

Coverage Status

Coverage increased (+0.09%) to 80.27% when pulling e759a44ea15f0f6ec325d6c08f717e8803fdcf79 on heuermh:adam-0.30.0 into 126d6b2fbb6773804f1d53a298b69a2cf355e35a on bigdatagenomics:master.

AmplabJenkins commented 4 years ago

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/mango-prb/917/ Test FAILed.

akmorrow13 commented 4 years ago

Looks like we need to modify the python code with the new API:

py4j.protocol.Py4JError: org.bdgenomics.mango.converters.GA4GHutil.alignmentRecordDatasetToJSON does not exist in the JVM

heuermh commented 4 years ago

Looks like we need to modify the python code with the new API...

Yep, I have not made the 0.30.0 python release to PyPI yet

akmorrow13 commented 4 years ago

@heuermh do you want me to make the release?

heuermh commented 4 years ago

Yeah, I feel like I should fix this issue at some point (by splitting Python ADAM to a separate repo?) but haven't got to it yet.

The release branch is https://github.com/bigdatagenomics/adam/tree/maint_spark2_2.11-0.30.0

Thanks!

akmorrow13 commented 4 years ago

Closing in favor of https://github.com/bigdatagenomics/mango/pull/548

heuermh commented 4 years ago

Thank you, @akmorrow13