Scripts overhaul - Githubissues

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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Scripts overhaul #579

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

Paraphrasing the commit msg from https://github.com/hammerlab/guacamole/commit/52666e1774b580fb0c8fd94f2dfa59faed2f3b06:

make scripts/guacamole wrap spark-submit
make scripts/guacamole-shell, a wrapper for spark-shell
both delegate to jar-finder and spark-env-setup scripts, .jars-rc and .spark-rc.
orient spark configuration around "spark properties" files, pointed to by $GUAC_SPARK_CONFS env var, which can take multiple paths to properties files which will be concatenated

This change is

coveralls commented 7 years ago

Coverage increased (+0.01%) to 78.583% when pulling 4bd4004a44464072365fc4326ecb78446ce9af64 on ryan-williams:scripts into a6771eeafed073e6858979e01b214b214d965a1f on hammerlab:master.

arahuja commented 7 years ago

LGTM

coveralls commented 7 years ago

Coverage increased (+0.2%) to 78.816% when pulling 6658f25ceb5c0a8c64550d95a352561b371bccf6 on ryan-williams:scripts into a3018fd15952ccd65307bcd83ad92600072e109d on hammerlab:master.

ryan-williams commented 7 years ago

Added in conf/kryo file and made it always get mixed in to the spark properties file.

coveralls commented 7 years ago

Coverage increased (+0.2%) to 78.816% when pulling 6aebaed5e20d81d236d00823ec7152cc2e9ed825 on ryan-williams:scripts into a3018fd15952ccd65307bcd83ad92600072e109d on hammerlab:master.

coveralls commented 7 years ago

Coverage decreased (-0.1%) to 78.826% when pulling 55b27e3df952c148742b0f2bc0fdc0598c6ce72c on ryan-williams:scripts into 2f860060b62e0a55a9e45a90a254912936607ed5 on hammerlab:master.