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DataBiosphere / toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
http://toil.ucsc-cgl.org/.
Apache License 2.0
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Setup script for Cactus missing `--recursive` option #4383

Open adamnovak opened 1 year ago

adamnovak commented 1 year ago

Cactus now ships a sonLib submodule, but the scritp we ship for the Cactus tutorial for Toil, in https://github.com/DataBiosphere/toil/blob/0afd209252406783aa1841387fafebf3110182f3/src/toil/test/cactus/pestis.tar.gz, doesn't use it. So Cactus fails to install.

We need to add --recursive to the script in the tar file and reupload it.

┆Issue is synchronized with this Jira Story ┆Issue Number: TOIL-1291

adamnovak commented 1 year ago

We could also drop the sudo calls since the Toil appliance ships no sudo binary.

adamnovak commented 1 year ago

And we could add -e to make the script fail fast.