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broadinstitute / viral-ngs-deploy

Deployment files related to https://github.com/broadinstitute/viral-ngs
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Add support for git based viral-ngs installs #13

Closed yesimon closed 7 years ago

yesimon commented 7 years ago

Allow relative install path variable $INSTALL_PATH

Use setup-git to install git based viral-ngs Use upgrade-deps to upgrade conda deps based on changes in git viral-ngs

Symlink instead of copying Snakefile Stop creating run-pipe_LSF.sh symlink Add run-pipe.sh symlink to run-pipe_UGER.sh

yesimon commented 7 years ago

@tomkinsc Can you take a look at this?

tomkinsc commented 7 years ago

Nice. It looks like this adds to the CLI without breaking past usage, right?

Can you add a test for the new setup-git install? Right now we only test basic setup, but it would be nice to have coverage of the other install types.

yesimon commented 7 years ago

I also had to add quiet flags to conda install and every because Travis was failing going over 4mb log file limit On Fri, Jun 9, 2017 at 11:49 AM Chris Tomkins-Tinch < notifications@github.com> wrote:

Nice. It looks like this adds to the CLI without breaking past usage, right?

Can you add a test https://github.com/broadinstitute/viral-ngs-deploy/blob/master/travis/tests-unit.sh#L10 for the new setup-git install? Right now we only test basic setup, but it would be nice to have coverage of the other install types.

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dpark01 commented 7 years ago

Huh, is the 4MB log limit new on Travis, or has it always been like that?

yesimon commented 7 years ago

It looks like it has always been like that, at least since 2013. I wish more tools supported wget option of selecting printing dots for progress (to prevent travis_wait output timeouts) instead of full progress bar ascii art.

yesimon commented 7 years ago

@tomkinsc Added a basic setup-git test.

tomkinsc commented 7 years ago

Is this ready to merge?