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Question: Bioblend: should I update, how do I update?
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gravatar for lachlan.simpson
9 months ago by
lachlan.simpson • 20
lachlan.simpson • 20 wrote:

I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9 installed, and that one of the changes in Bioblend 0.10 was "support for galaxy 17.09".

Actually, now that I've looked into how it was installed, I see that the virtualenv that's created when Galaxy is installed only has bioblend 0.7.0.

Can someone hip me to the easiest way to update bioblend?

Is it just to activate the venv and pip install -U bioblend?
upgrades bioblend • 310 views
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modified 9 months ago • written 9 months ago by lachlan.simpson • 20
1

Martin,

Thanks, that was the information I was after.

ADD REPLY • link written 9 months ago by lachlan.simpson • 20

Thanks Jen. I should have been clearer in my question.

  1. Is the proper place to update within galaxy's venv? (we have set that to be /path/to/galaxy/codebase/.venv)
  2. Is it safe to do so - ie should I expect things to "just work" after the update?
ADD REPLY • link written 9 months ago by lachlan.simpson • 20
1
gravatar for Martin Čech
9 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The upcoming 18.01 release of Galaxy has BioBlend 0.7.0 as a dependency however you do not need to have or use local Galaxy installation in order to use BioBlend.

You should not update Galaxy's requirements manually or install other things in the Galaxy's .venv manually, Galaxy will take care of its own dependency updates and it is better to keep its .venv clean from other software.

If you are using BioBlend directly please install it (or update to the latest) into an independent virtual environment and use it from there. BioBlend in general should work with any older Galaxy, the 'support for 17.09' means that it covers some/all features new in that version of Galaxy.
ADD COMMENT • link modified 9 months ago • written 9 months ago by Martin Čech ♦♦ 4.9k
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