Question: Galaxy 18.09 does not work with planemo (0.55.0)
gravatar for david.christiany
7 days ago by
david.christiany10 wrote:


I was using planemo with a git clone of galaxy 18.05 and everything was working fine.

I tried to upgrade to galaxy 18.09, first with :

$ git fetch origin && git checkout release_18.09 && git pull --ff-only origin release_18.09

and then with a new (and maybe cleaner) copy :

$ git clone -b release_18.09

When I run planemo on this new galaxy 18.09, all I got is a blank page on my web browser (firefox)

I got error from planemo :

.planemo/gx_venv/local/lib/python2.7/site-packages/sqlalchemy/sql/ SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert fromfloating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
  'storage.' %, dialect.driver))

I ran in the galaxy (18.09) folder to see if it can unlock the situation but it does not. I got another error :

Cannot uninstall 'certifi'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

I don't know if planemo can't handle the last version of galaxy yet or if it is an installation problem.

Does anyone had the same issue ?

planemo 18.09 galaxy • 27 views
ADD COMMENTlink modified 5 days ago by Bjoern Gruening5.1k • written 7 days ago by david.christiany10
gravatar for Bjoern Gruening
5 days ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:


you need to run make client-production inside your Galaxy directory, or use the latest planemo from github with pip install Nicola fix this bug today. What you are seeing is that with 18.09 the client (JS code) is not shipped with Galaxy anymore. So you need to build it.

Hope that helps, Bjoern

ADD COMMENTlink written 5 days ago by Bjoern Gruening5.1k
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