Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy) source my_galaxy_dir/.venv/bin/activate pip install scipy (dependency numpy also installed) ./run.sh But since the last update, i am having problems with this. Did something change? because it looks like it searches for an existing venv and then activates a new venv in my already active one?? Depending on what i try, when i execute my tool in galaxy, my messages range from ImportError: No module named scipy or ValueError: numpy.dtype has the wrong size, try recompiling <http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling> I tried running galaxy without a venv, re-creating my venv. renaming my venv installing numpy, then scipy, not using pip at all. removing numpy and reinstalling without cache. I also played around with pip, doing nothing after creating my venv, or first upgrading my pip, but then after i start galaxy i get this message: (.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2 And later on i get the message that i should upgrade my pip... I am confused...can someone tell me the correct way to start galalxy within or without my venv and how to correctly install my packages? Thanks! with regards, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker <linda.bakker@wur.nl> wrote:
Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy)
...
(.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2
And later on i get the message that i should upgrade my pip... I am confused...
From what I understand from following some of the relevant issues on GitHub, this is a side effect of Galaxy using its own modified version of pip as of Galaxy v16.01, although this isn't clear from the release notes:
https://docs.galaxyproject.org/en/master/releases/16.01_announce.html Nate (CC'd) can explain further I think. Regards, Peter
On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker <linda.bakker@wur.nl> wrote:
Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy)
...
(.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2
And later on i get the message that i should upgrade my pip... I am confused...
From what I understand from following some of the relevant issues on GitHub, this is a side effect of Galaxy using its own modified version of pip as of Galaxy v16.01, although this isn't clear from the release notes:
https://docs.galaxyproject.org/en/master/releases/16.01_announce.html
Nate (CC'd) can explain further I think.
I filed this specific issue on GitHub, https://github.com/galaxyproject/galaxy/issues/1845 An example of the pip upgrade warning: $ ./run.sh ... You are using pip version 8.0.2+gx2, however version 8.0.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. ... Peter
On Thu, Mar 3, 2016 at 3:24 AM, Linda Bakker <linda.bakker@wur.nl> wrote:
Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy)
source my_galaxy_dir/.venv/bin/activate pip install scipy (dependency numpy also installed) ./run.sh
But since the last update, i am having problems with this. Did something change? because it looks like it searches for an existing venv and then activates a new venv in my already active one??
Depending on what i try, when i execute my tool in galaxy, my messages range from
ImportError: No module named scipy or ValueError: numpy.dtype has the wrong size, try recompiling <http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling>
I tried running galaxy without a venv, re-creating my venv. renaming my venv installing numpy, then scipy, not using pip at all. removing numpy and reinstalling without cache. I also played around with pip, doing nothing after creating my venv, or first upgrading my pip, but then after i start galaxy i get this message:
Hi Linda, There are two options here: 1. You can install your dependencies inside Galaxy's virtualenv, (by default, .venv) 2. You can set up a separate virtualenv to be used only by jobs. Depending on how you run jobs, this one may also need to include Galaxy's dependencies (to run the metadata detection step). Details can be found here: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html And specifically, the instructions for setting up a separate virtualenv for job handlers: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#g... --nate
(.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2
And later on i get the message that i should upgrade my pip... I am confused...can someone tell me the correct way to start galalxy within or without my venv and how to correctly install my packages? Thanks!
with regards, Linda Bakker
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
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participants (3)
-
Linda Bakker -
Nate Coraor -
Peter Cock