# Galaxy 18.09 upgrade client build problem **URL:** \ **Category:** Uncategorized\ **Tags:** devops-administration\ **Created:** [January 9, 2019, 10:30am UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364 "2019-01-09T10:30:24Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![gerhard](https://avatars.discourse-cdn.com/v4/letter/g/b5e925/32.png) [@gerhard](https://help.galaxyproject.org/u/gerhard)\ **Post date:** [January 9, 2019, 10:30am UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/1 "2019-01-09T10:30:24Z")
After git pull and run.sh the client build part errors on npm trying to install yarn … So yarn is never installed into the .venv/lib/node\_modules directory. ENOENT: no such file or directory, chmod ‘/home/galaxy/.venv/lib/node\_modules/yarn/bin/yarn.js’ Is there a config missing here for npm?? Thanks, Gerhard ---
**Author:** ![nsoranzo](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/nsoranzo/32/77_2.png) [@nsoranzo](https://help.galaxyproject.org/u/nsoranzo)\ **Post date:** [January 9, 2019, 10:39am UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/2 "2019-01-09T10:39:04Z")
Hi Gerhard, I’m not an expert of these issues, but I’d remove the Galaxy virtualenv directory `.venv`, then start Galaxy and if the error is still present, copy&paste the relevant output to a gist on [https://gist.github.com/](https://gist.github.com/) and link that here. ---
**Author:** ![gerhard](https://avatars.discourse-cdn.com/v4/letter/g/b5e925/32.png) [@gerhard](https://help.galaxyproject.org/u/gerhard)\ **Post date:** [January 9, 2019, 12:26pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/3 "2019-01-09T12:26:39Z")
[[https://gist.github.com/gerhard1234/443938447dca0e66d8c76d60697bd5c7](https://gist.github.com/gerhard1234/443938447dca0e66d8c76d60697bd5c7)] Conda will not uninstall certifi so the process halts. I am looking around for a way to do this manually - perhaps you can recommend a way. The process you suggested seems to run fine until this point. Thanks for your suggestion! ---
**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\ **Post date:** [January 9, 2019, 3:59pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/4 "2019-01-09T15:59:43Z")
Galaxy is using pip to install its own dependencies, not conda. Moreover all the dependencies should be installed in the virtual environment so if you delete the `.venv` folder all should be gone. Are you using a non-default virtual environment? ---
**Author:** ![gerhard](https://avatars.discourse-cdn.com/v4/letter/g/b5e925/32.png) [@gerhard](https://help.galaxyproject.org/u/gerhard)\ **Post date:** [January 9, 2019, 4:32pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/5 "2019-01-09T16:32:07Z")
This galaxy installation uses supervisord to start. So there is a .venv stanza there and has been from the start - 18.05 was a clean install. I do not quite understand … there seems to be an either/or architecture with conda being incompatible with venv. Also the devs seem to be moving more towards conda. Then searches indicate problems with individual packages like devutils when they do not uninstall cleanly. Also in the .venv world yarn does not play nicely with npm. It looks like my previous galaxy installation is not upgrading in either the .venv paradigm or the conda paradigm because of some package that cant make way to be reinstalled by the upgrade. So to answer your question the virtual environment is the one that was created from the original clean install of 18.05. Would it be OK to remove the package that is causing the installation to fail by file deletion? I dont want to just try this without some reflection. ---
**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\ **Post date:** [January 9, 2019, 5:06pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/6 "2019-01-09T17:06:07Z")
Galaxy uses pip to install its own dependencies, it manages its own conda and it uses own conda to install dependencies for any Galaxy Tools you choose (but that only happens at tool installation time). You can override most of these settings and set up your own environments but that is generally not recommended unless you have a good reason. If you remove the whole `.venv` folder and execute `run.sh` it should recreate the folder and install all Galaxy dependencies using pip. In case you want to see what happens most of the dep-related startup stuff happens here: [https://github.com/galaxyproject/galaxy/blob/dev/scripts/common\_startup.sh](https://github.com/galaxyproject/galaxy/blob/dev/scripts/common_startup.sh) note that if you are using systemd configuration like the one here: [https://docs.galaxyproject.org/en/master/admin/scaling.html#supervisord](https://docs.galaxyproject.org/en/master/admin/scaling.html#supervisord) you are not running these startup scripts and have to maintain your dependencies yourself. ---
**Author:** ![gerhard](https://avatars.discourse-cdn.com/v4/letter/g/b5e925/32.png) [@gerhard](https://help.galaxyproject.org/u/gerhard)\ **Post date:** [January 9, 2019, 7:17pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/7 "2019-01-09T19:17:13Z")
Removing .venv results in … [galaxy@storage1 ~]$ sh run.sh Found conda at: /home/.galaxy/database/dependencies/\_conda/bin/conda Found Conda, virtualenv will not be used. To use a virtualenv instead, create one with a non-Conda Python 2.7 at .venv Activating Conda environment: \_galaxy\_18.09 And it then tries to establish a non-venv/conda installation which fails because of the certifi clash. The installation readme says to run the run.sh after the git pull to finalise the upgrade - so I dont see how starting the Galaxy installation from supervisord is involved in the maintenance of deps. The .venv version of the installation will not install yarn due to a similar issue with packages not agreeing on how they should be uninstalled. Seems to only happen on systems where the package scertifi and already exist and requires removal and reinstallation, or yarn must be installed by npm into a pre-existing .venv … Anyhow thanks for thinking about all this - hope we are not boring you 😉 ---
**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\ **Post date:** [January 9, 2019, 7:41pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/8 "2019-01-09T19:41:53Z")
The issue probably is that you are using the conda-built Python, which is non-standard to some extent. I think the best approach would be to use a different python 2.7.x to create the .venv but you can read details about this situation here: [https://docs.galaxyproject.org/en/master/admin/framework\_dependencies.html#conda](https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#conda) ---
**Author:** ![gerhard](https://avatars.discourse-cdn.com/v4/letter/g/b5e925/32.png) [@gerhard](https://help.galaxyproject.org/u/gerhard)\ **Post date:** [January 10, 2019, 8:13pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/9 "2019-01-10T20:13:11Z")
So we now have a working Galaxy 18.09. The workaround was to prevent the installation script from throwing its exception: by doing a clean install of 18.09 in a different location and dropping the yarn libs into the troubled installation’s .venv/lib/node\_modules The 18.09 upgrade proceeded smoothly from there on. Thanks all for your thoughts and comments. Gerhard ---
**Author:** ![KJW](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kjw/32/326_2.png) [@KJW](https://help.galaxyproject.org/u/KJW)\ **Post date:** [March 20, 2019, 9:33pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/10 "2019-03-20T21:33:26Z")
It sounds like you have figured it out. I’m a newbie and having trouble at the sh run.sh step which gives me the error kws-imac:~ kw$ sh run.sh \> sh: run.sh: No such file or directory. I’m trying to figure out how you changed the install but its not clear to me since the installation was installed automatically when installing by $ git clone -b release\_19.01 [https://github.com/galaxyproject/galaxy.git](https://github.com/galaxyproject/galaxy.git) . If you can point me in the right direction I would really appreciate it. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 20, 2019, 9:51pm UTC](https://help.galaxyproject.org/t/galaxy-18-09-upgrade-client-build-problem/364/11 "2019-03-20T21:51:07Z")
Please try the help in this reply to your original question: [Error when trying to run Galaxy on MacOs](https://help.galaxyproject.org/t/error-when-trying-to-run-galaxy-on-macos/353/10?u=jennaj) It looks like you are not running the `sh run.sh` command from inside of the galaxy directory, plus might need the python virtualenv created first.