I’m trying to install Galaxy and in the first time I run sh run.sh I have this message:
“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.”
Hi,
I installed Galaxy recently on top of Debian. No such an error. What is you Linux OS?
Did you try the to install certifi on you own before starting? May be this could help
Please never run run.sh as sudo, among other things this is a big security issue.
There is clearly something wrong with your setup.
Basic instructions are at https://galaxyproject.org/admin/get-galaxy/, if this doesn’t work feel free to post the complete error message here.
Hi Marius,
Having recently installed a server from scratch, may I suggest a few improvements in the documentation you pointed.
a) https://galaxyproject.org/admin/get-galaxy/#start-it-up should state about a default user to install and launch the run.sh script. Maybe this information is in another part of the doc, but as it is the entry point I think this could be useful for newbie as me.
b) https://galaxyproject.org/admin/get-galaxy/#become-an-admin should state how to become a registered user. It will sound very obvious to you and any other Galaxy users, but being more a sys admin than a end user, I was looking for a command to create users before using Galaxy (as in Linux, mysql, postgresql… installations).
My two cents, indirectly related to the question of the OP.
I follow exact these steps. Actually, I’ve made a full reinstall of my machine, from zero.
This time, after run git… galaxy was created in root, not under my user in home. Is that correct? If not, what should I do?
Again, it only runs with sudo. Without I receive this:
OSError: [Errno 13] Permission denied: ‘/galaxy/static/plugins/interactive_environments/neo/static’
From the path in your error, it doesn’t look as if you are cloning the Galaxy repository into your user home directory.
Important: Avoid moving a Galaxy install after running sh run.sh the first time. Start over instead by cloning Galaxy into the directory where you want it to be, or other problems will come up.
I’m not sure exactly what information is missing there, but you can click at the top of the site on “edit” and propose changes, this would be much appreciated.