Updating to current Galaxy

usegalaxy.org support
1

I’m running an old Galaxy release (from 2017), and would like to upgrade to the current stable release. I’ve downloaded from GitHub. However, I’m wondering if there is a standard update procedure.

  1. Can I simply unzip into my galaxy base directory (/home/galaxy/galaxy)?
  2. is there an install or update script I should use?
  3. How can I find the release ID of a particular distribution?
  4. How often should Galaxy be updated?

Thanks,

Brian

2

I normally update by using the command given in the installation page:

$ git fetch origin && git checkout release_20.01 && git pull --ff-only origin release_20.01

edit: oh to use the git command, you might need to install it here first: https://git-scm.com/

3

so I run:
git fetch origin && git checkout release_20.01 && git pull --ff-only origin release_20.01

with the following result:

error: Your local changes to the following files would be overwritten by checkout:
config/plugins/interactive_environments/jupyter/config/jupyter.xml
config/plugins/interactive_environments/jupyter/templates/jupyter.mako
config/plugins/interactive_environments/rstudio/static/js/rstudio.js
config/plugins/interactive_environments/rstudio/templates/rstudio.mako
config/plugins/tours/core.galaxy_ui.yaml
config/plugins/tours/core.history.yaml
config/plugins/tours/core.scratchbook.yaml
config/plugins/visualizations/charts/config/charts.xml
config/plugins/visualizations/charts/package.json
config/plugins/visualizations/charts/templates/charts.mako
config/plugins/visualizations/csg/templates/csg.mako
config/plugins/visualizations/graphviz/config/graphviz.xml
config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
config/plugins/visualizations/graphviz/templates/graphviz.mako
config/plugins/visualizations/scatterplot/templates/scatterplot.mako
config/tool_conf.xml.main
Please, commit your changes or stash them before you can switch branches.
Aborting

I then run “git commit” and a lot of files get modified, and it ends with untracked files:

Untracked files:
ca-cert.pem
client-cert.pem
client-key.pem
config/plugins/visualizations/charts/Gruntfile.js
config/plugins/visualizations/charts/static/app.css
config/plugins/visualizations/charts/static/app.js
config/plugins/visualizations/charts/static/charts/
config/plugins/visualizations/charts/static/library/
config/plugins/visualizations/charts/static/models/
config/plugins/visualizations/charts/static/plugins/
config/plugins/visualizations/charts/static/views/
config/plugins/visualizations/graphview/
paster.log.2017-05-26
static/cats/
static/images/avispa.png
static/images/biociph_biglogo.png
static/images/penn_fulllogo.png
static/majiq-cat
static/majiq_spel/
static/rbp-pokedex/
static/rnagroup/
static/voila/
tools/majiq_spel/
tools/prime/
xxx

no changes added to commit

then I run git push origin with the following result:

[root@paros-web galaxy]# git push origin
Username for ‘https://github.com’: bampolsk
Password for ‘https://bampolsk@github.com’:
remote: Permission to galaxyproject/galaxy.git denied to bampolsk.
fatal: unable to access ‘https://github.com/galaxyproject/galaxy.git/’: The requested URL returned error: 403

The password is accepted by git, but not by galaxy project.

I welcome any ideas…