Question: Upgrade Galaxy to new release
1
gravatar for md2587
6 months ago by
md258710
md258710 wrote:

Hi to everyone,

Is there any "step by step" procedure how to upgrade Galaxy to new release? My current Galaxy release is 16.04. I would like to upgrade it to new one (17.01) without to lose my changing and installed tools.

Thanks in advance.

Maki

upgrade new release galaxy • 204 views
ADD COMMENTlink modified 3 months ago by marija.djurdjevic30 • written 6 months ago by md258710
2
gravatar for Hotz, Hans-Rudolf
6 months ago by
Switzerland
Hotz, Hans-Rudolf1.6k wrote:

Hi Maki

There is no "step by step" guide, since there is just one (or two) step:

git checkout release_17.01 && git pull --ff-only origin release_17.01

and restarting the server.

(see also: https://galaxyproject.org/admin/get-galaxy/#updating-exiting )

You don't need to worry about your changes (e.g. the changes you have introduced to the file: 'galaxy.ini') and installed tools. These will not be reversed or deleted. Though, if you have made changes to the galaxy code, git will warn you about any potential conflicts.

If you are not familiar with all the possibilities of git, I recommend you first make a copy of your galaxy installation, so you can always go back and check, the old files. Also, make sure you have a copy of your PostgreSQL database. Well, you should have those as part of your back-ups anyway.

Of course, the update process depends on the settings of your installation. For example: are you the only user, or do you provide the Galaxy server for others. In the latter case, it is advisable to announce the upgrade and hence the galaxy downtime in advance. As it is not advisable to update the server while there are jobs running, unless you have several nodes and you do a rolling upgrade; but again, this all depends on your local set-up.

Hope this helps, Hans-Rudolf

ADD COMMENTlink written 6 months ago by Hotz, Hans-Rudolf1.6k

Hi Hans-Rudolf,

Thank you very much for your answer. I thought it's much more complicated procedure.

Thanks, Maki

ADD REPLYlink written 6 months ago by md258710
1
gravatar for marija.djurdjevic
3 months ago by
marija.djurdjevic30 wrote:

Hi all,

I have similar problem with galaxy upgrade. I tried to do git checkout release_17.05 && git pull --ff-only origin release_17.05. but since I have changes in some files I got error message:

Already on 'release_17.05'
From https://github.com/galaxyproject/galaxy
 * branch            release_17.05 -> FETCH_HEAD
Updating 5a97b8f..9dca211
error: Your local changes to the following files would be overwritten by merge:
        .ci/first_startup.sh
        .ci/flake8_blacklist.txt
        .ci/py3_sources.txt  
        ........

If I do git status:

On branch release_17.05 Changes not staged for commit:   (use "git add/rm <file>..." to update what will be committed)   (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   .ci/check_controller.sh
        modified:   .ci/check_mako.sh
        modified:   .ci/first_startup.sh
        modified:   .ci/flake8_blacklist.txt
        modified:   .ci/py3_sources.txt
        modified:   .coveragerc
        modified:   .gitignore
        modified:   .travis.yml
        ....
        Untracked files:
        (use "git add <file>..." to include in what will be committed)

        FETCH_HEAD
        config/plugins/interactive_environments/jupyter/config/allowed_images.yml
        config/plugins/interactive_environments/rstudio/config/allowed_images.yml
        current_files.summary
        file_list.txt
        static/CDAworkflow.html
        static/CDAworkflow.xml
        static/Capture.PNG
        static/Einladung_Galaxy_03_04_2017.pdf
        static/FTP.pdf
        static/Homo_sapiens.GRCh38.86.gtf
        ......
        no changes added to commit (use "git add" and/or "git commit -a")

My question is which step should I perform before upgrade? Should I do git add -A && git commit first and than git pull or git stash, git pull and git stash pop??? I know only git basics and therefore I am not sure which step should I perform first?

Thanks, Marija

ADD COMMENTlink written 3 months ago by marija.djurdjevic30
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