Question: How can I get the version of a running instance of galaxy ?
3
gravatar for plindenbaum
3.6 years ago by
plindenbaum90
France
plindenbaum90 wrote:

all is in the title: how can I get the version of a running instance of galaxy ?

 

version • 1.3k views
ADD COMMENTlink modified 21 months ago by Guy Reeves1.0k • written 3.6 years ago by plindenbaum90
3
gravatar for Martin Čech
3.6 years ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

I answered this here: https://www.biostars.org/p/98023/

Disclosing of Galaxy version/build/changeset entirely depends on the owner of the instance.

The official Main usegalaxy.org and Test instances contain changeset in the footer of the landing page (which usually is part of welcome.html in the galaxy /static folder). 

Your best choice, if you cannot find it on the page, is to write an email to the admin.

EDIT: we have added an API to show the instance's version, try https://usegalaxy.org/api/version

ADD COMMENTlink modified 20 months ago • written 3.6 years ago by Martin Čech ♦♦ 4.2k
1
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson23k wrote:

As a user:

On http://usegalaxy.org go to the home page and scroll all the way down. The galaxy-central changeset the server is running at is noted.

For other Galaxies, how and if to share this information is up to the administrator of the instance. I am not sure if there is an API method or not, but let's see if we get more comments/answers.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson23k
4
gravatar for Bjoern Gruening
3.6 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

The following answer is for developers with an own Galaxy instance.

Galaxy does not have any explicit version number. The only way you can identify a Galaxy version is by it's unique commit tag. You can get this, plus the date of the commit and a short description with:

hg tip

in your Galaxy root directory.

Cheers,

Bjoern

ADD COMMENTlink written 3.6 years ago by Bjoern Gruening4.8k

I am trying to get the version number. When I try

-bash-4.1$ cd galaxy -bash-4.1$ hg tip abort: There is no Mercurial repository here (.hg not found)!

Apparently we installed without using Mercurial but git.
any ideas how to get a version number. Thanks Guy

ADD REPLYlink written 21 months ago by Guy Reeves1.0k
1

This was back in old mercurial days. Today you need to do git log and have a look at the latest revision.

ADD REPLYlink written 21 months ago by Bjoern Gruening4.8k
0
gravatar for Guy Reeves
21 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

I did the 'git log' comand and got pages of messages and no recognisable version number. I guess this was because I was not running the latest version.
so I did 'git pull' and waited then I stopped and restarted the instance.

-bash-4.1$ git pull remote: Counting objects: 15635, done. remote: Compressing objects: 100% (29/29), done. remote: Total 15635 (delta 7831), reused 7827 (delta 7825), pack-reused 7781 Receiving objects: 100% (15635/15635), 30.21 MiB | 1.26 MiB/s, done. Resolving deltas: 100% (12577/12577), completed with 1639 local objects. From https://github.com/galaxyproject/galaxy ffb3de9..36d85e8 dev -> origin/dev da2cc58..5677c2e master -> origin/master 360a6ad..cee85ba release_14.10 -> origin/release_14.10 46e67b5..61cd045 release_15.01 -> origin/release_15.01 b23acda..0122040 release_15.03 -> origin/release_15.03 0bf60a5..c8e9845 release_15.05 -> origin/release_15.05 ed992b3..30608c1 release_15.07 -> origin/release_15.07 30b13bb..d225aeb release_15.10 -> origin/release_15.10 * [new branch] release_16.01 -> origin/release_16.01 * [new branch] revert-1537-handlebars.removal -> origin/revert-1537-handlebars.removal * [new tag] v14.10.3 -> v14.10.3 * [new tag] v15.01.4 -> v15.01.4 * [new tag] v15.03.4 -> v15.03.4 * [new tag] v15.05.2 -> v15.05.2 * [new tag] v15.07.1 -> v15.07.1 * [new tag] v16.01 -> v16.01 From https://github.com/galaxyproject/galaxy * [new tag] v15.10.1 -> v15.10.1 * [new tag] v15.10.2 -> v15.10.2 Updating ffb3de9..36d85e8 error: Your local changes to 'config/tool_conf.xml.main' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge.

have I done something wrong?

ADD COMMENTlink modified 21 months ago • written 21 months ago by Guy Reeves1.0k

You have local changes in config/tool_conf.xml.main ... never change on of these files. Only the tool_conf.xml. Do you remember what you changed? If not git diff will tell you. If you don't care about the changes remove this file and do a git pull again.

ADD REPLYlink written 21 months ago by Bjoern Gruening4.8k

I did change that file accidentally when manually installing a tool not present in the tools shed. I did actually mean to change config/tool_conf.xml.sample.
I deleted both after making a copy then ran

git pull

stopped and restarted my instance
-bash-4.1$ git pull Already up-to-date.

Which is great

but when I try to access galaxy through the browser I get this error

'Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team.'

Where is the error logged? Thanks Guy

I have submitted this as a new post 'Internal Server Error Galaxy was unable to successfully complete your request' where is the log?

ADD REPLYlink modified 21 months ago • written 21 months ago by Guy Reeves1.0k

You did you start Galaxy. With ./run.sh you should get all log into your terminal.

ADD REPLYlink written 21 months ago by Bjoern Gruening4.8k
0
gravatar for Guy Reeves
21 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

I am still a bit confused about how to get the version number from the git log command on

git log

gives a long list of messages

but as I understand it

git log origin/master

gives the version number

-*bash-4.1$ git log origin/master

commit 5677c2ee4fce70c9898ea5e6cae125b6147ae36a

Author: Nate Coraor nate@bx.psu.edu

Date: Wed Feb 24 15:29:14 2016 -0500

Update version to 16.01*

https://wiki.galaxyproject.org/Admin/GetGalaxy

ADD COMMENTlink modified 21 months ago • written 21 months ago by Guy Reeves1.0k
1

Try git describe

ADD REPLYlink written 21 months ago by Bjoern Gruening4.8k
1

we have added an API to show the instance's version, try https://usegalaxy.org/api/version

git log will never consistently give you the human readable version of Galaxy; check if you have the following file: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/version.py

If you do you know your version, if you don't you are pre- and will only know the revision (have to check against github/repo)

ADD REPLYlink written 20 months ago by Martin Čech ♦♦ 4.2k
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