Tutorial: Get Galaxy! Your own Local Server
7
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson24k wrote:

What's Galaxy?

Download and Installation

Release Notes

Server Administration

Search all Galaxy resources

ADD COMMENTlink modified 3 months ago • written 3.3 years ago by Jennifer Hillman Jackson24k
0
gravatar for Dendi Nugraha
3 months ago by
Osaka, Japan
Dendi Nugraha30 wrote:

Hi guys, I am totally new here and I want to set up my own galaxy but I face problem. When I follow your instruction (hg clone https://bitbucket.org/galaxy/galaxy-dist/), the response was:

Blockquote destination directory: galaxy-dist abort: destination 'galaxy-dist' is not empty

Does it mean I already have the galaxy? When I try to run using "sh run.sh", it says error:

Blockquote Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/dendinugraha/galaxy-dist/lib/galaxy/dependencies/__init__.py", line 10, in <module> from galaxy.util import asbool File "/Users/dendinugraha/galaxy-dist/lib/galaxy/util/__init__.py", line 41, in <module> import docutils.core as docutils_core File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/site-packages/docutils/core.py", line 20, in <module> from docutils import frontend, io, utils, readers, writers File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/site-packages/docutils/frontend.py", line 41, in <module> import docutils.utils File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 20, in <module> import docutils.io File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/site-packages/docutils/io.py", line 18, in <module> from docutils.utils.error_reporting import locale_encoding, ErrorString, ErrorOutput File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/site-packages/docutils/utils/error_reporting.py", line 47, in <module> locale_encoding = locale.getlocale()[1] or locale.getdefaultlocale()[1] File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/locale.py", line 543, in getdefaultlocale return _parse_localename(localename) File "/Users/dendinugraha/galaxy-dist/.venv/lib/python2.7/locale.py", line 475, in _parse_localename raise ValueError, 'unknown locale: %s' % localename ValueError: unknown locale: UTF-8

and also they want me to update pip (even I already try it many time, it still cant run the program) please what should I do?

ADD COMMENTlink written 3 months ago by Dendi Nugraha30

The post's instructions were no longer current. I've updated the links to point to the most current resources.

In short, use Github instead of Bitbucket. Or consider a Docker distribution.

Thanks! Jen, Galaxy team

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson24k
1

Thanks Jen!

Finally I can have my own galaxy. But, new problem appeared. After 3 times, I can run galaxy using 'sh run.sh' without problem (provide me the localhost address), but after I stop the galaxy using 'fg Ctrl+c' and try become an admin, my galaxy did not work again. When I re-run using 'sh run.sh', it says this following error:

Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/dendinugraha/galaxy/lib/galaxy/dependencies/__init__.py", line 126, in optional conditional = ConditionalDependencies(config_file) File "/Users/dendinugraha/galaxy/lib/galaxy/dependencies/__init__.py", line 21, in __init__ self.parse_configs() File "/Users/dendinugraha/galaxy/lib/galaxy/dependencies/__init__.py", line 25, in parse_configs self.config = load_app_properties(config_file=self.config_file) File "/Users/dendinugraha/galaxy/lib/galaxy/util/properties.py", line 64, in load_app_properties properties.update(dict(parser.items(config_section))) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ConfigParser.py", line 642, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: 'app:main'

Another problem, I try to become the admin, but I do not know how to do that. I have log in to my galaxy via chrome, but I still do not have admin option on my galaxy. Try to follow instruction using command : 'sed 's/#admin_users = None/admin_users = admin@email.edu/' config/galaxy.ini.sample > config/galaxy.ini' but it says I dont have such directory.

Can you help me out (again)?

ADD REPLYlink modified 3 months ago • written 3 months ago by Dendi Nugraha30
1

First, make sure that you are in the primary (root) galaxy directory when running the command to change the galaxy.ini file or executing the run.sh. For you, that means being in the working directory /Users/dendinugraha/galaxy. That said, any command can be run from a different location (directly or through a script) as long as the paths in the command are correct (full path or relative). For example, the full path for run.sh for you would be:

$ sh /Users/dendinugraha/galaxy/run.sh

The next item is to double check that you are actually using the 17.09 release. The command to clone the repository is:

$ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git

My guess is that you obtained either the master branch or some development branch instead of release_17.09. If you are not sure or think that some other action/config change might have corrupted the install, the existing galaxy clone could be deleted (the entire directory and contents) and a new clone created for a fresh start. Successfully set up an admin account before investing time/effort in other updates (advanced config changes).

I downloaded and configured admin using the instructions at http://getgalaxy.org on the 17.09 release branch yesterday without any issues (MAC OSX). I do have Miniconda installed on my laptop, but that is not really needed, and I didn't set up advanced dependency resolution for that testing server.

Steps:

  1. initialized the instance by executing run.sh
  2. stopped Galaxy Ctrl-c
  3. created a modified galaxy.ini file to set the admin email
  4. restarted Galaxy again
  5. opened the local Galaxy server up in a browser (I used Chrome)
  6. created a newly registered account in the GUI using same email address assigned to admin in the config
  7. refreshed the GUI browser window
  8. the Admin section was activated (displayed/accessible) in the masthead

This granted me full GUI admin access - to install tools, to create local data, to load data libraries, etc. Note that any email address you want can be used, but it must be exactly the same between the galaxy.ini setting and the GUI registered Galaxy account. Email addresses are case-sensitive, meaning that Me@admin.edu is not the same as me@admin.edu.

Please be aware that the next release will implement new methods for configuration. The admin documentation will be updated when that goes out. The current instructions for many admin functions, including how to become an admin, will change slightly. If interested, the ticket tracking the 18.01 release is here: https://github.com/galaxyproject/galaxy/issues/4920 and a related PR for the config change is here: https://github.com/galaxyproject/galaxy/pull/5105.

Hopefully, this info helps resolves the problems, but let us know!

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson24k
1

You are so cool. I deleted the galaxy directory and its whole content and re-install again using the command you provided me and it works! I guess I installed the master branch version. Now it works.

Then, I follow the steps from this to be an admin, but here I get confused.

  1. When I open the galaxy using chrome, should I log in directly from it?
  2. I have shut down the running galaxy using 'fg' and 'Ctrl-c'. After that, do I have to close the tab on chrome and perform the commands?
  3. I have tested the 'grep ....' command, and it works. The response is 'None', after that I perform the 'sed......' command, but nothing happen (there was no response).

How can I solve this?

I FOLLOW YOUR STEPS ABOVE, AND IT WORKS PERFECTLY (I noticed that what you have instructed me was different what with was written in the galaxy website, like there's no step to close and re-open the galaxy like that)

ADD REPLYlink modified 3 months ago • written 3 months ago by Dendi Nugraha30
1

Good, now you have the correct branch!

  1. Yes, open the application in Chrome (or Safari) and create a new registered account using the same email address as in the galaxy.ini admin setting. You can create this GUI account before or after changing the galaxy.ini file, but it will not be Admin until both are done, and Galaxy is restarted after the galaxy.ini change.

  2. If the Terminal window already has Galaxy running as the active process, there is no need to bring it into the foreground with fg before using Ctrl-c. Also, you can leave the browser window/tab open while making line command changes. The GUI application will not be available when Galaxy is shut down but will become active again once Galaxy is started up. You might need to refresh the page.

  3. The grep command is run twice and it is constructed a bit differently for each step. https://galaxyproject.org/admin/get-galaxy/#become-an-admin-example

    • The first grep is a query against the config/galaxy.ini.sample file (the default that comes with the distribution).
    • The sed command will not have a response (unless something goes wrong) - it just makes the line change using config/galaxy.ini.sample as an input and outputs that result in a new file named config/galaxy.ini.
    • The second grep is a query against the newly created config/galaxy.ini file with the admin_users line modified. This grep is a quick way to confirm that the sed command actually made the intended changes.

It sounds like you are getting closer!

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson24k

Thank you so much Jen! I have successfully installed Galaxy by following your help. Now I am on the way install some tools I need.

Just want to confirm, after I use my Galaxy and I want to close it, should I do it orderly:

Close the chrome tab without logging out --> command Ctrl-c on terminal --> then close the terminal or should I log out also from Chrome in the first place?

ADD REPLYlink written 3 months ago by Dendi Nugraha30
1

You can leave Chrome open or not. The GUI won't impact anything you are doing while Galaxy is shut down. You can even close the browser window while Galaxy is still running and any job(s) that are in progress will continue to run (example: tool installs, index creation, analysis jobs). Then you can open it up again at any point. The only exception I can think of is when a dataset upload has been started through the GUI but the data transfer isn't completed yet (and not necessary for all upload methods - probably just for local-file-browsing upload).

In short, the browser accesses Galaxy, and many admin changes can be made in the GUI, but Galaxy itself is an independent process that isn't dependent on the browser. Some power-users never even use the GUI, ever. Instead, they access Galaxy through the API with scripts.

If you are on a shared computer, then definitely log out within the GUI, or the next person to open Chrome to the URL hosting Galaxy might get access to your account (if Galaxy is running). A rare situation, but seems worth mentioning.

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson24k

When we rewrite the help, I'll try to make the exact steps clearer and all in the same place. The beginning and end of that help section state to shut down/restart Galaxy, and how to do that is in other sections (same FAQ), but if it is confusing, that matters and we should adjust it. The original idea was to keep the "become an admin" instructions simple and distinct (there are a few ways to do these same actions), but I agree that an overview connecting all of the steps would be helpful as a supplemental FAQ/tutorial.

Very glad this is working now!

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson24k
1

Thank you so much Jen!

You are my savior, now I can run everything perfectly and I am so happy. Start to do the Tn-Seq analysis. Cheers!

ADD REPLYlink written 3 months ago by Dendi Nugraha30
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