Best practices for a local install of Galaxy for only 1 user on a Mac

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Best practices for a local install of Galaxy for only 1 user on a Mac

Paul St.
I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly the install worked and I can use my local install. However, about 25% of the functional tests failed for me. And about 4 of the unit tests failed for me. Also, I can't seem to install anything from the toolshed (logged in as Admin). Below is what I did to install. Can any Galaxy/Mac gurus out there please fix the errors in the below install list so that we can have a good idea of the best practices for installing Galaxy on a Mac running the latest version of OSX? Also, tips for installing all of the dependencies would be great too.



Best practices for a local install of Galaxy for only 1 user on a Mac.

For Galaxy on a Mac (OSX 10.8):
To uninstall:
delete galaxy-dist folder (should anything else be done??)

To install Galaxy on a Mac (OSX 10.8):
1. Install Mercurial, download latest version from http://mercurial.selenic.com/mac/ and unzip and run installer.
2. Run the following in the terminal as a NON-root user (change "pst" to your user ID). (Is it better to create a "galaxy" user and install as user "galaxy"???) (Is it OK to use /Users/MacID/Applications as the install location, or is the home folder best??):
% cd /Users/pst/Applications
% hg clone https://bitbucket.org/galaxy/galaxy-dist/
% cd /Users/pst/Applications/galaxy-dist
% hg update stable
3. After install, run this to start the server and create defaults, then Control-C to quit the server:
% cd /Users/pst/Applications/galaxy-dist
% sh run.sh
% Ctrl-c in the terminal
4. Make the following changes to the universe_wsgi.ini file (found in /Users/pst/Applications/galaxy-dist/) using any text editor, save file as a UNIX text only file (TextWrangler works great for this) (What other changes should be made?).
library_import_dir = /Users/pst/Documents/GalaxyDataFiles
allow_library_path_paste = True
admin_users = [hidden email]
allow_user_dataset_purge = True
debug = False
use_interactive = False
cleanup_job = onsuccess
5. Set Up Visualizations:
% cd /Users/pst/Applications/galaxy-dist
% cp datatypes_conf.xml.sample datatypes_conf.xml
6. Get wigToBigWig and bedGraphToBigWig from (http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/) and copy the files to the /Users/pst/Applications/galaxy-dist/ folder.
7. Set both files to be executable:
% chmod +x /Users/pst/Applications/galaxy-dist/bedGraphToBigWig
% chmod +x /Users/pst/Applications/galaxy-dist/wigToBigWig
8. Test installation with:
% cd /Users/pst/Applications/galaxy-dist
% sh run_functional_tests.sh
9. Check test output. The above command will output an html file called "run_functional_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests.
10. Other tests:
% cd /Users/pst/Applications/galaxy-dist
% sh run_unit_tests.sh
11. Check test output. The above command outputs an html file called "run_unit_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests.
12. Install dependencies??




To start the local Galaxy server:
% cd /Users/pst/Applications/galaxy-dist
% sh run.sh

To use the local Galaxy server, enter this URL in your web browser:
http://localhost:8080

To stop the Galaxy server, just hit Ctrl-c in the terminal window from which Galaxy is running.

To see if new releases are available:
% cd /Users/pst/Applications/galaxy-dist
% hg incoming
If "no changes found" then you are up to date.
If changes are found, then add new versions with:
% hg pull -u

To update local galaxy:
% cd /Users/pst/Applications/galaxy-dist
% hg update stable





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Re: Best practices for a local install of Galaxy for only 1 user on a Mac

Florent Angly
Hi Paul,

I have Galaxy running on a small Mac workstation. I have made a specific
user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person.

Note also that you can install a daemon to start Galaxy automatically
when your computer starts:
https://bitbucket.org/galaxy/galaxy-central/src/d2d4b6ac2139f1623301990462a5e63b2952dcc1/contrib?at=default

I don't think I have ever waited long enough to see the end of the unit
tests. If some fail without any obvious reason (missing dependencies or
what not), you should probably raise this issue on the Galaxy mailing
list or bug tracker.

Cheers,

Florent



On 15/06/13 08:54, Paul St. Amand wrote:

> I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly the install worked and I can use my local install. However, about 25% of the functional tests failed for me. And about 4 of the unit tests failed for me. Also, I can't seem to install anything from the toolshed (logged in as Admin). Below is what I did to install. Can any Galaxy/Mac gurus out there please fix the errors in the below install list so that we can have a good idea of the best practices for installing Galaxy on a Mac running the latest version of OSX? Also, tips for installing all of the dependencies would be great too.
>
>
>
> Best practices for a local install of Galaxy for only 1 user on a Mac.
>
> For Galaxy on a Mac (OSX 10.8):
> To uninstall:
> delete galaxy-dist folder (should anything else be done??)
>
> To install Galaxy on a Mac (OSX 10.8):
> 1. Install Mercurial, download latest version from http://mercurial.selenic.com/mac/ and unzip and run installer.
> 2. Run the following in the terminal as a NON-root user (change "pst" to your user ID). (Is it better to create a "galaxy" user and install as user "galaxy"???) (Is it OK to use /Users/MacID/Applications as the install location, or is the home folder best??):
> % cd /Users/pst/Applications
> % hg clone https://bitbucket.org/galaxy/galaxy-dist/
> % cd /Users/pst/Applications/galaxy-dist
> % hg update stable
> 3. After install, run this to start the server and create defaults, then Control-C to quit the server:
> % cd /Users/pst/Applications/galaxy-dist
> % sh run.sh
> % Ctrl-c in the terminal
> 4. Make the following changes to the universe_wsgi.ini file (found in /Users/pst/Applications/galaxy-dist/) using any text editor, save file as a UNIX text only file (TextWrangler works great for this) (What other changes should be made?).
> library_import_dir = /Users/pst/Documents/GalaxyDataFiles
> allow_library_path_paste = True
> admin_users = [hidden email]
> allow_user_dataset_purge = True
> debug = False
> use_interactive = False
> cleanup_job = onsuccess
> 5. Set Up Visualizations:
> % cd /Users/pst/Applications/galaxy-dist
> % cp datatypes_conf.xml.sample datatypes_conf.xml
> 6. Get wigToBigWig and bedGraphToBigWig from (http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/) and copy the files to the /Users/pst/Applications/galaxy-dist/ folder.
> 7. Set both files to be executable:
> % chmod +x /Users/pst/Applications/galaxy-dist/bedGraphToBigWig
> % chmod +x /Users/pst/Applications/galaxy-dist/wigToBigWig
> 8. Test installation with:
> % cd /Users/pst/Applications/galaxy-dist
> % sh run_functional_tests.sh
> 9. Check test output. The above command will output an html file called "run_functional_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests.
> 10. Other tests:
> % cd /Users/pst/Applications/galaxy-dist
> % sh run_unit_tests.sh
> 11. Check test output. The above command outputs an html file called "run_unit_tests.html" (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests.
> 12. Install dependencies??
>
>
>
>
> To start the local Galaxy server:
> % cd /Users/pst/Applications/galaxy-dist
> % sh run.sh
>
> To use the local Galaxy server, enter this URL in your web browser:
> http://localhost:8080
>
> To stop the Galaxy server, just hit Ctrl-c in the terminal window from which Galaxy is running.
>
> To see if new releases are available:
> % cd /Users/pst/Applications/galaxy-dist
> % hg incoming
> If "no changes found" then you are up to date.
> If changes are found, then add new versions with:
> % hg pull -u
>
> To update local galaxy:
> % cd /Users/pst/Applications/galaxy-dist
> % hg update stable
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/