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

15 Jun 2013


      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 = yourID@yourLocation.com
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