[galaxy-dev] Best practices for a local install of Galaxy
On Jun 18, 2013, at 8:02 AM, galaxy-dev-requ...@lists.bx.psu.edu wrote: > 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 Thanks for the startup tip Florent. That would be useful for those using Galaxy daily. So you think that running the install as the current non-root but ADMIN user works OK? What about the install folder? Must it be the home folder or is a subfolder OK as I have it (/Users/pst/Applications/)? My test output "run_functional_tests.html" is 5.1MB. I suppose that is too much to post on the list. I think that most of the errors are not due to dependencies. How do I get help with that? Paul___ 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/
Re: [galaxy-dev] Best practices for a local install of Galaxy for only 1 user on a Mac
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 = you...@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 ___ 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:
[galaxy-dev] Best practices for a local install of Galaxy for only 1 user on a Mac
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 = you...@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 ___ 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/
