Re: [galaxy-dev] [galaxy-user] help
Because your questions are about a local installation of Galaxy, your email is best suited to the galaxy-dev mailing list, so I've moved it there. 1. FastQC not running . gives an error and doesn’t run on groomed or un-groomed FastQ file. The error message shows in the below pic. I don't see the pic, you probably need to install FastQC: (a) download the tool (b) put the fastqc script in the galaxy_home/tool-data/shared/jars/FastQC directory (c) make the script executable: %chmod 777 galaxy_home/tool-data/shared/jars/FastQC/fastqc 2. No reference genomein the drop down list in TOPHAT for illumine tool and TOPHAt2. See the section 'Setting Up the Reference Genomes for NGS Tools' on this page for help setting up genomes/indices: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J. ___ 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/
Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt
On May 9, 2012, at 10:37 AM, Tilahun Abebe wrote: Hi Jen, Thank you for the suggestions. I did try to log in to Galaxy under User --Login. The password is the one I use for the Galaxy Main. However, it gives me the error message No such user (please note that login is case sensitive). I do not see a place to set Admin password in the universe_wsgi.ini file. Here is how I setup the Admin permissions under Users and Security in the universe_wsgi.ini file: 1. id_secrete = gave a mix of numbers and letters 2. use_remote_user = True 3. remote_user_maildomain = tilahun.ab...@uni.edu Hi Tilahun, If you're using remote_user and your authentication is done upstream (e.g. in Apache) then you'll want to modify your remote_user_maildomain. That parameter should be everything after the @ sign, so if you authenticate in Apache and Apache sets the REMOTE_USER header to 'Tilahun.Abebe', then remote_user_maildomain should be set to 'uni.edu'. 4. remote_user_logout_href = None 5. Admin_users = tilahun.ab...@uni.edu 6. require_login = True 7. allow_user_creation = False 8. allow_user_deletion = True 9. allow_user_impersonation = True 10. allow_user_dataset_purge = True 11. new_user_dataset_access_role_default_private = True Can you check and let me know information I missed? If remote user authentication is correctly set up, you should not have a Log In link under the User menu. You should always see the Logged in as tilahun.ab...@uni.edu item in the menu instead, and that item would not be clickable. --nate Thanks. Tilahun -- On Tue, May 8, 2012 at 4:53 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Tilahun, Are you logged into your Galaxy instance UI using your admin account? This will display the Admin menu. Admin permissions are set up in the universe_wsgi.ini file: # -- Users and Security other items # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None Hopefully this solves the issue. Going forward, you'll probably find that the galaxy-...@bx.psu.edu mailing list is the most helpful for local install questions: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 5/8/12 2:10 PM, Tilahun Abebe wrote: Hi Galaxy users, I tried to install cutadapt for sequence trimming on a local Galaxy instance. I successfully installed Galaxy as an administrator. However, when Galaxy starts, I don't see the administrator option in the top menu bar with the Analyze Data, Workflow, Shared Data, Visualization, Help, and User. It looks like the only way I can install cutadapt is with an administrator option. Any suggestion how I can include the administrator option in the menu? Thanks for your help. Tilahun ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ 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/ ___ 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/
Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt
Hi Jen, Thank you for the suggestions. I did try to log in to Galaxy under User --Login. The password is the one I use for the Galaxy Main. However, it gives me the error message No such user (please note that login is case sensitive). I do not see a place to set Admin password in the universe_wsgi.ini file. Here is how I setup the Admin permissions under Users and Security in the universe_wsgi.ini file: 1. id_secrete = gave a mix of numbers and letters 2. use_remote_user = True 3. remote_user_maildomain = tilahun.ab...@uni.edu 4. remote_user_logout_href = None 5. Admin_users = tilahun.ab...@uni.edu 6. require_login = True 7. allow_user_creation = False 8. allow_user_deletion = True 9. allow_user_impersonation = True 10. allow_user_dataset_purge = True 11. new_user_dataset_access_role_default_private = True Can you check and let me know information I missed? Thanks. Tilahun -- On Tue, May 8, 2012 at 4:53 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Tilahun, Are you logged into your Galaxy instance UI using your admin account? This will display the Admin menu. Admin permissions are set up in the universe_wsgi.ini file: # -- Users and Security other items # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/**Admin/Interfacehttp://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None Hopefully this solves the issue. Going forward, you'll probably find that the galaxy-...@bx.psu.edu mailing list is the most helpful for local install questions: http://wiki.g2.bx.psu.edu/**Support#Mailing_Listshttp://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 5/8/12 2:10 PM, Tilahun Abebe wrote: Hi Galaxy users, I tried to install cutadapt for sequence trimming on a local Galaxy instance. I successfully installed Galaxy as an administrator. However, when Galaxy starts, I don't see the administrator option in the top menu bar with the Analyze Data, Workflow, Shared Data, Visualization, Help, and User. It looks like the only way I can install cutadapt is with an administrator option. Any suggestion how I can include the administrator option in the menu? Thanks for your help. Tilahun __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
