Re: [galaxy-dev] No Display at UCSC Main link.
Hello Luobin, Thanks for sending the additional information. It sounds as if you are using the default version of: tool-data/shared/ucsc/ucsc_build_sites.txt Adding hg19 to main in this file will add the link to the datasets. Hopefully this helps, Best, Jen Galaxy team On 2/17/12 1:58 PM, Luobin Yang wrote: Hi, Jen, I noticed that when I use hg18 or other database builds, the UCSC display link shows up, but when I use hg19 database builds, there is no UCSC display link. Thanks, Luobin On Wed, Feb 15, 2012 at 11:30 AM, Luobin Yang yangl...@isu.edu mailto:yangl...@isu.edu wrote: Hi, Jen, Thanks for your replay. Yes, it's an instance that I installed here at ISU, not the main instance at PSU. The dataset is BED and the database is hg19. In my universe_wsgi.ini file, I have the following lines: # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt ucsc_display_sites = main,test,archaea,ucla In my apache configuration file, I added the following: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1c9ec50d26246b3120bb238_1Location /root/display_as http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1c9ec50d26246b3120bb238_2 Satisfy Any Order deny,allow Deny fromall Allow fromhgw1.cse.ucsc.edu http://hgw1.cse.ucsc.edu Allow fromhgw2.cse.ucsc.edu http://hgw2.cse.ucsc.edu Allow fromhgw3.cse.ucsc.edu http://hgw3.cse.ucsc.edu Allow fromhgw4.cse.ucsc.edu http://hgw4.cse.ucsc.edu Allow fromhgw5.cse.ucsc.edu http://hgw5.cse.ucsc.edu Allow fromhgw6.cse.ucsc.edu http://hgw6.cse.ucsc.edu Allow fromhgw7.cse.ucsc.edu http://hgw7.cse.ucsc.edu Allow fromhgw8.cse.ucsc.edu http://hgw8.cse.ucsc.edu /Location One thing I would like to ask you about is for above Apache configuration, because my Galaxy is served as /galaxy subdirectory instead of the root directory, do I need to make changed to above location? for instance, instead of /root/display_as, use /galaxy/root/display_as ? Thanks so much! Luobin On Tue, Feb 14, 2012 at 10:51 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello again, The link is not a Galaxy Main public instance share link, which would start with: http://main.g2.bx.psu.edu Having the datatype as BED and the database as hg19 would (for all of the cases I can think of) bring up the View at UCSC link, if the instance is set up to have display at UCSC configured. So, the root cause of the problem is probably with how this other instance is set up. If this is not your instance, you will want to contact the folks running it to see if they have plans to configure UCSC display. If this is yours, follow the instructions on this wiki to get set up: http://wiki.g2.bx.psu.edu/__Admin/Config/Apache%20Proxy http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy See the section: Display at UCSC Hopefully this helps, Best, Jen Galaxy team On 2/14/12 9:26 PM, Luobin Yang wrote: Hi, Jen, The dataset is BED datatype and the database is hg19. Actually this history contains the same steps as those in Galaxy101 tutorial. I created the link for the history and here it is: So basically I do not see an option called Display at UCSC Main, but it has two other options, View in GeneTrack and Display at Ensemble Current Thanks, Luobin On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu mailto:j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Luobin, To display at UCSC, the datatype has to be a UCSC display type and the database has to be a UCSC genome browser. Often, small changes can be made to tune a dataset to help it fit into these requirements. Other times, a dataset will need to be transformed into another type or it can't be viewed at all because the genome is not available at UCSC. You should try to modify these attributes yourself first. Common UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of UCSC known datatypes, see: http://genome.ucsc.edu/FAQ/FAQformat.html http://genome.ucsc.edu/FAQ/__FAQformat.html http://genome.ucsc.edu/FAQ/__FAQformat.html http://genome.ucsc.edu/FAQ/FAQformat.html.
Re: [galaxy-dev] No Display at UCSC Main link.
Hi Luobin, To display at UCSC, the datatype has to be a UCSC display type and the database has to be a UCSC genome browser. Often, small changes can be made to tune a dataset to help it fit into these requirements. Other times, a dataset will need to be transformed into another type or it can't be viewed at all because the genome is not available at UCSC. You should try to modify these attributes yourself first. Common UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of UCSC known datatypes, see: http://genome.ucsc.edu/FAQ/FAQformat.html. Known databases would be any that you also can find at: http://genome.ucsc.edu as full genome assemblies. The short label used at UCSC should match the database assignment at Galaxy. For example, the most recent human would be hg19 at both. If you are still stuck and would like to send me a shared history link, I can provide feedback about how to modify (if possible) to view at UCSC. Use Options - Share or Publish, generate the link, and email this link directly back to me. Be sure to include the dataset #, so that I know which in your history you want to view at UCSC. Best, Jen Galaxy team On 2/14/12 11:50 AM, Luobin Yang wrote: Hi, I have a local instance of Galaxy, but I found there is no Display at UCSC Main link for some datasets that can be viewed in GeneTrack or displayed by Ensemble, what has been wrong? Thanks, Luobin ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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] No Display at UCSC Main link.
Hello again, The link is not a Galaxy Main public instance share link, which would start with: http://main.g2.bx.psu.edu Having the datatype as BED and the database as hg19 would (for all of the cases I can think of) bring up the View at UCSC link, if the instance is set up to have display at UCSC configured. So, the root cause of the problem is probably with how this other instance is set up. If this is not your instance, you will want to contact the folks running it to see if they have plans to configure UCSC display. If this is yours, follow the instructions on this wiki to get set up: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy See the section: Display at UCSC Hopefully this helps, Best, Jen Galaxy team On 2/14/12 9:26 PM, Luobin Yang wrote: Hi, Jen, The dataset is BED datatype and the database is hg19. Actually this history contains the same steps as those in Galaxy101 tutorial. I created the link for the history and here it is: So basically I do not see an option called Display at UCSC Main, but it has two other options, View in GeneTrack and Display at Ensemble Current Thanks, Luobin On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Luobin, To display at UCSC, the datatype has to be a UCSC display type and the database has to be a UCSC genome browser. Often, small changes can be made to tune a dataset to help it fit into these requirements. Other times, a dataset will need to be transformed into another type or it can't be viewed at all because the genome is not available at UCSC. You should try to modify these attributes yourself first. Common UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of UCSC known datatypes, see: http://genome.ucsc.edu/FAQ/__FAQformat.html http://genome.ucsc.edu/FAQ/FAQformat.html. Known databases would be any that you also can find at: http://genome.ucsc.edu as full genome assemblies. The short label used at UCSC should match the database assignment at Galaxy. For example, the most recent human would be hg19 at both. If you are still stuck and would like to send me a shared history link, I can provide feedback about how to modify (if possible) to view at UCSC. Use Options - Share or Publish, generate the link, and email this link directly back to me. Be sure to include the dataset #, so that I know which in your history you want to view at UCSC. Best, Jen Galaxy team On 2/14/12 11:50 AM, Luobin Yang wrote: Hi, I have a local instance of Galaxy, but I found there is no Display at UCSC Main link for some datasets that can be viewed in GeneTrack or displayed by Ensemble, what has been wrong? Thanks, Luobin _ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/__Support http://galaxyproject.org/wiki/Support -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
