[galaxy-user] How do I remove Histories shared with you by others?
Hello - I am trying to clean out my Histories shared with you by others page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking Unshare at the bottom of the page 2. clicking the drop down menu and then selecting Unshare In both cases, I get the error message History is not owned by the current user. This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in-order-to-delete-td4656453.html). Any ideas on what is going on here? Best regards, Casey signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How do I remove Histories shared with you by others?
Hi Casey, I just tested the UI unsharing for both of your cases and was unable to replicate the problem. Can you confirm that you are using the public Main Galaxy instance at http://usegalaxy.org ? And is this your account email? Please confirm and we can try to see what may be going on. For the other, prior, question you reference, that one was fully resolved and permissions were not a factor. The thread has a reply with a link to our sharing wiki/video. The UI is/was behaving as expected. To share/unshare, use the pull-down menus or use the forms available from the history menu. Let us know about where you are using Galaxy, and we can follow up with more testing, Thanks! Jen Galaxy team On 2/6/14 3:46 AM, Casey Bergman wrote: Hello - I am trying to clean out my Histories shared with you by others page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking Unshare at the bottom of the page 2. clicking the drop down menu and then selecting Unshare In both cases, I get the error message History is not owned by the current user. This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in-order-to-delete-td4656453.html). Any ideas on what is going on here? Best regards, Casey ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How do I remove Histories shared with you by others?
Hi Casey, I was able to confirm this issue and we’ll work on a fix for it. Thanks for reporting. Thanks for using Galaxy, Dan On Feb 6, 2014, at 10:25 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Casey, I just tested the UI unsharing for both of your cases and was unable to replicate the problem. Can you confirm that you are using the public Main Galaxy instance at http://usegalaxy.org ? And is this your account email? Please confirm and we can try to see what may be going on. For the other, prior, question you reference, that one was fully resolved and permissions were not a factor. The thread has a reply with a link to our sharing wiki/video. The UI is/was behaving as expected. To share/unshare, use the pull-down menus or use the forms available from the history menu. Let us know about where you are using Galaxy, and we can follow up with more testing, Thanks! Jen Galaxy team On 2/6/14 3:46 AM, Casey Bergman wrote: Hello - I am trying to clean out my Histories shared with you by others page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking Unshare at the bottom of the page 2. clicking the drop down menu and then selecting Unshare In both cases, I get the error message History is not owned by the current user. This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in-order-to-delete-td4656453.html). Any ideas on what is going on here? Best regards, Casey ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Help with Cuffdiff
Hello, I am new to cuff diff and just got my data output back and it doesn't look like anything is statistically significant. There are three treatment groups with two biological replicates each group. I am not sure if I made an error somewhere along the line, need to adjust the parameters, or if there really could be no change. The samples are from sheep and I have been using the OvisAries3.0 reference I downloaded from UCSC. Thanks Maria ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How do I remove Histories shared with you by others?
Hello again Casey, A correction has been created and it will be included in the next update to the public server. The ticket with the details is here: https://trello.com/c/wqQua5V4 We appreciate that you took the time to research and report the problem! Best, Jen Galaxy team On 2/6/14 8:07 AM, Daniel Blankenberg wrote: Hi Casey, I was able to confirm this issue and we’ll work on a fix for it. Thanks for reporting. Thanks for using Galaxy, Dan On Feb 6, 2014, at 10:25 AM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Casey, I just tested the UI unsharing for both of your cases and was unable to replicate the problem. Can you confirm that you are using the public Main Galaxy instance at http://usegalaxy.org ? And is this your account email? Please confirm and we can try to see what may be going on. For the other, prior, question you reference, that one was fully resolved and permissions were not a factor. The thread has a reply with a link to our sharing wiki/video. The UI is/was behaving as expected. To share/unshare, use the pull-down menus or use the forms available from the history menu. Let us know about where you are using Galaxy, and we can follow up with more testing, Thanks! Jen Galaxy team On 2/6/14 3:46 AM, Casey Bergman wrote: Hello - I am trying to clean out my Histories shared with you by others page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking Unshare at the bottom of the page 2. clicking the drop down menu and then selecting Unshare In both cases, I get the error message History is not owned by the current user. This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in-order-to-delete-td4656453.html). Any ideas on what is going on here? Best regards, Casey ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Help with Cuffdiff
Hi Maria, More details are needed to help. Would you like to share a history with me? You might also find the tutorials and other resources for RNA-seq analysis we have helpful. Many are linked from here: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq I've also added the latest sheep build to the set of genomes to be indexed for the RNA-seq mapping tools (bowtie bowtie2). I'll try to include them in the upcoming snapshot if at all possible. But if not this one (is nearing completion), will be added to the next. Please review the help, then send me a share link if the suggested protocols are not addressing your questions (direct). Jen Galaxy team On 2/6/14 9:09 AM, Maria Hoffman wrote: Hello, I am new to cuff diff and just got my data output back and it doesn't look like anything is statistically significant. There are three treatment groups with two biological replicates each group. I am not sure if I made an error somewhere along the line, need to adjust the parameters, or if there really could be no change. The samples are from sheep and I have been using the OvisAries3.0 reference I downloaded from UCSC. Thanks Maria ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Questions regarding Circster visualization
Hi, I just noticed that Circos plots are now incorporated into Galaxy's visualization methods which is awesome! However, I'm a bit lost as to what kinds of data I can load into Circos and I cannot find much documentation, so I hope you guys can help out. 1. I tested it using a bigWig and a BED file. Both were loaded nicely in Circos, but I was surprised to see that the visualization of both files looked exactly the same, i.e. both file types seemed to be interpreted as histograms/coverage data. From the Circos plots I've seen in publications, I assumed that BED files should be visualized as straight lines, indicating genome regions (rather than a coverage). Am I doing anything wrong? Or, rather, how should I modify the BED file so that its content is simply interpreted as genomic regions? 2. In the Galaxy publication (www.biomedcentral.com/1471-2164/14/397), line data is mentioned for displaying connecting lines in the center of the circle - could you give me an example line of how this kind of data needs to be formated? It would be great to make much more use of Circster! Thanks a lot! Best wishes, Friederike ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How do I remove Histories shared with you by others?
Dear Jen Dan Thanks for looking into this and providing a quick fix. Best regards, Casey On Feb 6, 2014, at 5:29 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello again Casey, A correction has been created and it will be included in the next update to the public server. The ticket with the details is here: https://trello.com/c/wqQua5V4 We appreciate that you took the time to research and report the problem! Best, Jen Galaxy team On 2/6/14 8:07 AM, Daniel Blankenberg wrote: Hi Casey, I was able to confirm this issue and we’ll work on a fix for it. Thanks for reporting. Thanks for using Galaxy, Dan On Feb 6, 2014, at 10:25 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Casey, I just tested the UI unsharing for both of your cases and was unable to replicate the problem. Can you confirm that you are using the public Main Galaxy instance at http://usegalaxy.org ? And is this your account email? Please confirm and we can try to see what may be going on. For the other, prior, question you reference, that one was fully resolved and permissions were not a factor. The thread has a reply with a link to our sharing wiki/video. The UI is/was behaving as expected. To share/unshare, use the pull-down menus or use the forms available from the history menu. Let us know about where you are using Galaxy, and we can follow up with more testing, Thanks! Jen Galaxy team On 2/6/14 3:46 AM, Casey Bergman wrote: Hello - I am trying to clean out my Histories shared with you by others page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking Unshare at the bottom of the page 2. clicking the drop down menu and then selecting Unshare In both cases, I get the error message History is not owned by the current user. This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in-order-to-delete-td4656453.html). Any ideas on what is going on here? Best regards, Casey ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
