Re: [galaxy-dev] Questions about Galaxy!

Dear Greg Von Kuster, I installed a local Galaxy instance for data submit test for our own GMap project. And I found a question: If I submit from GMap for the first time, then a error page appears. (attached the error information) However, if I use it from "Get Data" in Galaxy for the first time, it works very well. I guess the history_id does not exist when I submit from GMap for the first time. Also I found it's "Server error" if I submit data from UCSC table browser to the public Galaxy instance for the first time. I think I have the same question with them. Can you help to to find a solution? Thanks a lot! Best wishes, Kathleen 2010-01-19 发件人： Greg Von Kuster 发送时间： 2009-11-18 02:10:17 收件人： wangjun 抄送： galaxy-dev 主题： Re: [galaxy-dev] Questions about Galaxy! Kathleen, Please install a local instance of Galaxy and develop a data source tool that works between your Galaxy instance and GMap. You can download Galaxy from http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy . When you have your tool working, please submit it to us for possible inclusion in the public Galaxy instance. Thanks very much for your interest in doing this. Greg Von Kuster On Nov 17, 2009, at 11:27 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: > Hello Greg Von Kuster, > > You can access test GMap at http://202.38.125.5:8383/. > Click the big button "search" and submit using the default params, > then > you can see four tracks. You can click the entry of the second > track, for > example the red one, then you can see the detail info in the right > panel. > Click the "view sequence", there is a button "submit to Galaxy", > you can > try it. > > Thanks a lot! > Kathleen > >> Kathleen, sorry, I thought you had your own local Galaxy instance. >> Can you give us more information on GMap? Do you have a wiki or >> something we can access online to read about it? >> >> Thanks! >> >> On Nov 17, 2009, at 10:37 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: >> >>> Hello Greg Von Kuster, >>> >>> I am talking about your public Galaxy instance, and we don't have >>> local one. >>> We find that UCSC's data can be saved in your site directly, so we >>> hope >>> that Galaxy can also save our GMap data directly. We use the same >>> post >>> method like UCSC and the data can be saved now, but the data >>> title is >>> wrong. So I am writing to you to hope that you can help us. >>> >>> Thanks you. >>> >>> Kathleen >>> >>>> Hello Kathleen, >>>> >>>> Are you talking about your own local Galaxy instance or our main >>>> public Galaxy instance that is hosted here at Penn State >>>> University? >>>> >>>> Greg Von Kuster >>>> >>>> On Nov 17, 2009, at 10:10 AM, WangJun wrote: >>>> >>>>> Hello Greg Von Kuster, >>>>> >>>>> Thanks for your reply, but I think you misunderstood my meaning. >>>>> I am now working on a genome browser project GMap, and I hope >>>>> that >>>>> I can post request from GMap to Galaxy, then Galaxy can retrieve >>>>> and save the data in the History space like the UCSC request. >>>>> Untill now, I can post a request, including a url and params, and >>>>> Galaxy can retrieve the data and save it. However, the title of >>>>> the >>>>> data is still "UCSC Main". I think that's because of the tool_id >>>>> param's value is still "ucsc_table_direct1". I mean whether you >>>>> can >>>>> support us by adding a new tool_id named "CBI GMap". Then our >>>>> post >>>>> data can be shown with title "CBI GMap", not "UCSC Main". >>>>> >>>>> Thanks a lot! >>>>> Kathleen >>>>> >>>>> >>>>> 发件人： Greg Von Kuster >>>>> 发送时间： 2009-11-17 21:49:22 >>>>> 收件人： WangJun >>>>> 抄送： >>>>> 主题： Re: [galaxy-dev] Questions about Galaxy! >>>>> Kathleen, >>>>> >>>>> I'm not sure I understand the question, but if you are simply >>>>> creating a new tool that is very similar to the >>>>> "ucsc_table_direct1" tool , and you want the ID of your new >>>>> tool to >>>>> be "CBIGMap" ( I would advise against space characters in the >>>>> tool >>>>> ID ), then your tools config tag can be something like this: >>>>> >>>>>> <tool id="CBIGMap" name="CBIG Map" version="1.0.0" >>>>>> hidden="false" >>>>>> tool_type="data_source" URL_method="post"> >>>>> >>>>> If you have questions about how to add a new tool to your Galaxy >>>>> instance, see our wiki at http://bitbucket.org/galaxy/galaxy- >>>>> central/wiki/AddToolTutorial >>>>> >>>>> >>>>> On Nov 17, 2009, at 8:38 AM, WangJun wrote: >>>>> >>>>>> Hello Greg Von Kuster, >>>>>> >>>>>> Now I have solved the second problem.:) >>>>>> And for the first one, could you help me to add a new tool_id >>>>>> named "CBI GMap" to support our data source? >>>>>> This is a project in Center for Bioinformatics in Peking >>>>>> University in China. And I am a PhD student working on it. If >>>>>> you >>>>>> have other questions, please email me.:) >>>>>> <tool id="ucsc_table_direct1" name="UCSC Main" version="1.0.0" >>>>>> hidden="false" tool_type="data_source" URL_method="post"> >>>>>> Thanks a lot! >>>>>> >>>>>> Best, >>>>>> Kathleen >>>>>> 20091117 >>>>>> >>>>>> = >>>>>> = >>>>>> = >>>>>> ================================================================ >>>>>> = >>>>>> Hello Greg Von Kuster, >>>>>> >>>>>> Thanks a lot for your reply. >>>>>> But I still have a question: >>>>>> >>>>>> I have a url, and I include three necessary params in the >>>>>> following form. After I post it to Galaxy, I can see that Galaxy >>>>>> fetch the data. However, there are two point that I want to ask: >>>>>> 1. the "tool_id" param. My data's title is still "UCSC Main", I >>>>>> think that's because I use the "ucsc_table_direct1" value for >>>>>> "tool_id", right? Then how do I change this title? Can I >>>>>> adjust it >>>>>> by other param to change the title? >>>>>> 2. If I submit data from UCSC, then I can see a white box >>>>>> containing the data in the History part. However, I can only see >>>>>> the data info without data if I submit from my own site. (You >>>>>> can >>>>>> refer to attachment for detail. The No.20 data is from UCSC, >>>>>> and I >>>>>> can see the sequence. While the No.22 data is from my site, >>>>>> and I >>>>>> can not see the sequence.) And I don't know why. >>>>>> >>>>>> <form method="POST" action="http://main.g2.bx.psu.edu/tool_runner >>>>>> "> >>>>>> <input type="HIDDEN" value="ucsc_table_direct1" >>>>>> name="tool_id"/> >>>>>> <input type="HIDDEN" value="http://202.38.125.5:8383/entry/ >>>>>> rice_nucleotide_frame_galaxy.jsp" name="URL"/> >>>>>> <input type="HIDDEN" value="<%=id%>" name="id"/> >>>>>> <input type="HIDDEN" value="<%=trackName%>" >>>>>> name="trackName"/> >>>>>> <input type="HIDDEN" value="<%=type%>" name="type"/> >>>>>> <input type="HIDDEN" value="rice" name="db"/> >>>>>> <input type="HIDDEN" value="Rice" name="org"/> >>>>>> <input type="SUBMIT" value="Send query to Galaxy" >>>>>> name="submitGalaxy"/> >>>>>> </form> >>>>>> >>>>>> (test data: http://202.38.125.5:8383/entry/ >>>>>> rice_nucleotide_frame_galaxy.jsp? >>>>>> id=LOC_Os02g01370&trackName=MSU_Osa1_Rice_Loci&type=seq ) >>>>>> >>>>>> Thank a lot! >>>>>> Best, >>>>>> Kathleen >>>>>> 20091117 >>>>>> >>>>>> >>>>>> 发件人： Greg Von Kuster >>>>>> 发送时间： 2009-11-17 04:50:55 >>>>>> 收件人： WangJun >>>>>> 抄送： galaxy-user(a)bx.psu.edu; galaxy-dev(a)bx.psu.edu >>>>>> 主题： Re: [galaxy-dev] Questions about Galaxy! >>>>>> Hello Kathleen, >>>>>> >>>>>> Please see our wiki at http://bitbucket.org/galaxy/galaxy-central/ >>>>>> wiki/DataSources for details about how Galaxy communicates with >>>>>> external data sources. Your "dataset platform" will need to >>>>>> build >>>>>> an url that includes all of the parameters that are needed to >>>>>> retrieve the data, and send that url to Galaxy in the URL >>>>>> parameter so that Galaxy can execute the post. >>>>>> >>>>>> >>>>>> On Nov 16, 2009, at 9:06 AM, WangJun wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> This is a question about Galaxy interaction with UCSC data. >>>>>>> >>>>>>> I hava a dataset platform, and I want to add a button like the >>>>>>> UCSC's "Send query to Galaxy". >>>>>>> >>>>>>> I find that it's actually a form: >>>>>>> <form method="POST" action="http://main.g2.bx.psu.edu/ >>>>>>> tool_runner"> >>>>>>> <input type="HIDDEN" value="ucsc_table_direct1" >>>>>>> name="tool_id"/> >>>>>>> <input type="HIDDEN" value="http://genome.ucsc.edu/cgi-bin/ >>>>>>> hgTables" name="URL"/> >>>>>>> <input type="HIDDEN" value="296389734" name="hguid"/> >>>>>>> <input type="HIDDEN" value="hg18" name="db"/> >>>>>>> <input type="HIDDEN" value="Human" name="org"/> >>>>>>> <input type="HIDDEN" value="multiz28way" name="hgta_table"/> >>>>>>> <input type="HIDDEN" value="multiz28way" name="hgta_track"/> >>>>>>> <input type="HIDDEN" value="range" name="hgta_regionType"/> >>>>>>> <input type="HIDDEN" value="primaryTable" >>>>>>> name="hgta_outputType"/> >>>>>>> <input type="HIDDEN" value="chr3:130734948-130736581" >>>>>>> name="position"/> >>>>>>> <input type="HIDDEN" value="get output" >>>>>>> name="hgta_doTopSubmit"/> >>>>>>> <input type="HIDDEN" value="146683120" name="hgsid"/> >>>>>>> <input type="SUBMIT" value="Send query to Galaxy" >>>>>>> name="hgta_doGalaxyQuery"/> >>>>>>> </form> >>>>>>> >>>>>>> I have a url and three params, and I tried. But I can't see my >>>>>>> data in the right-side green box. >>>>>>> And what's the tool_id param used for? >>>>>>> >>>>>>> Thanks in advance! >>>>>>> >>>>>>> Best, >>>>>>> Kathleen >>>>>>> 2009-11-16 >>>>>>> _______________________________________________ >>>>>>> galaxy-dev mailing list >>>>>>> galaxy-dev(a)lists.bx.psu.edu >>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>>>> >>>>>> Greg Von Kuster >>>>>> Galaxy Development Team >>>>>> greg(a)bx.psu.edu >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> Greg Von Kuster >>>>> Galaxy Development Team >>>>> greg(a)bx.psu.edu >>>>> >>>>> >>>>> >>>>> >>>> >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> greg(a)bx.psu.edu >>>> >>>> >>>> >>>> >>> >>> >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> >> > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu <Snap1.png>