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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > Greg Von Kuster > Galaxy Development Team > greg@bx.psu.edu > > > >
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap1.png>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button in http://genome.ucsc.edu/cgi-bin/hgTables, then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy!
Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Kathleen,
I'm on a Mac, so I do not have an IE browser, but I cannot reproduce this error in either Firefox or Safari. What version of IE are you using? Galaxy supports the IE browser, but I believe some versions of IE have problems. Clearing the browser cache before going to the UCSC table browser should not have this effect.
On Jan 19, 2010, at 9:33 PM, WangJun wrote:
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button in http://genome.ucsc.edu/cgi-bin/hgTables , then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> Greg Von Kuster >> Galaxy Development Team >> greg@bx.psu.edu >> >> >> >> > > Greg Von Kuster > Galaxy Development Team > greg@bx.psu.edu > > > >
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap3.png>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hello Greg Von Kuster,
I tested in IE 7. And this error appears also in my safari 4 public beta (528.16) and Opera 9.64. (attached) Because I have some important data in FireFox, I did not try in my FireFox. I do not know what is wrong with my instance. I add a tool config file under data_source in tools (attached the GMap cofig file) and also add it in tool_conf.xml and universe_wsgi.ini. Please help me to have a look, thanks a lot.
Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 10:44:48 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy!
Hi Kathleen,
I'm on a Mac, so I do not have an IE browser, but I cannot reproduce this error in either Firefox or Safari. What version of IE are you using? Galaxy supports the IE browser, but I believe some versions of IE have problems. Clearing the browser cache before going to the UCSC table browser should not have this effect.
On Jan 19, 2010, at 9:33 PM, WangJun wrote:
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button in http://genome.ucsc.edu/cgi-bin/hgTables, then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap1.png>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap3.png>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
This is the reproducible error shown in the server log when starting at ucsc with a fresh browser cache. Galaxy tries to load a history, but the user has no history yet.
128.118.200.27 - - [20/Jan/2010:08:51:36 -0400] "POST /tool_runner HTTP/1.0" 500 - "http://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_2; en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/4.0.4 Safari/531.21.10" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'id' URL: http://main.g2.bx.psu.edu/tool_runner File '/galaxy/home/g2main/galaxy_main/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/home/g2main/galaxy_main/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/home/g2main/galaxy_main/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/web/framework/base.py', line 125 in __call__ body = self.call_body_method( method, trans, kwargs ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/web/framework/base.py', line 144 in call_body_method return method( trans, **kwargs ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/web/controllers/tool_runner.py', line 51 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py', line 791 in handle_input out_data = self.execute( trans, incoming=params ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py', line 1063 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/actions/__init__.py', line 129 in execute db_dataset = trans.db_dataset_for( input_dbkey ) File '/galaxy/home/g2main/galaxy_main/lib/galaxy/web/framework/__init__.py', line 654 in db_dataset_for .filter_by( deleted=False, history_id=self.history.id, extension="len" ) AttributeError: 'NoneType' object has no attribute 'id'
CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'close' HTTP_HOST: 'main.g2.bx.psu.edu' HTTP_ORIGIN: 'http://genome.ucsc.edu' HTTP_REFERER: 'http://genome.ucsc.edu/cgi-bin/hgTables' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_2; en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/4.0.4 Safari/531.21.10' HTTP_X_FORWARDED_FOR: '128.118.200.27' HTTP_X_FORWARDED_HOST: 'main.g2.bx.psu.edu' ORGINAL_HTTP_HOST: 'galaxy_app' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/tool_runner' REMOTE_ADDR: '128.118.200.27' REQUEST_METHOD: 'POST' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9980' SERVER_PROTOCOL: 'HTTP/1.0'
Configuration ------------- __file__: '/galaxy/home/g2main/galaxy_main/universe_wsgi.webapp.ini' admin_users: 'nate@bx.psu.edu,greg@bx.psu.edu,anton@bx.psu.edu,dan@bx.psu.edu,james.taylor@emory.edu,gua110@bx.psu.edu,ross.lazarus@gmail.com,rc@bx.psu.edu,guru@psu.edu,cap142@psu.edu,dsg4@psu.edu' allow_user_deletion: 'True' cluster_files_directory: 'database/tmp/pbs' database_connection: 'postgres://g2main:norzOgtep6@main-db1.g2.bx.psu.edu/galaxy_main' database_engine_option_max_overflow: '20' database_engine_option_pool_size: '10' database_engine_option_strategy: 'threadlocal' datatype_converters_config_file: 'datatype_converters_conf.xml' datatype_converters_path: '/galaxy/home/g2main/galaxy_main/lib/galaxy/datatypes/converters' datatype_indexers_path: '/galaxy/home/g2main/galaxy_main/lib/galaxy/datatypes/indexers' debug: 'False' enable_job_running: 'False' enable_pages: 'True' error_email_to: 'galaxy-bugs@bx.psu.edu' file_path: 'database/files' gbrowse_display_sites: 'main,test,tair' here: '/galaxy/home/g2main/galaxy_main' id_secret: 'gHdf984t3ojldfGgdfggG93sdfmls9dlMellvm955kl' job_scheduler_policy: 'FIFO' job_walltime: '94:00:00' job_working_directory: 'database/tmp/job_working_directory' library_import_dir: '/galaxy/home/g2main/import' log_events: 'True' log_level: 'DEBUG' log_memory_usage: 'False' mailing_join_addr: 'galaxy-user-join@bx.psu.edu' new_file_path: 'database/tmp' nginx_upload_path: '/_upload' nginx_upload_store: 'database/tmp/upload_store' nginx_x_accel_redirect_base: '/_x_accel_redirect' output_size_limit: '214748364800' outputs_to_working_directory: 'True' sendmail_path: '/usr/sbin/sendmail' session_data_dir: '/galaxy/home/g2main/galaxy_main/database/beaker_sessions' session_key: 'galaxysessions' session_secret: 'LKhioo2HGopLy86HFtjkjvgsiy75ikIK' session_type: 'file' set_metadata_externally: 'False' smtp_server: 'mail.bx.psu.edu' static_cache_time: '360' static_dir: '/galaxy/home/g2main/galaxy_main/static/' static_enabled: 'True' static_favicon_dir: '/galaxy/home/g2main/galaxy_main/static/favicon.ico' static_images_dir: '/galaxy/home/g2main/galaxy_main/static/images' static_scripts_dir: '/galaxy/home/g2main/galaxy_main/static/scripts/' static_style_dir: '/galaxy/home/g2main/galaxy_main/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml' tool_data_path: 'tool-data' tool_path: 'tools' ucsc_display_sites: 'main,archaea,ucla' use_beaker_session: 'True' use_interactive: 'False' use_lint: 'False' use_new_layout: 'true'
WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x5d7ad10> paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x5d6eed0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xe5c990> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_post_vars: (MultiDict([('tool_id', 'ucsc_table_direct1'), ('URL', 'http://genome.ucsc.edu/cgi-bin/hgTables'), ('hguid', '321992688'), ('db', 'hg19'), ('org', 'Human'), ('hgta_table', 'knownGene'), ('hgta_track', 'knownGene'), ('hgta_regionType', 'range'), ('hgta_outputType', 'primaryTable'), ('position', 'chr21:33031597-33041570'), ('hgta_doTopSubmit', 'get output'), ('hgsid', '150111503'), ('hgta_doGalaxyQuery', 'Send query to Galaxy')]), <FakeCGIBody at 6dd78d0 viewing MultiDict([('to...y')])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------
On Jan 19, 2010, at 9:33 PM, WangJun wrote:
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button inhttp://genome.ucsc.edu/cgi-bin/hgTables, then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> Greg Von Kuster >> Galaxy Development Team >> greg@bx.psu.edu >> >> >> >> > > Greg Von Kuster > Galaxy Development Team > greg@bx.psu.edu > > > >
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap1.png>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
<Snap3.png>_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hello Kathleen,
I've opened the following ticket for this issue - you can "follow" it in bitbucket if you want.
http://bitbucket.org/galaxy/galaxy-central/issue/271/loading-the-tool_runner...
Thanks for reporting this error,
Dan
On Jan 19, 2010, at 9:33 PM, WangJun wrote:
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button inhttp://genome.ucsc.edu/cgi-bin/hgTables, then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> Greg Von Kuster >> Galaxy Development Team >> greg@bx.psu.edu >> >> >> >> > > Greg Von Kuster > Galaxy Development Team > greg@bx.psu.edu > > > >
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Hello Dan,
I just return from my winter holiday. And I find you have solved this problem. I have updated it and it works well now. Thank you so much for your help.
best,
Kathleen
发件人： Daniel Blankenberg 发送时间： 2010-01-20 22:16:53 收件人： WangJun 抄送： Greg Von Kuster; kongl@mail.cbi.pku.edu.cn; galaxy-dev 主题： Re: [galaxy-dev] Questions about Galaxy!
Hello Kathleen,
I've opened the following ticket for this issue - you can "follow" it in bitbucket if you want.
http://bitbucket.org/galaxy/galaxy-central/issue/271/loading-the-tool_runner...
Thanks for reporting this error,
Dan
On Jan 19, 2010, at 9:33 PM, WangJun wrote:
Hello Greg Von Kuster,
Thank you very much for your reply. I used the method you said to add GMap into my local instance. If I visit Galaxy main page first then submit data, it works well. However, if I clear the whole browsing history, then submit data from GMap, the error occurs. For UCSC, I clear the history first in IE, then click the "get output" button inhttp://genome.ucsc.edu/cgi-bin/hgTables, then "Send query to Galaxy", the "Server error" appears at this time. (attached the snapshot) I tried in three computers, the results are the same. Please help me to have a look. Be careful to clear the history first, otherwise it will be OK.
Thanks a lot. Best, Kathleen
发件人： Greg Von Kuster 发送时间： 2010-01-20 05:44:24 收件人： WangJun 抄送： galaxy-dev; kongl@mail.cbi.pku.edu.cn 主题： Re: [galaxy-dev] Questions about Galaxy! Hello Kathleen,
I'm not seeing the server error behavior when sending a request to Galaxy from the UCSC table browser. Instead, the data is sent to Galaxy as expected. Are you using the main UCSC table browser or another instance of the browser?
If your GMap app is configured to send data to Galaxy when the request originates from GMap, then your GMap app will simply need point to your Galaxy instance, including the same "parameters" that are sent in the URL parameter if the request originates from Galaxy.
On Jan 19, 2010, at 7:42 AM, WangJun wrote:
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@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@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@bx.psu.edu; galaxy-dev@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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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