Hello Kathleen,
I've opened the following ticket for this issue - you can "follow" it in
bitbucket if you want.
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(a)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(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>
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
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