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

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