[galaxy-dev] Galaxy server configuration question

2012-02-07 Thread Huayan Gao
Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely?

Re: [galaxy-dev] Galaxy server configuration question

2012-02-09 Thread Huayan Gao
. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? Thanks, Best, Huayan On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: Dear Sir or Madam, I am installing

Re: [galaxy-dev] Galaxy server configuration question

2012-02-13 Thread Huayan Gao
Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved. Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file

Re: [galaxy-dev] Galaxy server configuration question

2012-02-14 Thread huayan gao
Good point, Nate! I will move galaxy out of my documentroot then. Best, Huayan On Tue, Feb 14, 2012 at 1:21 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name

[galaxy-dev] Welcome.html page

2012-03-07 Thread huayan gao
Hi Nate, I got a silly question for you. My galaxy is running now but I'd like to customize it. I've changed the welcome.html page but the galaxy mirror site is showing the old one. Do I need to change some other files or other configurations? Also, I add lable in tool_conf.xml file but it does

Re: [galaxy-dev] Galaxy server configuration question

2012-03-12 Thread Huayan Gao
. I've tried different ways but no luck. Best, Huayan On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote: On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed

Re: [galaxy-dev] Galaxy server configuration question

2012-03-15 Thread Huayan Gao
galaxy-dist/run.sh I could not figure it out what is wrong. Any suggestions? Best, Huayan On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote: On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote: Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot /var

Re: [galaxy-dev] Galaxy server configuration question

2012-05-18 Thread Huayan Gao
Dear Nate, Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working. Could it possible to send me your httpd.conf file for reference? Best, Huayan On 16 May, 2012, at 3:57 AM, Nate Coraor wrote: On Mar 14, 2012, at 9:16 PM, Huayan Gao

Re: [galaxy-dev] Galaxy server configuration question

2012-05-22 Thread Huayan Gao
Hi Nate, Thanks for helping. I've tried this part already but it is still not working. Still scratching my head here... Best, Huayan On 18 May, 2012, at 9:41 PM, Nate Coraor wrote: On May 18, 2012, at 2:37 AM, Huayan Gao wrote: Dear Nate, Thanks for checking. No, it is still

Re: [galaxy-dev] Galaxy server configuration question

2012-05-22 Thread Huayan Gao
, at 1:37 AM, Huayan Gao wrote: Dear Nate, Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working. Could it possible to send me your httpd.conf file for reference? Best, Huayan Huayan, The permission denied error might

[galaxy-dev] Question about default input files

2012-08-19 Thread Huayan Gao
Dear Nate, I am writing a tool of my own. I have a question about the default input files. I'd like to include some test files for my tool so anyone who is using the tool can run the tool with my default files or the files they upload. How can I set it up or where should I put the default

[galaxy-dev] hardware requirement for galaxy

2012-11-29 Thread Huayan Gao
Hi there, I'm interested in the specifics of your Penn State setup. Can you send it to me? Thanks, Huayan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy

Re: [galaxy-dev] hardware requirement for galaxy

2012-11-30 Thread Huayan Gao
-td4136963.html http://dev.list.galaxyproject.org/Local-Galaxy-concept-system-hardware-spec-questions-td4655904.html There's a lot more. Dave C On Thu, Nov 29, 2012 at 11:21 PM, Huayan Gao huayan...@gmail.com wrote: Hi there, I'm interested in the specifics of your Penn State setup. Can

[galaxy-dev] How to refresh the tool panel in Galaxy?

2012-12-06 Thread Huayan Gao
Hi, I am trying to add a tool into Galaxy. So far everything is ok except that I need to restart the server to make the tool showing up in the tool panel. So my question is that how to refresh the tool panel without restarting the server? After I install a tool from toolshed, I can see the tool

Re: [galaxy-dev] How to refresh the tool panel in Galaxy?

2012-12-26 Thread Huayan Gao
anything to the server. On Thu, Dec 13, 2012 at 12:10 PM, Huayan Gao huayan...@gmail.com wrote: Dear all, I just want to follow up with this question(see email below). I am afraid that it is lost in the traffic. Thanks, Huayan On Fri, Dec 7, 2012 at 12:48 PM, Huayan Gao huayan

[galaxy-dev] envirtual and import numpy problem

2013-01-15 Thread Huayan Gao
Hi, First it started with the error message: self.check_version_conflict(). So I use the virtualenv as instructed in wiki. But I got a new error: ImportError: No module named rpy/numpy... I will not have this importerror if I dont use the virtualenv. How to solve this problem? Thanks, Huayan

[galaxy-dev] How to add images/pictures into Galaxy Published Pages?

2013-03-12 Thread Huayan Gao
Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. Thanks, Huayan ___ Please keep all replies on

Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?

2013-03-12 Thread Huayan Gao
Thanks Bjoern! I figured it out too. I put the pictures in the static/images/Pages folder, then use them in the page. The main idea is to find a place with valid URL to store the pictures first. :-) Best, Huayan On Tue, Mar 12, 2013 at 5:41 PM, Björn Grüning

[galaxy-dev] Help with Send output to Galaxy function

2013-07-10 Thread Huayan Gao
Hi, I am trying to connect my local database/webpages to my local galaxy server. But I have a hard to implement send output to galaxy function. Right now I have a sending page to send a form to galaxy and it looks like everything goes well. From the variable json_params(data_source.py), I can see

[galaxy-dev] Help with two questions about transfering data to galaxy local instance

2014-01-23 Thread Huayan Gao
Hi, I am doing a data transferring interface in galaxy. I want to accomplish two things. First, when user enters a number, the interface will show some related information or search results (eg, related files) by this unique number. Then user can select the files they wanted to put into galaxy

[galaxy-dev] Bowtie2 and tophat2 data library set up

2014-03-19 Thread Huayan Gao
Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks,

Re: [galaxy-dev] Bowtie2 and tophat2 data library set up

2014-03-19 Thread Huayan Gao
PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page

Re: [galaxy-dev] Bowtie2 and tophat2 data library set up

2014-03-19 Thread Huayan Gao
Hi Martin, Actually I want a NGS Toolbox Beta tool panel exactly like the usegalaxy.org. How can I achieve this? I found myself looking for the tools and put them to tool_conf.xml which is very tedious. Is there a better way to do it? Best, Huayan On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao