[galaxy-dev] Bowtie2 and tophat2 data library set up
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, 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 lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 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 or send me the documents please? 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 lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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 huayan...@gmail.com wrote: Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 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 or send me the documents please? 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 lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Help with two questions about transfering data to galaxy local instance
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 history panel for further data analysis. So my question is, can add a button in xml interface or python code to show the search results? The second question is that the files could be big. How can I transfer the files faster to my local galaxy instance? The current copy is just too slow. Thanks! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Help with Send output to Galaxy function
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 that all parameters have been received by galaxy. But the problem is that how I get my parameters from my getfile.php file(This is used in the Galaxy_URL too, the callback function)? I tried to print out $_POST, $_GET, $_REQUEST, nothing shows up. I did see some output from $_Server. I am using php. Please help! Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to add images/pictures into Galaxy Published Pages?
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 the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?
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 bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Huayan, in your page-editor you have a picture symbol. As you mentioned you need to specify a path to an image. For my pages I created a history where I store all my pictures. Afterwards I copy the full URL of that picture to the page. So use galaxy to store you image collection :) Hope that helps, Bjoern 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 the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] envirtual and import numpy problem
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to refresh the tool panel in Galaxy?
Thank you Alex and Ross. This is a totally new tool so there is not record yet. So I guess it will not work without restarting the server. Best, Huayan On Sat, Dec 15, 2012 at 1:36 AM, Oleksandr Moskalenko o...@hpc.ufl.eduwrote: There's also a shortcut that avoids having to click through the menus every time. You can use a reload URL. For instance, if you were working with a local instance and developing the tool 'mytool'. You can open the following url, keep that page open and reload it when necessary to update the modified wrapper in the galaxy. http://localhost:8080/admin/reload_tool?reload_tool_button=Reloadtool_id=mytool Regards, Alex On Dec 12, 2012, at 9:21 PM, Ross ross.laza...@gmail.com wrote: After making changes to the tool xml, you can refresh any tool using the admin menu Reload a tool's configuration option. This only works for tools loaded at startup and AFAIK there is currently no way to load a brand new tool after Galaxy has started other than via the toolshed installation option or a server restart. If you edit a wrapper (eg perl or python) script that is called by a tool xml, it loads afresh for every subsequent job - no need to do 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...@gmail.com wrote: 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 immediately from the tool panel. This is exactly the function I want to implement in python. I was reading the code but too complicated. Could you point me the right place(code)? Thanks a lot. Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] How to refresh the tool panel in Galaxy?
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 immediately from the tool panel. This is exactly the function I want to implement in python. I was reading the code but too complicated. Could you point me the right place(code)? Thanks a lot. Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] hardware requirement for galaxy
Dear Dave, Thanks very much for your reply. It is very useful. Best, Huayan On Fri, Nov 30, 2012 at 11:14 PM, Dave Clements cleme...@galaxyproject.orgwrote: Huayan, Take a look at http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults for an idea of what infrastructure many Galaxy production servers use. That survey was taken this year. I also went to http://galaxyproject.org/search/mailinglists/ and found: http://dev.list.galaxyproject.org/Galaxy-Main-Server-Tool-Repository-td4363452.html http://user.list.galaxyproject.org/Recommended-spec-for-Galaxy-server-box-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 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 lists, please use the interface at: http://lists.bx.psu.edu/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] hardware requirement for galaxy
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 lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Question about default input files
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 input files? 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 lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy server configuration question
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 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 Hi Huayan, I don't have Galaxy running behind Apache here, so I don't have a full example to send. Can you check that all of the directories: /home /home/galaxy /home/galaxy/galaxy-dist /home/galaxy/galaxy-dist/static Are accessible by the user that Apache runs as? In addition, check that a Directory directives that would cover /home/galaxy/galaxy-dist/static do not contain Deny from all, Many configurations by default have an entry like: Directory / Some options... Deny from all /Directory You would need to add something like: Directory /home/galaxy/galaxy-dist/static Order deny,allow Allow from all /Directory --nate On 16 May, 2012, at 3:57 AM, Nate Coraor wrote: On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote: Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, Forbidden……You don't have permission to access /galaxy/static/welcome.html…. I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/... Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history Hi Huayan, Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or Directory directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist. --nate I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh 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/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate 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 the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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
Re: [galaxy-dev] Galaxy server configuration question
Hi Shantanu, I checked the status of SELinux, it is disabled. [root@galaxy ~]# sestatus SELinux status: disabled Not sure where I went wrong. Right now I am running Galaxy under root. Best, Huayan On 18 May, 2012, at 10:19 PM, Shantanu Pavgi wrote: On May 18, 2012, 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 be coming because of selinux setting. If you have selinux in enforcing mode then try either of these options: 1. set selinux in permissive or disabled mode 2. modify selinux context on related files HTH.. -- Shantanu On 16 May, 2012, at 3:57 AM, Nate Coraor wrote: On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote: Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, Forbidden……You don't have permission to access /galaxy/static/welcome.html…. I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/... Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history Hi Huayan, Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or Directory directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist. --nate I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh 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/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate 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 the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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
Re: [galaxy-dev] Galaxy server configuration question
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 wrote: Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, Forbidden……You don't have permission to access /galaxy/static/welcome.html…. I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/... Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history Hi Huayan, Maybe you've already fixed this problem, but if not, you'll need to adjust filesystem permissions or Directory directives such that the user running the Apache server can access the files in /home/galaxy/galaxy-dist. --nate I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh 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/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate 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 the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all
Re: [galaxy-dev] Galaxy server configuration question
Yes, I did read the page and followed the instructions. But somehow, I keep getting the error message, Forbidden……You don't have permission to access /galaxy/static/welcome.html…. I did add +x to all files under folder /static. -rwxrwxr-x 1 galaxy galaxy 1108 Mar 15 17:19 welcome.html I did change the rewrite rule path to /home/galaxy/galaxy-dist/... Here is the output from error_log of apache server, (13)Permission denied: access to /galaxy/static/style/history.css denied, referer: http://server/galaxy/history I run galaxy through the virtual env. (galaxy_env)[galaxy@galaxy ~]$ sh 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/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate 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 the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy server configuration question
Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot /var/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. 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 the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Welcome.html page
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 not show up either. Is there another file I need to change too? Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy server configuration question
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 is galaxy-dist. After I changed the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy server configuration question
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 and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. 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 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? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy server configuration question
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? Best, 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 lists, please use the interface at: http://lists.bx.psu.edu/
