Re: [galaxy-user] Accessing Galaxy on the cloud from http
Colleen; Yoy definitely only want to select a single security group: the CloudMan one. Selecting multiple groups like uses the most conservative settings in the union of the groups, so won't have the right ports open for CloudMan. The ami I've been mainly using is ami-da58aab3 (although I've tried a few others). I don't believe this will work with NX, which would explain being able to connect with ssh and not NX. NX requires a username/password. The latest CloudBioLinux images do this and support CloudMan: http://cloudbiolinux.org/ You need to enter a freenxpass: option to the user data with the password to use for access and it will setup the server on the back end. However, it would be worth tackling this second, after getting CloudMan working. The user data may be where I am messing up: I have a few questions I'm not clear on, I think I've tried may options here.. 1. Is cluster name just something I make up? Yes. It's used so you can restart the same cluster with saved data, and have multiple clusters with different names. 2. Are the characters part of the yaml structure? (I've tried both). No. From the log you pasted it looks like you have those around your secret key. Could you try without it, and a single security group, on a clean cluster and see if that fixes the issue? 3. Do I need to specify the default information? No. cluster_name, password, access_key and secret_key would be enough. It looks like you are nearly there. Hope this does it, Brad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Accessing Galaxy on the cloud from http
Thanks for the help! I was able to successfully connect and get galaxy running. The items I had incorrect and needed to change were: One security group User data with NO and only a space between the : and the data (Not a tab). Thanks f the quick responses and advice, I would have been forever trying the different variables. On Tue, Sep 27, 2011 at 7:49 PM, Brad Chapman chapm...@50mail.com wrote: Colleen; Yoy definitely only want to select a single security group: the CloudMan one. Selecting multiple groups like uses the most conservative settings in the union of the groups, so won't have the right ports open for CloudMan. The ami I've been mainly using is ami-da58aab3 (although I've tried a few others). I don't believe this will work with NX, which would explain being able to connect with ssh and not NX. NX requires a username/password. The latest CloudBioLinux images do this and support CloudMan: http://cloudbiolinux.org/ You need to enter a freenxpass: option to the user data with the password to use for access and it will setup the server on the back end. However, it would be worth tackling this second, after getting CloudMan working. The user data may be where I am messing up: I have a few questions I'm not clear on, I think I've tried may options here.. 1. Is cluster name just something I make up? Yes. It's used so you can restart the same cluster with saved data, and have multiple clusters with different names. 2. Are the characters part of the yaml structure? (I've tried both). No. From the log you pasted it looks like you have those around your secret key. Could you try without it, and a single security group, on a clean cluster and see if that fixes the issue? 3. Do I need to specify the default information? No. cluster_name, password, access_key and secret_key would be enough. It looks like you are nearly there. Hope this does it, Brad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Accessing Galaxy on the cloud from http
Hello, I am having trouble setting up access to the galaxy cloud instance and may have missed something in the tutorial (I am following this one:http://wiki.g2.bx.psu.edu/Admin/Cloud) I am able to launch the instance I can access it through ssh, but when I try to access it through firefox or chrome it just times out. I am using the public DNS provided by amazon I DO add the /cloud I do have the http port added in the security group for GalaxyWeb that I set up (I also tried to add https just in case) Would someone be willing to work through this with me? I suspect I have incorrectly set up my security group, but I have tried many versions of the options. I have been through the amazon security faqs and I don't see what the issue could be (other than maybe IPv4 vs IPv6). Any advice or links for further help would be greatly appreciated Thank you! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Accessing Galaxy on the cloud from http
Colleen; I am having trouble setting up access to the galaxy cloud instance and may have missed something in the tutorial (I am following this one:http://wiki.g2.bx.psu.edu/Admin/Cloud) I am able to launch the instance I can access it through ssh, but when I try to access it through firefox or chrome it just times out. It does sound like something with the security group setting. Could you include a screenshot of what your security group looks like? As a reference, here is mine: http://tinypic.com/view.php?pic=jzy07qs=7 Did you also remember to select this security group, and not the default, when starting the image in the console? I sometimes make that mistake and then wonder for a while why I'm having connectivity issues. Hope this helps, Brad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Accessing Galaxy on the cloud from http
Hi Brad and All, Some more info (in case it gives you or anyone else any hints as to what I am doing wrong): If I start apache2, I can access the instance through http, so I guess it isn't with my security settings. I get: It works! This is the default web page for this server. The web server software is running but no content has been added, yet. I am obviously missing the cloudman startup, but I'm not sure what step I skipped that does that part. I see on this page (http://wiki.g2.bx.psu.edu/Admin/Cloud/UserData) that I can specify in the userData.yaml an optional boot_script_name, but it is not clear that I should explicitly include that in the userdata when I launch the instance. Just to be safe I also tried accessing it with just galaxy2 security settings (not also including default). I can still access it by ssh, but no access to it via http. Again if I start apache2, I can access via http, but there is nothing running. If I try to connect via NX it also fails (details provided by NX below) Again, thanks so much for the help with this! Colleen NXPROXY - Version 3.5.0 Copyright (C) 2001, 2011 NoMachine. See http://www.nomachine.com/ for more information. Info: Proxy running in client mode with pid '14459'. Session: Starting session at 'Mon Sep 26 17:42:34 2011'. Warning: Connected to remote version 3.4.0 with local version 3.5.0. Info: Connection with remote proxy completed. Info: Using ADSL link parameters 512/24/1/0. Info: Using cache parameters 4/4096KB/16384KB/16384KB. Info: Using pack method 'adaptive-7' with session 'gnome'. Info: Using ZLIB data compression 1/1/32. Info: Using ZLIB stream compression 4/4. Info: No suitable cache file found. Info: Forwarding X11 connections to display ':0.0'. Info: Listening to font server connections on port '12000'. Session: Session started at 'Mon Sep 26 17:42:34 2011'. Info: Established X server connection. Info: Using shared memory parameters 1/4096K. Session: Terminating session at 'Mon Sep 26 17:43:34 2011'. On Mon, Sep 26, 2011 at 5:25 PM, Colleen Doherty cdohe...@ucsd.edu wrote: Thank you for the quick answer. Here is a screenshot of my security groups (I have 2 galaxy ones, because I've been trying various options, but neither seem to work). As far as I can tell it looks similar to yours (thanks for that, it makes it easier to check that I typed everything in OK). http://s1232.photobucket.com/albums/ff373/c_doherty/?action=viewcurrent=Screenshot-1.png One difference is that I have been selecting BOTH default and galaxy2 security groups, maybe I should just select only galaxy2, I'll try that next. Looking at it through my ssh, I think I may be missing an even bigger point because it does not seem like cloudman is running There is nothing in the /tmp file except for my userData.yaml (and it looks from various websites that I should have a tmp/cm dir) So maybe I missed a major step in the setup? Thanks again for any advice! Colleen On Mon, Sep 26, 2011 at 5:09 PM, Brad Chapman chapm...@50mail.com wrote: Colleen; I am having trouble setting up access to the galaxy cloud instance and may have missed something in the tutorial (I am following this one:http://wiki.g2.bx.psu.edu/Admin/Cloud) I am able to launch the instance I can access it through ssh, but when I try to access it through firefox or chrome it just times out. It does sound like something with the security group setting. Could you include a screenshot of what your security group looks like? As a reference, here is mine: http://tinypic.com/view.php?pic=jzy07qs=7 Did you also remember to select this security group, and not the default, when starting the image in the console? I sometimes make that mistake and then wonder for a while why I'm having connectivity issues. Hope this helps, Brad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
