Re: [galaxy-dev] apache proxy configuration
I've installed galaxy locally and it works fine but I can't get the apache proxy to work. I've followed the instructions on the wiki first by serving galaxy at the web server root with: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] At the risk of making stupid suggestions: * You can see the galaxy instance directly at http://localhost:8080, yes? * Galaxy is running and Apache is running? * You're restarted Apache? It has the whiff of something being wrong with Apache, so you might want to switch on logging: RewriteLog /etc/httpd/logs/rewrite_log RewriteLogLevel 9 and see what that says. Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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 login session query
Harendra chawla wrote: Hi, Thanks a lot Mr.Lazarus, this solution worked out. I have one more (last) query related to sessions. When a user logs out from galaxy and in the next page uses the back button, the user session doesn't expire. The user can't see the previously saved history but it shows that the user is still logged in. Can anyone or Mr.Lazarus can suggest how this problem can be solved. Hi Harendra, This is a function of browsers that we can't really do anything about. The best solution is to instruct users to close their browser after logging out. Since the user is logged out, if anyone does hit the back button, it would not be possible to view any of that user's private data. --nate Regards Harendra On Sun, May 15, 2011 at 10:42 PM, Ross ross.laza...@gmail.com wrote: Harendra, Welcome to Galaxy! As far as I know, there's currently no parameter in universe_wsgi.ini other than the cookie path but in [galaxyroot]/lib/galaxy/web/framework/__init__.py you might be able to change the default from 90 days - I have NOT tested this so YMMV. All the calls to set_cookie I found appear to rely on the default age... def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): Convenience method for setting a session cookie # The galaxysession cookie value must be a high entropy 128 bit random number encrypted # using a server secret key. Any other value is invalid and could pose security issues. self.response.cookies[name] = value self.response.cookies[name]['path'] = path self.response.cookies[name]['max-age'] = 3600 * 24 * age # 90 days tstamp = time.localtime ( time.time() + 3600 * 24 * age ) self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) self.response.cookies[name]['version'] = version On Sun, May 15, 2011 at 12:44 PM, Harendra chawla chawla.haren...@gmail.com wrote: Hi everyone, I am new to Galaxy and I have a specific requirement regarding the user session. When a user logs in to galaxy his session dose not expire until he logs out. I want that when a user logs in his session automatically expires in 3 days and he will be asked to login again. Can anyone suggest how or where this can be done. Regards Harendra ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] Auto file convert
Jason, Thanks for pointing this error out - it's now fixed in galaxy-central and appears to be working on test. This fix will be on main after the next scheduled update. On Sun, May 15, 2011 at 8:43 PM, Ellul Jason jason.el...@petermac.org wrote: Hi All, I am installing and testing galaxy-dist locally and I have installed all the rgenetics tools and have them working but there seems to be a one problem. If I upload a lped file, then edit the attributes and convert it to a plink pbed file the tools such as QC reports and Case Control will work. If however I select (as pbed) RgeneticsData to run the tool directly I receive the following error: input data 1 is in error state I don't think this error is strictly related to rgenetics but something goes wrong after tools/parameters/basic.py gets called. Thanks for producing a fantastic resource and I would appreciate any help, -- Jason Ellul Bioinformatician Cancer Research Division Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.el...@petermac.org Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] User list and disk space?
Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the query variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods. Regards, L-A ___ 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] A tool with no inputs
One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). It is admittedly a fairly niche use-case and we could put in a dummy field and simply not use it, but that seems inelegant. Any suggestions? Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **___ 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] A tool with no inputs
Doesn't this violate one of the basic tenets of Galaxy - reproducibility? Without the ability to provide full traceability to the inputs, one can make no guarantees about the outputs. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Paul-Michael Agapow Sent: Monday, May 16, 2011 7:45 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] A tool with no inputs One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). It is admittedly a fairly niche use-case and we could put in a dummy field and simply not use it, but that seems inelegant. Any suggestions? Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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] apache proxy configuration
Hi Nate and Paul, thanks for your answers. It works now, I just didn't edit the right configuration file. I also tried with nginx, seems much more straightforward to configure than apache! Thanks again, best, Yann On 05/16/2011 06:30 AM, Nate Coraor wrote: Yann Surget-Groba wrote: Hi all, I've installed galaxy locally and it works fine but I can't get the apache proxy to work. I've followed the instructions on the wiki first by serving galaxy at the web server root with: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] if I go to http://localhost/ I get the default apache page, not galaxy I also tried serving galaxy at a sub directory but then if I go to http://localhost/galaxy I get a not found page Any idea of what is wrong with my configuration? I'm running apache v2.2.17 on a Debian system and mod_proxy, mod_http_proxy, and mod_rewrite are enabled. Hi Yann, Could you set RewriteLog, raise RewriteLogLevel to 9, restart Apache, and see if anything is logged? You may also want to set LogLevel debug and check your error_log for anything interesting. --nate Thanks, Yann ___ 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/
