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apache proxy configuration
by Yann Surget-Groba 16 May '11

16 May '11

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. Thanks, Yann

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Auto file convert
by Ellul Jason 16 May '11

16 May '11

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.ellul(a)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.

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Re: [galaxy-dev] galaxy login session query
by Harendra chawla 16 May '11

16 May '11

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. Regards Harendra On Sun, May 15, 2011 at 10:42 PM, Ross <ross.lazarus(a)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.harendra(a)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; >

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Re: [galaxy-dev] apache proxy configuration
by Paul-Michael Agapow 16 May '11

16 May '11

> 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.agapow(a)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 **************************************************************************

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galaxy login session query
by Harendra chawla 15 May '11

15 May '11

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

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More on multiple inputs to a workflow
by Dave Walton 13 May '11

13 May '11

So we loaded the change set that was developed at the hack-a-thon to our instance of galaxy. For the case where I have a directory of input files, where I want to run the same workflow for each, this change works great. There is one new issue I see, that I'd be interested in input on, and an old issue that I'd like a status on. First the new... So I have a workflow that does analysis on paired end mRNA Seq data. My workflow for single end works great, but with paired end, I can see an obvious way to submit two lists of files (one for the forward and one for the reverse), which can then be submitted to a series of the same workflow. Once I've chosen the forward to allow selection of multiple input files, the option to allow the reverse to also allow selection of multiple input files becomes disabled. This makes perfect sense, as, unless you've implemented it to associate pairs of files together, this probably wouldn't work anyway. Is there anyone out there working on a solution to this? If not, does anyone have suggestion as to how we could make it work? Now the old... A while back I suggested that it would be useful while editing a workflow, if there were a way to grab the name of an input file as a variable, and then use this variable in naming all later output files (this way I can propagate a sample name all the way through the workflow). Especially in a case where we are using the option to select multiple files to run the same workflow, this feature is very important. Is anyone working on this? If not, could someone point me in the right direction if I were to start trying to implement this feature? Thanks, Dave

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Reload ".loc" files without restarting Galaxy system?
by Luobin Yang 13 May '11

13 May '11

Hi, The "reload a tool's configuration" menu avoids restarting Galaxy system when a tool's web interface changed, but it doesn't seem to reload the ".loc" files that a tool's XML file uses. I am wondering if it's possible to reload the ".loc" file also? Thanks, Luobin

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Restoring galaxy database return few empty tables.
by Vipin TS 12 May '11

12 May '11

Dear Galaxy Team, I am switching our Galaxy production service to a new machine, We are using Postgres as database server. The existing database belongs to postgres version 8.3 and I took my instance's dump using postgres version 8.4. I am able to restore my database on postgres 8.4, Except few tables were empty and with few strange error message left on log file. I am not sure how many tables are empty, but I found table called 'job' returns 0 rows. Original job table returns me 40733 rows. excerpts from error log: ERROR: insert or update on table "history_dataset_association_annotation_association" violates foreign key constraint "history_dataset_association_a_history_dataset_association__fkey" DETAIL: Key (history_dataset_association_id)=(284985) is not present in table "history_dataset_association". STATEMENT: ALTER TABLE ONLY history_dataset_association_annotation_association ADD CONSTRAINT history_dataset_association_a_history_dataset_association__fkey FOREIGN KEY (history_dataset_association_id) REFERENCES history_dataset_association(id); ERROR: insert or update on table "history_dataset_association_tag_association" violates foreign key constraint "history_dataset_association_t_history_dataset_association__fkey" DETAIL: Key (history_dataset_association_id)=(387932) is not present in table "history_dataset_association". STATEMENT: ALTER TABLE ONLY history_dataset_association_tag_association In my knowledge we didn't do any manual transactions on Galaxy database and Could anyone let me know something wrong at my end. I'm sure this has been covered somewhere but I haven't been able to find it on the Wiki or by searching the archives. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

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Javascript out of date - history widgets don't expand.
by James Bullard 12 May '11

12 May '11

This is probably not a galaxy problem at all, however it is manifesting itself in the history pane of galaxy. The history widgets don't expand -- everything else works fine. The relevant javascript error looks to be: Uncaught TypeError: Cannot call method 'init' of undefined init_history_items galaxy.base.js:468 updater history:32 jQuery.extend.ready jquery.js:392 DOMContentLoaded jquery.js:745 I saw a previous post which is related to an update of galaxy, however, I haven't updated galaxy, but rather my OS (in fact the problem occurs in Firefox/Chrome; I'm ubuntu 11.04). Creating a new user doesn't help, restarting server doesn't help. Any thoughts on this, and once again I apologize for the fact that this isn't galaxy per se. jim

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param type="float" optional="true" doesn't work
by Leandro Hermida 12 May '11

12 May '11

Hi, how do you make float parameter types fully optional? optional="true" doesn't work. -Leandro

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