galaxy-dev November 2010

galaxy-dev@lists.galaxyproject.org

63 participants
98 discussions

MySQL timeout problem
by David Hoover 03 Nov '10

03 Nov '10

I am using MySQL as the backend database. If I leave a Galaxy browser session sitting for more than 30 minutes, the MySQL connection goes to sleep. Then, when I try some action, there is an error displayed on the browser window and in the logfile. It looks something like this: Error - sqlalchemy.exc.OperationalError: (OperationalError) (2013, 'Lost connection to MySQL server during query') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['911e5446281a234467a4812eab1cad30', 1] I have seen this sleeping problem for other applications that use MySQL. There are couple of ways to fix this. The simplest is to capture the MySQL error and retry the operation if the error is 'Lost connection'. Another is to continuously 'ping' the MySQL server periodically with very short requests. Does anyone have a fix for this problem, or am I the first to notice this? David Hoover Helix Systems Staff http://helix.nih.gov

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Correction to docstring for Tool.build_param_dict
by Peter 03 Nov '10

03 Nov '10

Hi all, Here is a small fix to the docstring for Tool.build_param_dict. Peter diff -r 53d1fa98fa05 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Oct 21 16:10:26 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 22 13:32:31 2010 +0100 @@ -1333,7 +1333,7 @@ line. Each value is wrapped in a `InputValueWrapper`, which allows all the attributes of the value to be used in the template, *but* when the __str__ method is called it actually calls the - `to_param_dict_value` method of the associated input. + `to_param_dict_string` method of the associated input. """ param_dict = dict() # All parameters go into the param_dict

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Re: [galaxy-dev] [galaxy-user] installation problem
by Nate Coraor 03 Nov '10

03 Nov '10

Wei,Xintao wrote: > Dear Sir., > > We are going to install Galaxy local server on our Windows PC. Are there any requirements for the hardware, for example the size of CUP or other things, in order to run Galaxy smoothly? Hi Xintao, I've moved this over to the galaxy-dev list since it is better suited for local installation discussion. There aren't any hardware requirements beyond a system that is not terribly outdated, and that has the CPU/memory/disk capacity to run the tools which you plan to run. Galaxy itself is not very resource intensive except when doing certain tasks like setting the metadata on datasets. Resources used for that specific task will depend on the data format and size. Galaxy is not officially supported under Windows, nor have we known of anyone running it under Windows recently. That said, there should not be any code in Galaxy which would not work under Windows. Cygwin is a requirement, however, since Galaxy needs a POSIX-like environment in which to run. Unless you have a specific need to use Windows, you may want to look in to using some sort of virtualization technology (VirtualBox, for example) under which you can run Linux. Running Galaxy under Linux would be simpler and would allow us to provide better support for any problems you may encounter. --nate > > Thank you! > > Xintao > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Workflow outputs
by SHAUN WEBB 03 Nov '10

03 Nov '10

Hi, I have a suggestion regarding outputs from a workflow. The new feature that allows you to mark the shown outputs and hide the rest is a great idea but I wonder if this could be implemented at the run stage rather than the design stage as sometimes I require different outputs from the same workflow. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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server for galaxy
by Andreu Alibés 03 Nov '10

03 Nov '10

Hi, This one is for the people that have a Galaxy instance running on their institutes/companies, but probably not for the people running the main galaxy website: What would you say the requirements of Galaxy are in terms of disk space, cpu/memory, etc..? Thanks, Andreu -- -------------------------------------------- Andreu Alibés, PhD Bioinformatics Core & EMBL-CRG Systems Biology Unit Center for Genomic Regulation C/ Dr. Aiguader 88, 08003 Barcelona, Spain Phone: +34 93 316 0202 http://sites.google.com/site/aalibes

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Limited access tools
by Dave Walton 03 Nov '10

03 Nov '10

We are interested in making some of our tools only available to a subset of users. It looks to me like all galaxy tools are available to all galaxy users. We were thinking about patching our local galaxy to use the same roles that are used for data files for tools as well. Is this something others are interested in? Is this something that's already being worked on by the galaxy core team? (We'd hate to duplicate effort if someone is already doing this) Thanks, Dave

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Re: [galaxy-dev] trouble with authentication through Apache
by Ross 02 Nov '10

02 Nov '10

On Tue, Nov 2, 2010 at 10:48 AM, David Hoover <hooverdm(a)helix.nih.gov> wrote: > I tried a number of things, but the only one that works is a hack to the galaxy remoteuser.py script. > > I am authenticating with Kerberos, and this introduces a string in the HTTP_COOKIE variable Odd - according to http://onlamp.com/pub/a/onlamp/2003/09/11/kerberos.html?page=2 the Kerberos module is supposed to automagically set REMOTE_USER to the full userid (email and all)? That http_remote_user hack is sure ugly - there must be a better way? Looking at our setup for LDAP we have the user id in the uid attribute, so RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e works for us without all the other stuff suggested in http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy Any suggestions Nate? > newuser=[userid] > > So, in remoteuser.py, I match the alphanumerical characters of the userid and set HTTP_REMOTE_USER directly. > > $ diff remoteuser.py remoteuser.py.ORIG > 6d5 > < import re > 79,81d77 > < match = re.search('newuser=([0-9a-zA-Z]+)',environ['HTTP_COOKIE']) > < if match: > < environ['HTTP_REMOTE_USER'] = match.group(1) > > This is really bad, because every time galaxy is updated I will need to change this script. Ultimately, it would be better if galaxy could access the $REMOTE_USER variable like perl and mod_cgi do. > > David > > On Nov 1, 2010, at 8:55 PM, Ross wrote: > > David, > > Please feel free to write some notes to summarize what you've learned > about Kerberos and apache? > > If you could contribute what you have learned in a form that we could > use to improve the documentation - telegraphic notes or longer > narratives are always welcome - we'll make sure they're added to our > wiki to help future users. > > Thanks for using and helping us improve Galaxy! > > > > On Mon, Nov 1, 2010 at 5:43 PM, David Hoover <hooverdm(a)helix.nih.gov> wrote: >> Ah, well the documentation on the wiki is not entirely complete... >> >> I figured out that the REMOTE_USER is not passed when Kerberos is used to authenticate, so I figured out a roundabout way of doing it using HTTP_COOKIE instead. Quite brutal. It's very similar to the problem with mod_authnz_ldap. >> >> David >> >> On Oct 29, 2010, at 7:46 PM, Ross wrote: >> >> David, the section "Serving Galaxy at a sub directory (such as /galaxy) " >> in http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy >> might help? >> >> On Fri, Oct 29, 2010 at 5:32 PM, David Hoover <hooverdm(a)helix.nih.gov> wrote: >>> >>> Hi, >>> >>> I'm trying to set up a Galaxy mirror, and I'd like to authenticate via Apache. I can get Galaxy going when I don't authenticate. >>> >>> It's running on the same machine as the Apache server, listening on port 8081. >>> >>> I've added the mod_rewrite stuff from http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy, but I'm' still getting an error: >>> >>> Access to Galaxy is denied >>> >>> Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. >>> >>> Please contact your local Galaxy administrator. >>> >>> Here's the block from our Apache configuration: >>> >>> <Location "/galaxy"> >>> AuthName "NIH Login -- all lowercase, not prefixed with NIH\!" >>> AuthType Kerberos >>> Krb5Keytab /etc/auth_kerb.keytab >>> KrbAuthRealm NIH.GOV >>> KrbMethodNegotiate off >>> KrbSaveCredentials off >>> KrbVerifyKDC off >>> Require valid-user >>> RewriteCond %{IS_SUBREQ} ^false$ >>> RewriteCond %{LA-U:REMOTE_USER} (.+) >>> RewriteRule . - [E=RU:%1] >>> RequestHeader set REMOTE_USER %{RU}e >>> </Location> >>> >>> RewriteRule ^/galaxy$ /galaxy/ [R] >>> RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] >>> RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] >>> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] >>> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] >>> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] >>> RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] >>> >>> Any ideas? >> >> > > -- Ross Lazarus MBBS MPH Associate Professor, Harvard Medical School Director of Bioinformatics, Channing Laboratory 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850

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trouble with authentication through Apache
by David Hoover 02 Nov '10

02 Nov '10

Hi, I'm trying to set up a Galaxy mirror, and I'd like to authenticate via Apache. I can get Galaxy going when I don't authenticate. It's running on the same machine as the Apache server, listening on port 8081. I've added the mod_rewrite stuff from http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy, but I'm' still getting an error: Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Please contact your local Galaxy administrator. Here's the block from our Apache configuration: <Location "/galaxy"> AuthName "NIH Login -- all lowercase, not prefixed with NIH\!" AuthType Kerberos Krb5Keytab /etc/auth_kerb.keytab KrbAuthRealm NIH.GOV KrbMethodNegotiate off KrbSaveCredentials off KrbVerifyKDC off Require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] Any ideas? David Hoover Helix Systems Staff http://helix.nih.gov

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galaxy-dev November 2010