February 2009 - galaxy-user - lists.galaxyproject.org

An idea for sharing tools
by James Casbon 11 Jun '09

11 Jun '09

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

7 8

Exception when using remote_user.
by MORITA Hideyuki 10 Jun '09

10 Jun '09

Hi, The following error will occur under certain condition when using remote_user. AttributeError: 'NoneType' object has no attribute 'user' This error is thrown when: 1. using remote_user 2. browser has a valid session (cookie) 3. after logged in with an email address other than previously used This is caused by None value in prev_galaxy_session variable at L.231 in lib/galaxy/web/framework/__init__.py. I understand that galaxy_session instead of prev_galaxy_session should be referenced here. I created a patch to fix this problem by replacing prev_galaxy_session with galaxy_session. =================================================================================== diff -r a4214de3752e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900 @@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau invalidate_existing_session = True user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, prev_galaxy_session.user.email ) + remote_user_email, galaxy_session.user.email ) else: # No session exists, get/create user for new session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) =================================================================================== Thanks. MORITA Hideyuki

3 2

Galaxy source code revision question
by Assaf Gordon 25 Feb '09

25 Feb '09

Hello, When I clone the galaxy code from http://www.bx.psu.edu/hg/galaxy - which version am I getting: is that the 'test' version or some kind of an internal build ? I'm asking because running "hg incoming" shows the tip at revision 1760, while the 'dev' mailing lists only goes up to rev 1735. Is it safe to pull up to the tip ? Thanks, Gordon. P.S. should these kind of questions go to the "user" to "dev" mailing lists ?

1 1

Galaxy + Apache + External Authentication
by Assaf Gordon 20 Feb '09

20 Feb '09

Hello, I'm trying to setup galaxy to run with apache and external authentication - and I can't get this to work. (This is a not a galaxy question per se, more of an apache question, but hopefully you can still help me). First step was to setup apache/galaxy with mode rewrite - works perfectly. I've added these two lines to a 'conf' file in /etc/httpd/conf.d: ReWriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] Browsing to http://myserver/galaxy indeed goes to galaxy and works ok. Then, I've tested a simple authentication directive (independent of galaxy): Alias /galaxy "/home/gordon/galaxy" <Directory /home/gordon/galaxy> AuthType Basic AuthName "Restricted Files" AuthUserFile /home/gordon/httpd_passwords Require user gordon </Directory> And this also works OK. Now I want to combine the two - but it doesn't work. My "ReWriteRule" are ignored when they are inside a <Directory> clause. I've also tried <Location> - same results. Any ideas ? Thanks, Gordon

2 2

Uploading large files
by Johannes Waage 16 Feb '09

16 Feb '09

Hi, I have problems uploading large BED files (>250 MB) to galaxy; both Safari and Firefox on Mac OS X 10.5.6 just hangs, waiting for a page response, even though the file has been sent (as per the Activity Monitor). I did try uploading the files to an web-server, and pasting the address into the URL/Text-field... same result. Any help or tips would be appreciated.. Thank you in advance, J Waage, Biotech Research and Innovation Center, University of Copenhagen

2 1

GALAXY + GBrowse
by Erick Antezana 09 Feb '09

09 Feb '09

Hi, I managed to link my local GBrowse (version 2.0) and Galaxy by following the suggestions at http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options and by adapting a bit the following files: gbrowse_build_sites.txt tool_conf.xml adding my own data source in XML... Everything seems to work fine. However, I was wondering whether there is some more documentation (screencast or whatever) to define such brigde between Galaxy and GGB? I was not sure for instance whether adding another entry to the following parameter (in universe_wsgi.ini) would also be necessary since without it, it still does the trick: gbrowse_display_sites = elegans,flybase, myDB any suggestions are very welcome! thanks, Erick

1 0

Canales, Roger is out of the office.
by Roger D Canales 06 Feb '09

06 Feb '09

I will be out of the office starting 02/04/2009 and will not return until 02/09/2009. Please expect delays in response time.

1 0

access_libraries.xml missing?
by Erick Antezana 05 Feb '09

05 Feb '09

Hi, I have successfully installed Galaxy, and played a bit with it (jobs, workflows, etc). However, I was curious about an error message I got when launching the daemon: IOError: [Errno 2] No such file or directory: './tools/data_source/access_libraries.xml' that file (access_libraries.xml) seems to be missing. Any suggestions? Thanks, Erick

2 1

Fwd: [Genome] Stitch MAF blocks given a set of genomic intervals
by Stein Aerts 03 Feb '09

03 Feb '09

Dear Galaxy, I was wondering whether I might be able to get the source of the online feature "Stitch MAF blocks", to use locally? Thanks you so much, in advance! Best regards, Stein Aerts VIB, Belgium Begin forwarded message: > From: Brooke Rhead <rhead(a)soe.ucsc.edu> > Date: Sat 31 Jan 2009 01:09:25 GMT+01:00 > To: Stein Aerts <stein.aerts(a)med.kuleuven.be> > Cc: genome(a)soe.ucsc.edu > Subject: Re: [Genome] Stitch MAF blocks given a set of genomic > intervals > > Hello Stein, > > There is not a tool to do this in the Kent source tree. From one of > our developers: > > --- > We don't have good tools to do this, partially because the > transformation isn't necessarily possible (not all maf's can be > converted to a global alignment like FASTA is, and also maf blocks > don't necessarily contain all the sequence that are in the species). > > The user may grab the corresponding sequences using the maf, and run > their own global aligner (e.g. clustalw, MUSCLE). > --- > > You might be able to get Galaxy's source for this. If you haven't > already contacted them, their helpdesk address is galaxy-user(a)bx.psu.edu > . > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/30/09 03:25, Stein Aerts wrote: >> Hi, >> I am looking for a standalone solution to extract MAF blocks and >> then 'stitch' those together for each species into a fasta file, >> starting from a genomic interval of one species? Galaxy has this >> feature online so I was wondering whether there is a script or >> similar code in the Kent source (or a combination of scripts) to >> accomplish this locally in an efficient way? >> Many thanks in advance, >> Stein Aerts >> Belgium >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> _______________________________________________ >> Genome maillist - Genome(a)soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome > Stein Aerts, PhD Laboratory of Neurogenetics VIB-KULeuven Belgium http://perswww.kuleuven.be/~u0038182/ http://med.kuleuven.be/cme-mg/lng/

2 1