An idea for sharing tools
by James Casbon
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
12 years, 7 months
Exception when using remote_user.
by MORITA Hideyuki
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
12 years, 7 months
Galaxy source code revision question
by Assaf Gordon
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 ?
12 years, 10 months
Galaxy + Apache + External Authentication
by Assaf Gordon
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
12 years, 11 months
Uploading large files
by Johannes Waage
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
12 years, 11 months
GALAXY + GBrowse
by Erick Antezana
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
12 years, 11 months
Canales, Roger is out of the office.
by Roger D Canales
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.
12 years, 11 months
access_libraries.xml missing?
by Erick Antezana
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
12 years, 11 months
Fwd: [Genome] Stitch MAF blocks given a set of genomic intervals
by Stein Aerts
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/
12 years, 11 months
