I'm trying to visualise some of our genome data using Trackster. Initial
input is 790,000 lines of GFF3. When I try and create the visualisation, I
get errors from two tools:
Convert GFF to Interval Index on data 3
-- an out of memory error - I'll try and fix this by upping the memory
limit for our Galaxy jobs
Convert BED, GFF, or VCF to BigWig on data 3
-- bedtools and bedGraphToBigWig not found errors. I tried to resolve these
by installing the ucsc-tools and bedtools packages - and they did install
correctly - but I still get these file not found errors.
Any idea how to fix this second problem?
P.S. as an alternative to Trackster, does anyone have Galaxy interfaced to
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh
-sid ...'. A few of the tests fail. When I go back and run the tool tests
individually, they succeed. So I looked into why they fail when running
them in batch, and it turns out to be a database lock. I'm using the
default sqllite database that run_tests.sh creates. Does this need to be
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched
Error - <class 'sqlalchemy.exc.OperationalError'>: (OperationalError)
database is locked u'SELECT api_keys.id AS api_keys_id,
api_keys.create_time AS api_keys_create_time, api_keys.user_id AS
api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE
api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
line 149 in __call__
app_iter = self.application(environ, sr_checker)
line 84 in __call__
return self.application(environ, start_response)
line 633 in __call__
return self.application(environ, start_response)
line 132 in __call__
return self.handle_request( environ, start_response )
line 159 in handle_request
trans = self.transaction_factory( environ )
line 71 in <lambda>
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
line 102 in transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
line 194 in __init__
self.error_message = self._authenticate_api( session_cookie )
line 283 in _authenticate_api
provided_key = self.sa_session.query( self.app.model.APIKeys ).filter(
self.app.model.APIKeys.table.c.key == api_key ).one()
File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331
OperationalError: (OperationalError) database is locked u'SELECT api_keys.id
AS api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM
api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
Where are you executing this? You'll need to be in the galaxy/config
directory, where galaxy.ini.sample exists.
I'm looping the mailing list back in on this so other people might also be
able to help.
On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha <ADAVENP3(a)gru.edu> wrote:
> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no
> such file or directory
> -------- Original message --------
> From: Dannon Baker <dannon.baker(a)gmail.com>
> Date: 06/15/2015 3:14 PM (GMT-05:00)
> To: "Davenport, Aneisha" <ADAVENP3(a)gru.edu>
> Subject: Re: [galaxy-dev] Galaxy admin access
> I'm not sure what you mean. You can edit the file using any text
> editor, try 'nano', or emacs or vim if you're more comfortable with those.
> Does the file exist or not? If not, simply "cp galaxy.ini.sample
> galaxy.ini" will do it.
> On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha <ADAVENP3(a)gru.edu>
>> How do I create it and edit it on terminal?
>> Aneisha Davenport
>> From: Dannon Baker [dannon.baker(a)gmail.com]
>> Sent: Friday, June 12, 2015 9:44 PM
>> To: Davenport, Aneisha; galaxy-dev(a)lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Galaxy admin access
>> Hi Aneisha,
>> When you say you cannot alter config/galaxy.ini, what do you mean? You
>> should be able to create (if not there) and edit this file in your regular
>> terminal on that machine.
>> Does a different user own the file, perhaps a 'galaxy' one? If so, you
>> could change to that user and then edit.
>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha <ADAVENP3(a)gru.edu
>> <mailto:ADAVENP3@gru.edu>> wrote:
>> Hi, I work at the It service desk at the GRU Health and Science campus Ed
>> Commons GB building and I have a customer trying to get admin access for
>> the local installation of galaxy. We tried to follow the online
>> instructions "In order to control your new Galaxy through the UI
>> (installing tools, managing users, creating groups etc.) you have to become
>> an administrator. First register as a new user and then give the user admin
>> privileges like this: You add the Galaxy login ( email ) to the Galaxy
>> configuration file (config/galaxy.ini). If the file does not exist you can
>> copy it from the provided sample (config/galaxy.ini.sample). Note that you
>> have to restart Galaxy after modifying the configuration for changes to
>> take effect.
>> # this should be a comma-separated list of valid Galaxy users
>> admin_users = user1(a)example.com<mailto:firstname.lastname@example.org>,
>> user2(a)example.com<mailto:email@example.com>" but we cannot alter the
>> config/galaxy.ini file. Can you please give us assistance? Do you run in
>> console or Terminal (this is a Macbook Air Laptop)?
>> Aneisha Davenport
>> 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:
>> To search Galaxy mailing lists use the unified search at:
I think a bug was introduced into galaxy-dist between the 15.03 and
15.05 releases, for the "Share history with user" function. The function
works for 15.03 but fails in 15.05.
1. Click on the "cog" icon for a history and select "Share or publish"
2. Under "Share History with Individual Users" click "Share with a user"
3. Enter the email of another user on the system and click submit
In 15.03 this returns to the sharing screen and indicates that the
history has been shared with the specified user; in 15.05 this produces
a stack trace (or "internal server error" in a production setting").
The following patch appears to fix the problem:
diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15
15:20:17 2015 -0400
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17
12:51:41 2015 +0100
@@ -899,7 +899,7 @@
for history_id in ids:
history_id = self.decode_id( history_id )
history = self.history_manager.get_owned( history_id,
trans.user, current_history=trans.history )
- histories.append( )
+ histories.append( history )
def _get_users( self, trans, user, emails_or_ids ):
also available via this gist:
Apologies if this has already been reported/fixed elsewhere, or if
there's a better way to submit this fix (if so then please let me know)
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
I have installed "package_r_ggplot2_0_9_3" in my galaxy instance as
dependency for "gatk2". The weird stuff is that in the web interface it
says the installation completed correctly but in the galaxy log file I get
As example, in the log file I get these errors:
ERROR: this R is version 2.11.0, package 'stringr' requires R >= 2.14
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called 'colorspac
ERROR: this R is version 2.11.0, package 'ggplot2' requires R >= 2.14
installation of package 'reshape2_1.2.2.tar.gz' had non-zero exit status
But at the end of the logfile I get this:
tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,229
Changing status for tool dependency ggplot2 from Installing to
tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,277
Tool dependency ggplot2 version 0.9.3 has been installed in
And in the webui it says the tool has been installed correctly (green).
Is this normal? can I ignore the errors or I should worry about them?
here you can see the complete log file when installing
thanks in advance for any advice.
Hi I was wandering how I can make the tool panel and history (left and right panels) to be hidden when the Galaxy instance starts. In the older versions you had to modify some .mako files but the newest setup has me a little confused.
I'd appreciate any help.
I have a custom tool_conf.xml in gbs_tools/gbs_tool_conf.xml
It is added to the config and loaded without problems.
But when I want to install tools from a toolshed (test and main)
to it ("Shed tool configuration file"), it reports Error during
Clicking on the tool, it says "This repository is not installed
correctly (see the Repository installation error below). [...]"
But there is no "Repository installation error".
So, how can I find out, what the problem is?
Installing in the default tool_shed_conf.xml works.
I also checked if it's a problem with the tool_path (I assume it
points to the galaxy root). So I created a directory gbs_tools
in gbs_tools, in case it is relative to the xml file directory.
Thanks for help!
the config/galaxy.ini is being overwritten when restarting Galaxy
via the CloudMan Console.
Unfortunately I can't find the file, that is used as template.
I searched on the whole machine for "*.cloud", "galaxy.ini*" and
"universe_wsgi.ini*". The only file I found was
"/mnt/cm/installed_files/universe_wsgi.ini.cloud". Changes to this
file doesn't have an effect.
The corresponding bucket also doesn't contain this file.
Where is this blueprint coming from?
And where can I change it?
I am using the next version of CloudMan (dev).
I created an own instance with the Cloud Man playbook.
Thanks a lot!
In the workflow editor, if you add an Input dataset collection, the
"Collection Type:" shows list. No dropdown arrow appears using Firefox. A
dropdown arrow appears when you mouse over using Chrome.
In Firefox, if you mouse over where the dropdown box should be, you can
still click to choose "list of datasets..."
For the longest time, I thought this was broken until a co-worker showed me
it works with Chrome. I'd make a Trello card for this but I can't access
Trello from behind the company firewall....