Re: [galaxy-dev] Cannot update Cloudman from a clean install on EC2?
Hey Brian,
Sorry for the delayed response on this one, what you're seeing is a
consequence of how Galaxy's tool migration scripts work -- all you
should need to do is click restart one more time in the cloudman admin
UI.
-Dannon
On Thu, Mar 14, 2013 at 10:56 PM, Brian Lin brian@tufts.edu wrote:
Hi guys, I'm running into a problem with updating a completely squeaky clean
fresh cloudman install using the current ami-da58aab3
Once it is up and running, I have SSHed in and made sure the sample files in
run.sh are complete.
I hit the update button, and 3 or 4 minutes later when the daemon tries to
restart, I get status= error.
Is anyone else having this issue?? The only threads and posts I have found
are from a year ago, and the line is in my run.sh.
The ultimate goal of all this was just so that I could have a cufflinks
version that is not 0.5.
Thanks for any help anyone can provide.
Brian
Here are the logs:
paster.log:
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is:
/mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading
references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference
to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference
to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database version
114
tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643
psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
File
/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py,
line 37, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 54, in
__init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File
/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py,
line 145, in verify_tools
raise Exception( msg )
Exception:
Console Log:
02:46:56 - Removing 'Galaxy' service
02:46:56 - Shutting down Galaxy...
02:47:25 - Starting Galaxy...
02:47:25 - Galaxy service state changed from 'Shut down' to 'Starting'
02:47:26 - Saved file 'persistent_data.yaml' to bucket
'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
02:48:28 - Galaxy daemon not running.
02:48:28 - Galaxy service state changed from 'Starting' to 'Error'
02:48:29 - Saved file 'persistent_data.yaml' to bucket
'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
02:49:30 -
[galaxy-dev] Galaxy dont work on my Bio-Linux
Hello, please could you help me, how to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there is GALAXY already install. When I try to open it, it is state that: The Galaxy server doesn't seem to be running on your machine. You may need to start it with the command: sudo start galaxy Or else Galaxy may still be starting up (it takes a couple of minutes to get going on the first run). When I open terminal and write sudo start galaxy it is state that galaxy start/running... But when I trying to open galaxy (just double clic on the icon) it still state problem which I write above. Could you help me please how to fix it?? Thank you very much for your reply! Have a nice day, Petr. ___ 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/
Re: [galaxy-dev] customtrack visualisation
Hello, Shaun Which revision of galaxy-central or galaxy-dist are you using in your local install? Thanks, Carl On Wed, Mar 20, 2013 at 12:52 PM, Shaun Webb swe...@staffmail.ed.ac.ukwrote: Hi Jen, I should have said this is in my own install. It works fine at the main server. I only noticed this as I was running a tutorial I created last year. So I can only say that something has changed in the last year.. I was wondering where in the configuration files or scripts galaxy is told to provide this link for this type of dataset, perhaps there is something I need to reconfigure. Thanks Shaun Quoting Jennifer Jackson j...@bx.psu.edu on Wed, 20 Mar 2013 07:08:13 -0700: Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = customtrack - database = hg18 display at UCSC main is functional, and it is the only external display (this is expected). If you want to share a history with me, please send a link and note the dataset with the problem. Thanks, Jen Galaxy team On 3/19/13 2:44 AM, Shaun Webb wrote: Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __**_ 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/ ___ 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/
Re: [galaxy-dev] Displaying track into UCSC (update)
Hi Julien, This was fixed in changeset 6cd4058d7b32 (https://bitbucket.org/galaxy/galaxy-dist/commits/6cd4058d7b32/). Can you update your Galaxy instance and see if the issue is resolved for you? Thanks for using Galaxy, Dan On Mar 20, 2013, at 4:53 AM, Julien SEILER wrote: Hello Carl, We are using galaxy-dist on revision a4113cc1cb5e. When we talk about private dataset, we mean datasets that have been uploaded to a user history through the Upload file tool. The access permission is allowed only to the current user role for these datasets. Anonymous user are not allowed on our galaxy instance. Regards, Julien Le 19 mars 2013 à 22:45, Carl Eberhard carlfeberh...@gmail.com a écrit : Hello, Stephanie and Julien What revision are you using IGBMC? Can you clarify what you mean by a private dataset? Are non-owners importing into a history via a shared history, or are they being passed a direct link to the UCSC display viewer from the owner? Thanks for the information, Carl On Tue, Mar 19, 2013 at 1:27 PM, Stephanie LE GRAS sleg...@igbmc.fr wrote: Hi all, Here is an update regarding the problem we are facing with Julien with our local instance of Galaxy. As Julien said we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) We have worked for hours on it today and we have identified that datasets that can be uploaded to UCSC are actually public datasets and that Julien can upload all his datasets to UCSC because they are all public by default. What is interesting now is that we've seen that the path to the data in the UCSC error message is : http://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interv al_as_bed/main/bea5029fce8b957e/data/galaxy.bed: While it should be : http://www.galaxy-igbmc.fr/display_at(Š)/galaxy.bed Because the right function to use in order to check whether the dataset can be uploaded to UCSC should be display_at but not display_application. Any ideas of what could cause Galaxy not to use the right function? Thank you in advance, Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97 Le 18/03/13 19:20, « Julien SEILER » seil...@igbmc.fr a écrit : Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien ___ 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/ ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] workflow parameters
Hi Brad, Thanks for reporting this issue. I have confirmed that there is an issue with workflow parameter substitution not working properly when inside of Grouping constructs (such as the paired end/single end conditional). We've opened a Trello card (https://trello.com/c/DvAea8kr) and Dannon, the developer of this feature, will work on a fix when he has a chance. Thanks for using Galaxy, Dan On Mar 15, 2013, at 9:35 PM, Langhorst, Brad wrote: Hi Dan: I've transplanted that fix - looks good in workflow editing. When i try to run the workflow though, I get this stack trace: URL: http://galaxy.neb.com/workflow/run?id=b3c161103f7e2a00 File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1514 in run enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 171 in render_body __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), , step, None, used_accumulator ))) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 40 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 429 in render_do_inputs __M_writer(unicode(do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used ))) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 340 in do_inputs return render_do_inputs(context,inputs,values,errors,prefix,step,other_values,already_used) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 435 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used ))) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 338 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used) File '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py', line 571 in render_row_for_param p_text = p_text.replace(rematch, 'span style=background-color:%s class=wfpspan wf_parm__%s%s/span' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1])) KeyError: 'min_insert' I'll hack a bit on it to see why min_insert is not in wf_params... Brad On Mar 15, 2013, at 5:28 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Brad, Thanks for reporting this issue. It has been fixed in -central and will be available in the next stable release:
Re: [galaxy-dev] Cloudman on openstack
Hi Zeeshan, There has actually been quite a bit of work on supporting CloudMan on OpenStack. The whole NECTAR deployment in Australia is based on OpenStack. What there has not been, as far as I know, is documentation about it. I suggest creating a Trello card on this (see http://wiki.galaxyproject.org/Issues#Create_an_Issue). That will allow others to comment on it and up-vote it, which will make it get done sooner. Sorry not to be of more help right now. Dave C On Wed, Mar 20, 2013 at 1:24 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, any update for cloudman with openstack . the page seems quite old http://wiki.galaxyproject.org/CloudMan/OpenStack -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/
