[galaxy-dev] Create select list parameter from input
Hi all, Is it possible to read id's from a column of an input dataset and create a checkbox parameter with the unique id's of that column within the same tool? The only remotely similar action that I found is on the sorting tool where it reads the number of the columns of that dataset and creates a dropdown select list. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Set output dbkey from parameter value
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I want to use is genome.
conditional name=bedgraph
param name=check type=select label=Produce BedGraph
output help=Can be displayed directly on UCSC browser. One file per
normalisation method.
option value=no selected=TrueNo/option
option value=yesYes/option
/param
when value=yes
param name=bed_file type=data format=bed
label=Transcripts ins BED format help=12 column BED file containing
trancript definitions. /
param name=genome type=text label=Genome Build
help=E.g. hg19 /
param name=track_name type=text label=Track
Name size=20 value=Track Name /
/when
when value=no /
/conditional
and this is how I've set the output:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
action type=metadata name=dbkey
option type=from_param name=bedgraph.genome
param_attribute=value /
/action
/data
When I run the tool the dbkey isn't set to the output file. Does
anyone know a workaround?
Bests,
Nikos
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Re: [galaxy-dev] Set output dbkey from parameter value
Hi Daniel,
Thanks for the response.
I've edited the output to:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
actions
conditional name=bedgraph.check
when value=yes
action type=metadata name=dbkey
option type=from_param
name=bedgraph.genome param_attribute=value /
/action
/when
/conditional
/actions
/data
Now I'm getting a tool execution error.
Error executing tool: 'unicode' object has no attribute 'value'
I've tried to change the param_attribute to ext, dbkey (ones that
I know that exist) and got a similar error.
Bests,
Nikos
On 15 October 2014 16:58, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Nikos,
In the very least, you’ll want to make sure that you have a bounding
actions/actions tag set around your actions. It is probably also
advisable to add a set of conditional/whens around the action, since you’re
only setting the dbkey under certain circumstances.
Thanks for using Galaxy,
Dan
On Oct 15, 2014, at 6:37 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I want to use is genome.
conditional name=bedgraph
param name=check type=select label=Produce BedGraph
output help=Can be displayed directly on UCSC browser. One file per
normalisation method.
option value=no selected=TrueNo/option
option value=yesYes/option
/param
when value=yes
param name=bed_file type=data format=bed
label=Transcripts ins BED format help=12 column BED file containing
trancript definitions. /
param name=genome type=text label=Genome Build
help=E.g. hg19 /
param name=track_name type=text label=Track
Name size=20 value=Track Name /
/when
when value=no /
/conditional
and this is how I've set the output:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
action type=metadata name=dbkey
option type=from_param name=bedgraph.genome
param_attribute=value /
/action
/data
When I run the tool the dbkey isn't set to the output file. Does
anyone know a workaround?
Bests,
Nikos
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Re: [galaxy-dev] Set output dbkey from parameter value
Yes!
Thank you very much Daniel.
On 15 October 2014 18:14, Daniel Blankenberg d...@bx.psu.edu wrote:
Does removing the ‘param_attribute=“value' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi Daniel,
Thanks for the response.
I've edited the output to:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
actions
conditional name=bedgraph.check
when value=yes
action type=metadata name=dbkey
option type=from_param
name=bedgraph.genome param_attribute=value /
/action
/when
/conditional
/actions
/data
Now I'm getting a tool execution error.
Error executing tool: 'unicode' object has no attribute 'value'
I've tried to change the param_attribute to ext, dbkey (ones that
I know that exist) and got a similar error.
Bests,
Nikos
On 15 October 2014 16:58, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Nikos,
In the very least, you’ll want to make sure that you have a bounding
actions/actions tag set around your actions. It is probably also
advisable to add a set of conditional/whens around the action, since you’re
only setting the dbkey under certain circumstances.
Thanks for using Galaxy,
Dan
On Oct 15, 2014, at 6:37 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I want to use is genome.
conditional name=bedgraph
param name=check type=select label=Produce BedGraph
output help=Can be displayed directly on UCSC browser. One file per
normalisation method.
option value=no selected=TrueNo/option
option value=yesYes/option
/param
when value=yes
param name=bed_file type=data format=bed
label=Transcripts ins BED format help=12 column BED file containing
trancript definitions. /
param name=genome type=text label=Genome Build
help=E.g. hg19 /
param name=track_name type=text label=Track
Name size=20 value=Track Name /
/when
when value=no /
/conditional
and this is how I've set the output:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
action type=metadata name=dbkey
option type=from_param name=bedgraph.genome
param_attribute=value /
/action
/data
When I run the tool the dbkey isn't set to the output file. Does
anyone know a workaround?
Bests,
Nikos
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[galaxy-dev] Set a new metadata attribute
Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bioblend dependency error
Hi all,
after the latest galaxy update I've experienced the following error while
trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in t
he egg distribution.
galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util
/pastescript/serve.py, line 1055, in invoke
exit_code = runner.run(args)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('bioblend')
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 409, in require
return c[req.project_name].require()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 237, in require
dists = self.resolve()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('mock'))
First I got and error about the python module 'requests' missing, fixed it
using 'pip install', and then got the error above.
Regards,
Nikos
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Re: [galaxy-dev] Bioblend dependency error
Dannon,
`python scripts/fetch_eggs.py` failed with errors about more packages
(pycrypto, poster).
After installing them and running the 'fetch_eggs' script successfully I'm
getting this error upon starting the server:
galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency bioblend requires
simplejson
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('bioblend')
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 409, in require
return c[req.project_name].require()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 237, in require
dists = self.resolve()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('simplejson'))
Simplejson is installed in the system and the library folder is in the
galaxy user's PYTHONPATH.
On 4 June 2014 15:32, Evan Bollig boll0...@umn.edu wrote:
Dannon,
Do you guys have a web page that documents all of the script/ utilities? I
know most of my deployment and upgrade problems have been resolved by
various scripts in there, but I have no idea what's available until I turn
to this mailing list.
-E
On Wednesday, June 4, 2014, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Nikos,
I think you're seeing the same issue from this trello card here:
https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
That should re-fetch galaxy's eggs and you should be up and running again.
On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi all,
after the latest galaxy update I've experienced the following error
while trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in t
he egg distribution.
galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1
[galaxy-dev] (New) error in Galaxy Reports
Hi all, a similar error with this one ( http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html) has appeared in Galaxy reports after the last update. It also occurs only when I'm trying to view the completed jobs in a certain day. Thanks in advance. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (New) error in Galaxy Reports
False alarm, the error went away when I restated the webapp. 2014-04-24 15:36 GMT+02:00 Nikos Sidiropoulos nikos.sid...@gmail.com: Hi all, a similar error with this one ( http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html) has appeared in Galaxy reports after the last update. It also occurs only when I'm trying to view the completed jobs in a certain day. Thanks in advance. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in Galaxy Reports
Hi Sam, thank you for the quick reply but I can't seem to find the revision, or maybe don't know how to pull it. I tried to check galaxy-dist on BitBucket but couldn't find any updates related to Galaxy Reports. Bests, Nikos 2014-02-13 17:35 GMT+01:00 sam guerler aysam.guer...@gmail.com: Hi Nikos, Thank you so much for your report. This issue should be fixed now. Please update your revision and try again. Thanks, Sam On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, after the February 2014 galaxy update I'm experiencing errors in Galaxy Reports. It only occurs when I'm trying to see which jobs were ran at a specific date (e.g. I can see how many jobs were ran today, but when I click on the number to see which ones it returns the following error): URL: http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13 Module paste.exceptions.errormiddleware:*144* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# body *=* method*(* trans*,* kwargs *)* Module galaxy.webapps.reports.controllers.jobs:*177* in specified_date_handler http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*specified_date_list_grid*(* trans*,* kwd *)* Module galaxy.web.framework.helpers.grids:*296* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# kwargs*=*kwargs *)* Module galaxy.web.framework:*1184* in fill_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*1199* in fill_template_mako http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* template*.*render*(* data *)* Module mako.template:*296* in render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs *)* Module mako.runtime:*718* in _exec_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# callable_*(*context*,* ***args*,* kwargs*)* Module _base_mako:*45* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _grid_base_mako:*134* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*self*.*load*(**)**)**)* Module _grid_base_mako:*108* in render_load http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# self*.*grid_javascripts*(**)* Module _grid_base_mako:*517* in render_grid_javascripts http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*h*.*to_json_string*(*self*.*grid_config*)**)**)* Module json:*231* in dumps http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* _default_encoder*.*encode*(*obj*)* Module json.encoder:*200* in encode http://localhost:9001/jobs
[galaxy-dev] Parsing input format in galaxy tools
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's format
(bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests,
Nikos
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Re: [galaxy-dev] Error in Galaxy Reports
Thanks so much Martin! 2014-02-14 19:32 GMT+01:00 Martin Čech mar...@bx.psu.edu: Hi, this has been resolved in galaxy-central repo (not dist). You can apply the patch manualy, it is less than one-liner. https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1 Martin On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi Sam, thank you for the quick reply but I can't seem to find the revision, or maybe don't know how to pull it. I tried to check galaxy-dist on BitBucket but couldn't find any updates related to Galaxy Reports. Bests, Nikos 2014-02-13 17:35 GMT+01:00 sam guerler aysam.guer...@gmail.com: Hi Nikos, Thank you so much for your report. This issue should be fixed now. Please update your revision and try again. Thanks, Sam On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, after the February 2014 galaxy update I'm experiencing errors in Galaxy Reports. It only occurs when I'm trying to see which jobs were ran at a specific date (e.g. I can see how many jobs were ran today, but when I click on the number to see which ones it returns the following error): URL: http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13 Module paste.exceptions.errormiddleware:*144* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# body *=* method*(* trans*,* kwargs *)* Module galaxy.webapps.reports.controllers.jobs:*177* in specified_date_handler http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*specified_date_list_grid*(* trans*,* kwd *)* Module galaxy.web.framework.helpers.grids:*296* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# kwargs*=*kwargs *)* Module galaxy.web.framework:*1184* in fill_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*1199* in fill_template_mako http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* template*.*render*(* data *)* Module mako.template:*296* in render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data *)* Module mako.runtime:*660* in _render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=* kwargs*)* Module mako.runtime:*718* in _exec_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# callable_*(*context*,* ***args*,* kwargs*)* Module _base_mako:*45* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _grid_base_mako:*134* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*self*.*load*(**)**)**)* Module _grid_base_mako:*108* in render_load http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# self*.*grid_javascripts*(**)* Module _grid_base_mako:*517* in render_grid_javascripts
Re: [galaxy-dev] Parsing input format in galaxy tools
Worked.
Thanks Björn!
2014-02-14 19:41 GMT+01:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Nikos,
try $input.ext ...
Cheers,
Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's
format (bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests,
Nikos
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[galaxy-dev] Error in SICER tool
Hi all, I'm getting the following error whenever I'm trying to run SICER Traceback (most recent call last): File /steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py, line 158, in module if __name__==__main__: __main__() File /steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py, line 154, in __main__ raise e IOError: [Errno 2] No such file or directory: '/NextGenSeqData/galaxy-data/database/tmp/tmpHPGhcN/input_bed_file-W200-G600-E0.01.scoreisland' Do you know if there's a workaround for this error? I have installed SICER from the toolshed (devteam) Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error in Galaxy Reports
Hi all, after the February 2014 galaxy update I'm experiencing errors in Galaxy Reports. It only occurs when I'm trying to see which jobs were ran at a specific date (e.g. I can see how many jobs were ran today, but when I click on the number to see which ones it returns the following error): URL: http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13 Module paste.exceptions.errormiddleware:*144* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# body *=* method*(* trans*,* kwargs *)* Module galaxy.webapps.reports.controllers.jobs:*177* in specified_date_handler http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*specified_date_list_grid*(* trans*,* kwd *)* Module galaxy.web.framework.helpers.grids:*296* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# kwargs*=*kwargs *)* Module galaxy.web.framework:*1184* in fill_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*1199* in fill_template_mako http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* template*.*render*(* data *)* Module mako.template:*296* in render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# callable_*(*context*,* ***args*,* kwargs*)* Module _base_mako:*45* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _grid_base_mako:*134* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*self*.*load*(**)**)**)* Module _grid_base_mako:*108* in render_load http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# self*.*grid_javascripts*(**)* Module _grid_base_mako:*517* in render_grid_javascripts http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*h*.*to_json_string*(*self*.*grid_config*)**)**)* Module json:*231* in dumps http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* _default_encoder*.*encode*(*obj*)* Module json.encoder:*200* in encode http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# chunks *=* self*.*iterencode*(*o*,* _one_shot*=*True*)* Module json.encoder:*263* in iterencode http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* _iterencode*(*o*,* *0**)* Module json.encoder:*177* in default http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *raise* TypeError*(*repr*(*o*)* *+* is not JSON serializable*)* *TypeError: datetime.datetime(2014, 2, 13, 12, 12, 24, 966618) is not JSON serializable* Bests, Nikos
[galaxy-dev] Create user error
Hi all, Although users were able to create accounts till recently, now the following error pops up whenever someone is trying to register as a new user after filling the fields and clicking submit. Select the user's type and information Is anyone familiar with this error? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create user error
I found the error in the logs: Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'id' URL: http://galaxy.bric.dk/user/manage_user_info?cntrller=user File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py', line 926 in manage_user_info status=status ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1002 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1017 in fill_template_mako return template.render( **data ) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/ base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/user/ manage_info.mako.py', line 93 in render_body __M_writer(unicode(trans.security.encode_id( user_type_form_definition.id))) AttributeError: 'NoneType' object has no attribute 'id' 2014/1/14 Nikos Sidiropoulos nikos.sid...@gmail.com Hi all, Although users were able to create accounts till recently, now the following error pops up whenever someone is trying to register as a new user after filling the fields and clicking submit. Select the user's type and information Is anyone familiar with this error? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create user error
Hi Martin, I have just found the workaround. Apparently there was a User information form in the Definition forms. I don't remember creating it but it was there anyway. After deleting it's able to register as a new user. Thanks for the help! Bests, Nikos 2014/1/14 Martin Čech mar...@bx.psu.edu Hi Nikos, did you update your galaxy version recently? Did you use galaxy form definitions at any time? Martin On Tue, Jan 14, 2014 at 8:30 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: I found the error in the logs: Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'id' URL: http://galaxy.bric.dk/user/manage_user_info?cntrller=user File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py', line 926 in manage_user_info status=status ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1002 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1017 in fill_template_mako return template.render( **data ) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/ base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/user/ manage_info.mako.py', line 93 in render_body __M_writer(unicode(trans.security.encode_id( user_type_form_definition.id ))) AttributeError: 'NoneType' object has no attribute 'id' 2014/1/14 Nikos Sidiropoulos nikos.sid...@gmail.com Hi all, Although users were able to create accounts till recently, now the following error pops up whenever someone is trying to register as a new user after filling the fields and clicking submit. Select the user's type and information Is anyone familiar with this error? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bismark error
Hi again You were right. Restarting all processes solved the problem and Bismark in now up and running. Bests, Nikos 2013/9/4 Nate Coraor n...@bx.psu.edu On Sep 4, 2013, at 10:08 AM, Nikos Sidiropoulos wrote: Hi Nate Yes, it is a multiprocess setup. But is it because we have more than one web-servers, handlers or both? Because if it's just the web-servers I could just scale it down to one since it doesn't seem necessary with our number of users. It's would be nice not to have to restart even for the tool-shed tools. The problem in this case is that one of the web server processes loaded the shed tool but none of the handlers did. Scaling back to a single web process won't solve the problem since the handler(s) will still need to load the tool. Unfortunately you'll have to restart all processes (except, technically, the one web process which happened to install the tool). The only way to avoid the restart is to have a single process for all tasks (web serving and job handling), which comes at a performance penalty. --nate Bests, Nikos 2013/9/4 Nate Coraor n...@bx.psu.edu On Sep 4, 2013, at 9:17 AM, Nikos Sidiropoulos wrote: Hi Bjørn that does not look like a bismark error. Is it happen with other tools as well? No, I have only experienced it with Bismark. Not sure, sorry. But you should migrate to the new job configuration, better sooner than later. I am starting to get that idea. There are jobs still running on the server. When they're done I'll migrate it and get back to you if the problem is fixed or not. Hi Nikos, The old-style configuration is still supported for now. I suspect this may be a problem of the tool not loading in the handler application. Are you running a multiprocess Galaxy setup? If so, you will need to restart all Galaxy processes after installing tools from the tool shed. --nate Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Scaling and hardware requirements
Hi all, I have a couple of questions regarding a server setup dedicated on Galaxy. The idea is to buy a 64 core 256GB RAM server. From my experience I believe that Galaxy will be able to scale up to 64 cpu's but I would like some more feedback on this. Also, is 4GB RAM per CPU core enough for NGS data? (including de-novo assembly) Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Scaling and hardware requirements
Hi Peter It's going to be one big machine, running both Galaxy server and the jobs. It's going to be a multi-process configuration. If that idea is terribly bad please let me know so I can give back the feedback. De novo assembly can also be for the human/mouse genome. Bests, Nikos 2013/9/11 Peter Cock p.j.a.c...@googlemail.com On Wed, Sep 11, 2013 at 1:03 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, I have a couple of questions regarding a server setup dedicated on Galaxy. The idea is to buy a 64 core 256GB RAM server. From my experience I believe that Galaxy will be able to scale up to 64 cpu's but I would like some more feedback on this. Also, is 4GB RAM per CPU core enough for NGS data? (including de-novo assembly) Bests, Nikos Hi Nikos, Is this going to be one server both for running Galaxy (which needs fairly low resources) and running jobs for Galaxy, like de novo assemblies (which need high resources)? i.e. You have one big machine only, no cluster? For de novo assembly the RAM per core/CPU isn't important, it is the total RAM on the machine. How much RAM you need depends on which assembler you use, the organism (both size and also complexity) and the volume of data. What you've described should be fine for bacterial assemblies and smaller eukaryotes - beyond that you'll need to give more details. Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Scaling and hardware requirements
I'm not sure how easy it would be to setup your Galaxy to only allow one de novo assembly at a time - which would seem a sensible precaution given you may have multiple users (or the same user) trying to run assemblies in parallel. I guess I could dedicate a handler to run this specific tool and in order to run it again, the first job will have to be completed. Thank you for all the help and suggestions! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bismark error
Hi all I installed bismark from the toolshed (bgruening) with all dependencies having been installed successfully and I generated the genomes according to the instructions. While trying to test the tool I got the following error. galaxy.jobs.handler ERROR 2013-09-04 13:14:26,267 Failed to generate job destination Traceback (most recent call last): File /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 287, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 617, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 163, in get_job_destination self.__cache_job_destination( params ) File /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' galaxy.datatypes.metadata DEBUG 2013-09-04 13:14:26,905 Cleaning up external metadata files galaxy.jobs.handler ERROR 2013-09-04 13:14:27,034 (1316) Error checking job readiness I'm using the old style job configuration (the one in universe_wsgi.ini). Could that be the issue? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bismark error
Hi Bjørn that does not look like a bismark error. Is it happen with other tools as well? No, I have only experienced it with Bismark. Not sure, sorry. But you should migrate to the new job configuration, better sooner than later. I am starting to get that idea. There are jobs still running on the server. When they're done I'll migrate it and get back to you if the problem is fixed or not. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bismark error
Hi Nate Yes, it is a multiprocess setup. But is it because we have more than one web-servers, handlers or both? Because if it's just the web-servers I could just scale it down to one since it doesn't seem necessary with our number of users. It's would be nice not to have to restart even for the tool-shed tools. Bests, Nikos 2013/9/4 Nate Coraor n...@bx.psu.edu On Sep 4, 2013, at 9:17 AM, Nikos Sidiropoulos wrote: Hi Bjørn that does not look like a bismark error. Is it happen with other tools as well? No, I have only experienced it with Bismark. Not sure, sorry. But you should migrate to the new job configuration, better sooner than later. I am starting to get that idea. There are jobs still running on the server. When they're done I'll migrate it and get back to you if the problem is fixed or not. Hi Nikos, The old-style configuration is still supported for now. I suspect this may be a problem of the tool not loading in the handler application. Are you running a multiprocess Galaxy setup? If so, you will need to restart all Galaxy processes after installing tools from the tool shed. --nate Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Postgres renaming to postgresql
Hi all After updating to the last stable galaxy when I'm trying to upgrade the database I'm getting the following message: /steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://user:pass@host/dbname If I change the line in universe_wsgi.ini from database_connection = postgresql://galaxy:password@localhost:5432/galaxydb to ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tophat2 output issue on LWR runner
Hi John Thank you for the reply. In the lwr_staging directory all the runs from tophat are kept in (separate folders for each run) which means that the job failed to finish. In the paster.log the most common error is HTTPNotFound: No file found with path lwr_staging/uniquejobstring/working/insertions.bed That's the case when tophat's output is set at default and the outputs are under working/tophat_out/. If I change this in the wrapper and redirect the output in working/ I get the following error. Traceback (most recent call last): File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, work_dir, output) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 174, in __raw_download_output output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 26, in execute with open(output_path, 'wb') as output: TypeError: coercing to Unicode: need string or buffer, file found or one time I got this Groomed 75 sanger reads into sanger reads. Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina Input ASCII range: 'B'(66) - 'b'(98) Input decimal range: 33 - 65 In the last two cases, no error was logged in lwr/paster.log Bests, Nikos 2013/6/18 John Chilton chil...@msi.umn.edu Hey Nikos, Thanks for the interest in the LWR and frankly I am excited to hear that bowtie worked properly. Some of these core NGS tools that require implicit indices spanning multiple files are not really addressed by the LWR currently, it only knows how to stage files that actually appear in the command-line or a config file. I guess if you are just using files from the history this is not a problem, but it is something to be aware of if you plan to start using .loc files. My first thought is that the LWR might not support 'from_work_dir' outputs in nested subdirectories. I will have to look more closely at that. Something that will help me though, is knowing if TopHat produced the outputs. Can you look at the LWR staging directory and tell me if these files were created (by default when a job fails, it is not cleaned up this is configurable in galaxy-central but not in galaxy-dist right now)? Also, does the LWR have any useful logs available? These will likely be in paster.log in the LWR directory. Also, the tip of galaxy-central includes improved error logging and exception handling so it is possible it would produce a better error message than this admittedly cryptic problem. I know it is not always possible to upgrade, but if it is easy it is something worth considering doing. -John On Tue, Jun 18, 2013 at 8:18 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi We are running the latest stable distribution on our server. We want tophat2 (along with other tools) to be executed on another machine. LWR is setup based on the online documentation (http://wiki.galaxyproject.org/Admin/Config/LWR, https://lwr.readthedocs.org/en/latest/) Bowtie2 is working as should but it looks like LWR is unable to return the outputs from tophat2. In universe_wsgi.ini the runner is configured like this: [galaxy:tool_runners] bowtie2 = lwr://https://uniquestring@chaos:8913 tophat2 = lwr://https://uniquestring@chaos:8913 When running tophat2 the following error message is returned. Traceback (most recent call last): File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, work_dir, output) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 174, in __raw_download_output output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 21, in execute response = self._url_open(request, data) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 12
[galaxy-dev] Tophat2 output issue on LWR runner
Hi We are running the latest stable distribution on our server. We want tophat2 (along with other tools) to be executed on another machine. LWR is setup based on the online documentation ( http://wiki.galaxyproject.org/Admin/Config/LWR, https://lwr.readthedocs.org/en/latest/) Bowtie2 is working as should but it looks like LWR is unable to return the outputs from tophat2. In universe_wsgi.ini the runner is configured like this: [galaxy:tool_runners] bowtie2 = lwr://https://uniquestring@chaos:8913 tophat2 = lwr://https://uniquestring@chaos:8913 When running tophat2 the following error message is returned. Traceback (most recent call last): File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, work_dir, output) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 174, in __raw_download_output output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 21, in execute response = self._url_open(request, data) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 12, in _url_open return urllib2.urlopen(request, data) File /usr/lib/python2.7/urllib2.py, line 127, in urlopen return _opener.open(url, data, timeout) File /usr/lib/python2.7/urllib2.py, line 407, in open response = meth(req, response) File /usr/lib/python2.7/urllib2.py, line 520, in http_response 'http', request, response, code, msg, hdrs) File /usr/lib/python2.7/urllib2.py, line 445, in error return self._call_chain(*args) File /usr/lib/python2.7/urllib2.py, line 379, in _call_chain result = func(*args) File /usr/lib/python2.7/urllib2.py, line 528, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error We tried to specify tophat's output folder either directly in lwr's working or output directory without success. Is there a solution to this? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] memdump
Hi everybody Has anybody used the profile memory usage feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] memdump
Hi everybody Has anybody used the profile memory usage feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] User expiration date
Hi Is it possible to set an expiration date for specific user accounts? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
