Re: [galaxy-dev] workflow parameters
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, '%s' % (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
mailto: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:
https://bitbucket.org/galaxy/galaxy-central/commits/b9afd514145740b4d5999158d51bd7dc4a409a99
Thanks for using Galaxy,
Dan
On Mar 15, 2013, at 5:04 PM, Langhorst, Brad wrote:
Workflow parameters still seem to be broken for me.
I'm seeing the same problem as Liisa Koski
http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html
(this message comes up when i edit a workflow with ${mininsert} set on a
bowtie2 job)
Problems were encountered loading this workflow (possibly a result of tool
upgrades). Please review the following parameters and then save.
* Step 9: Bowtie2
* Value no longer valid f
Re: [galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
Thanks Dave for your super-quick response! Works like a charm. -jorrit On Mar 15, 2013, at 12:16 PM, Dave Bouvier wrote: > Jorrit, > > Thank you for reporting this issue, I've committed a fix in the default > branch at 9077:62bd6fe0e9aa, and it will be updated in stable at our next > release. > > --Dave B. > > On 3/13/13 18:11:27.000, jorrit poelen wrote: >> To add some information to my earlier post - >> >> It seems that the remote repository is updated, but the commandline returns >> a confusing abort message. >> >> Trying on a private test toolshed, I see the following in the >> community-webapp.log: >> >> 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET >> /repos/testjorrit/testrepo?cmd=capabilities HTTP/1.1" 200 130 "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET >> /repos/testjorrit/testrepo?cmd=batch HTTP/1.1" 200 43 "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET >> /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1" 200 48 "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET >> /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1" 200 48 "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET >> /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1" 200 - "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - testjorrit [13/Mar/2013:22:08:23 +] "POST >> /repos/testjorrit/testrepo?cmd=unbundle HTTP/1.1" 200 - "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:24 +] "GET >> /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1" 200 58 "-" >> "mercurial/proto-1.0" >> 173.11.123.170 - - [13/Mar/2013:22:08:24 +] "POST >> /repos/testjorrit/testrepo?cmd=pushkey HTTP/1.1" 401 - "-" >> "mercurial/proto-1.0" >> >> Which seems to indicate that most http get/post succeed, but the last one, >> pushkey, fails to authenticate. >> >> I am wondering whether I am the only one seeing this confusing behaviour and >> what I can do to stop this from happening. >> >> thx, >> -jorrit >> >> On Mar 13, 2013, at 2:37 PM, jorrit poelen wrote: >> >>> Hey y'all, >>> >>> Even through >>> http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line >>> shows a working example of a hg push, I have not been able to push changes >>> to a remote toolshed successfull. Here's an example of an unsuccessful >>> attempt:. >>> >>> $ vi README >>> $ hg commit -m 'bla' -u jorrit >>> $ hg push >>> pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest >>> searching for changes >>> http authorization required >>> realm: >>> user: jorrit >>> password: >>> abort: authorization failed >>> >>> >>> tried this with hg versions: >>> Mercurial Distributed SCM (version 2.4.2+20130102) >>> and >>> Mercurial Distributed SCM (version 2.0.2) >>> >>> Curious to hear how I can get a hg push to remote repo to work from >>> commandline! >>> >>> -jorrit >>> >>> >>> ___ >>> 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. It has been fixed in -central and will be
available in the next stable release:
https://bitbucket.org/galaxy/galaxy-central/commits/b9afd514145740b4d5999158d51bd7dc4a409a99
Thanks for using Galaxy,
Dan
On Mar 15, 2013, at 5:04 PM, Langhorst, Brad wrote:
> Workflow parameters still seem to be broken for me.
>
> I'm seeing the same problem as Liisa Koski
> http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html
>
> (this message comes up when i edit a workflow with ${mininsert} set on a
> bowtie2 job)
>
> Problems were encountered loading this workflow (possibly a result of tool
> upgrades). Please review the following parameters and then save.
> Step 9: Bowtie2
> Value no longer valid for 'Minimum insert size for valid paired-end
> alignments', replaced with default
>
>
> but Im running a release release_2013.02.08
> and I've verified that this commit is present in the running code
>
> https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5
>
> any ideas?
>
>
>
> Brad
> --
> Brad Langhorst
> langho...@neb.com
>
>
>
>
>
> ___
> 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/
[galaxy-dev] workflow parameters
Workflow parameters still seem to be broken for me.
I'm seeing the same problem as Liisa Koski
http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html
(this message comes up when i edit a workflow with ${mininsert} set on a
bowtie2 job)
Problems were encountered loading this workflow (possibly a result of tool
upgrades). Please review the following parameters and then save.
* Step 9: Bowtie2
* Value no longer valid for 'Minimum insert size for valid paired-end
alignments', replaced with default
but Im running a release release_2013.02.08
and I've verified that this commit is present in the running code
https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5
any ideas?
Brad
--
Brad Langhorst
langho...@neb.com
___
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[galaxy-dev] configure loacl galaxy cluster question!
I have followed the instructions on how to setup a local cluster closely (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Frankly, the (Galaxy Configuration) section was not clear for me. I am not sure if those outlined steps should be applied to the server's universe_wsgi.ini or to the nodes'? So I might have overlooked some steps there but here is a summary of what I am doing at the server: All my nodes have been configured so the galaxy user can ssh/scp between nodes without pwd. Also the galaxy is a sudo in the galaxy (server). Torque has been configured and tested between the nodes. So the cluster is working fine. In universal_wsgi.ini file at the server node -- Start_job_runners=pbs,drama Drama_external_runjob_~ Drama_external_killer~ External_chown_~ Pbs_application_server = galaxyhost (server) Pbs_stage_path=/tmp/galaxy_stage/ Pbs_dataset_server= galaxyhost (server) ##This is the same like pbs_application_server Also, ln -s /nfsexport/galaxy_stage /usr/local/galaxy/galaxy-dis/database/tmp outputs_to_working_directory= False (if I changed this to True, the galaxy will not start) - After restarting the galaxy at the server node. The job seems to be submitted and its status is "R". When I "top" the processes on the node where the job was sent to, I see two processes; ssh and scp ran by the galaxy server. This tells me something is being copied over to the node. But I am not sure what and to where? After while the job status changed to "W". qstat Job idName UserTime Use S Queue - --- - - 68.ngsgalaxy01 ...x...@idtdna.com galaxy 0 W batch Here is what I say from the log when the job is sent. >> galaxy.jobs DEBUG 2013-03-15 15:34:54,183 (341) Working directory for job is: /usr/local/galaxy/galaxy-dist/database/job_working_directory/000/341 galaxy.jobs.handler DEBUG 2013-03-15 15:34:54,183 dispatching job 341 to pbs runner galaxy.jobs.handler INFO 2013-03-15 15:34:54,231 (341) Job dispatched galaxy.tools DEBUG 2013-03-15 15:34:54,309 Building dependency shell command for dependency 'samtools' galaxy.jobs.runners.pbs DEBUG 2013-03-15 15:34:54,391 (341) submitting file /usr/local/galaxy/galaxy-dist/database/pbs/341.sh galaxy.jobs.runners.pbs DEBUG 2013-03-15 15:34:54,391 (341) command is: PACKAGE_BASE=/usr/local/galaxy/software/samtools/0.1.16; export PACKAGE_BASE; . /usr/local/galaxy/software/samtools/0.1.16/env.sh; samtools flagstat "/usr/local/galaxy/galaxy-dist/database/files/000/dataset_319.dat" > "/usr/local/galaxy/galaxy-dist/database/files/000/dataset_384.dat" galaxy.jobs.runners.pbs DEBUG 2013-03-15 15:34:54,394 (341) queued in default queue as 70.ngsgalaxy01.idtdna.com galaxy.jobs.runners.pbs DEBUG 2013-03-15 15:34:54,966 (341/70.ngsgalaxy01.idtdna.com) PBS job state changed from N to R >> Here is the log when the ssh/scp on the node is finished. galaxy.jobs.runners.pbs DEBUG 2013-03-15 15:37:00,815 (341/70.ngsgalaxy01.idtdna.com) PBS job state changed from R to W Here is the log when I qdel that job galaxy.jobs.runners.pbs WARNING 2013-03-15 15:39:20,016 Exit code was invalid. Using 0. galaxy.jobs DEBUG 2013-03-15 15:39:20,033 (341) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /usr/local/galaxy/galaxy-dist/database/job_working_directory/000/341 galaxy 10020 galaxy.jobs ERROR 2013-03-15 15:39:20,071 (341) Failed to change ownership of /usr/local/galaxy/galaxy-dist/database/job_working_directory/000/341, failing Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 336, in finish self.reclaim_ownership() File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 909, in reclaim_ownership self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 895, in _change_ownership assert p.returncode == 0 AssertionError galaxy.datatypes.metadata DEBUG 2013-03-15 15:39:20,160 Cleaning up external metadata files galaxy.jobs.runners.pbs WARNING 2013-03-15 15:39:20,172 Unable to cleanup: [Errno 2] No such file or directory: '/usr/local/galaxy/galaxy-dist/database/pbs/341.o' galaxy.jobs.runners.pbs WARNING 2013-03-15 15:39:20,173 Unable to cleanup: [Errno 2] No such file or directory: '/usr/local/galaxy/galaxy-dist/database/pbs/341.e' galaxy.jobs.runners.pbs WARNING 2013-03-15 15:39:20,173 Unable to cleanup: [Errno 2] No such file or directory: '/usr/local/galaxy/galaxy-dist/database/pbs/341.ec' 10.7.10.201 - - [15/Mar/2013:15:39:22 -0500] "GET /api/histories/5a1cff6882ddb5b2 HTTP/1.0"
Re: [galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
Jorrit, Thank you for reporting this issue, I've committed a fix in the default branch at 9077:62bd6fe0e9aa, and it will be updated in stable at our next release. --Dave B. On 3/13/13 18:11:27.000, jorrit poelen wrote: To add some information to my earlier post - It seems that the remote repository is updated, but the commandline returns a confusing abort message. Trying on a private test toolshed, I see the following in the community-webapp.log: 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET /repos/testjorrit/testrepo?cmd=capabilities HTTP/1.1" 200 130 "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET /repos/testjorrit/testrepo?cmd=batch HTTP/1.1" 200 43 "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1" 200 48 "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1" 200 48 "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:19 +] "GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1" 200 - "-" "mercurial/proto-1.0" 173.11.123.170 - testjorrit [13/Mar/2013:22:08:23 +] "POST /repos/testjorrit/testrepo?cmd=unbundle HTTP/1.1" 200 - "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:24 +] "GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1" 200 58 "-" "mercurial/proto-1.0" 173.11.123.170 - - [13/Mar/2013:22:08:24 +] "POST /repos/testjorrit/testrepo?cmd=pushkey HTTP/1.1" 401 - "-" "mercurial/proto-1.0" Which seems to indicate that most http get/post succeed, but the last one, pushkey, fails to authenticate. I am wondering whether I am the only one seeing this confusing behaviour and what I can do to stop this from happening. thx, -jorrit On Mar 13, 2013, at 2:37 PM, jorrit poelen wrote: Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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] Conditional tool options based on input file format?
On Fri, Mar 15, 2013 at 2:51 PM, John Chilton wrote: > Hey Peter, > > I wonder if it is better to ask the user what type they would like to > select and then have the input param inside the conditional. That is doable now, but I'm not sure it is optimal for usability. > My > concern about you approach is who it would interplay with workflows. > Say you build a workflow that processes XML files with one input, say > an XML file. If that input param had let you select multiple formats > (format="tabular,xml"), then I believe the workflow input will as well > even though the options as well, even though the workflow would not be > valid for the other types. > > -John Good point... I'm not sure what the workflow would currently allow here - just XML, or both tabular and XML. I guess a side effect of my format specific options would be that a workflow using such a tool should be locked to just the one format. Is that such a bad thing? 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/
Re: [galaxy-dev] Conditional tool options based on input file format?
Hey Peter, I wonder if it is better to ask the user what type they would like to select and then have the input param inside the conditional. My concern about you approach is who it would interplay with workflows. Say you build a workflow that processes XML files with one input, say an XML file. If that input param had let you select multiple formats (format="tabular,xml"), then I believe the workflow input will as well even though the options as well, even though the workflow would not be valid for the other types. -John On Fri, Mar 15, 2013 at 9:43 AM, Peter Cock wrote: > On Wed, Apr 18, 2012 at 12:01 PM, Peter Cock > wrote: >> Dear all, >> >> I've looked over the wiki and as far as I can see, 'when' tags used inside >> 'conditional' tags only work on another input variable's values. >> >> I would like to be able to do is a conditional based on the file format >> of an input file. For instance, a tool might take XML or tabular files, >> and need to show additional parameters for one input type but not the >> other. >> >> Does this enhancement idea seem useful? >> >> Peter > > Hello again, > > I'd still like to be able to show different tool parameters for different > input file formats - is anyone else interested in using or working on > this? > > Thanks, > > 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/ ___ 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] Conditional tool options based on input file format?
Hi Peter, > > I've looked over the wiki and as far as I can see, 'when' tags used inside > > 'conditional' tags only work on another input variable's values. > > > > I would like to be able to do is a conditional based on the file format > > of an input file. For instance, a tool might take XML or tabular files, > > and need to show additional parameters for one input type but not the > > other. > > > > Does this enhancement idea seem useful? > > > > Peter > > Hello again, > > I'd still like to be able to show different tool parameters for different > input file formats - is anyone else interested in using or working on > this? Yes! Im using that for a few of my tools, but currently the user need to choose the file format, that is suboptimal :( But i have no time for a proper solution, a few of your reviews are also waiting ... :( Sorry, Bjoern > Thanks, > > 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/ ___ 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] Conditional tool options based on input file format?
On Wed, Apr 18, 2012 at 12:01 PM, Peter Cock wrote: > Dear all, > > I've looked over the wiki and as far as I can see, 'when' tags used inside > 'conditional' tags only work on another input variable's values. > > I would like to be able to do is a conditional based on the file format > of an input file. For instance, a tool might take XML or tabular files, > and need to show additional parameters for one input type but not the > other. > > Does this enhancement idea seem useful? > > Peter Hello again, I'd still like to be able to show different tool parameters for different input file formats - is anyone else interested in using or working on this? Thanks, 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/
[galaxy-dev] Issue with viz of mapped data in Trackster
Hi all, Since the last updata of Galaxy, I was not able anymore to view newly added tracks to existing or newly created visualisations. In the webhandler, I have traced down this error: 193.191.128.2 - - [14/Mar/2013:11:02:13 +0200] "GET /api/datasets/407a09c0b5976b4e?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr4 HTTP/1.1" 500 - "http://galaxy.bits.vib.be/visualization/trackster?id=1ec2297821c7f2cb"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+" galaxy.webapps.galaxy.api.datasets ERROR 2013-03-14 11:03:02,409 Error in dataset API at listing contents: : Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 41, in show is_true( kwd.get( 'retry', False ) ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 814, in has_data st = summary_tree_from_file( self.converted_dataset.file_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py", line 114, in summary_tree_from_file st = cPickle.load( st_file ) EOFError Thanks for any assistance, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] Tool config for accordian-like subpanels?
Hi Ted, this would fit well as another feature for the new section grouping construct I'm going to implement one of these days. There is a trello car if you want to add a comment, I'll update the spec. -- jt (composed on my phone) On Mar 13, 2013, at 3:01 PM, Ted Goldstein wrote: > I have a single tool with several different major modes. Each mode has its > own uniques group of options that can be managed separately. Rathan than make > five different tools, I would like to put it together and simply have the > user interface show just the options for the selected mode. People do this > in web pages sometimes using Jquery "Accordian" tabs. > > Is there any support to have something like Jquery accordion grouping of > options? see that the drill down , but it is only used for setting binary > options. > > Thanks,Ted > ___ > 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/
[galaxy-dev] Login issue with apache proxy
Hello all, I recently installed a galaxy server in my lab with Apache proxy and load balancing. Just after the installation, I was able to login correctly and everything seemed to work fine. The day after, login issues appeared. Login from the login page is not possible while login from other page seems to wrok even if the main page display the same login menu (Login/register) and not the user options. I have searched in the mailing list archive and saw some related issues linked to caching in browser. So I have tried to clear several time all my history (cookies and others) but the login issue remains. I am using firefox because I know Chrome causes some other issues. I have installed Galaxy from the last tarball obtained from thelink in the page http://wiki.galaxyproject.org/Admin/Get%20Galaxy Can somebody tell me how can I solve this issue? Thanks regards Lionel ___ 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/
