Re: [galaxy-dev] Opening Galaxy with a specified History Name -- how to convert the clear text history id to an encrypted id?

2015-10-26 Thread rbrown1422
Good afternoon John, Your patch works great for opening Galaxy with a specific History, but one needs to know the encrypted version of the History ID. How does one obtain that, or convert the clear text version to an encrypted id? Thanks again, Bob From: John Chilton Cc:

[galaxy-dev] Error in sh manage_db.sh -c ./config/galaxy.ini upgrade

2015-11-05 Thread rbrown1422
Dear Galaxy Dev Team, We upgraded our Galaxy instance to the git repository from mercurial old Galaxy-dist to Galaxy. When running the sh manage_db.sh -c ./config/galaxy.ini upgrade we get the following error. Can you explain this error and more importantly how to correct the problem>

[galaxy-dev] Opening Galaxy with a specified History Name

2015-09-05 Thread rbrown1422
To all, I would like to open a Galaxy session programmatically (schedule Galaxy with their user name and password) and have the Galaxy session open with a history name I specify. So if there was work done previously under that history name, those output files will appear in the history

Re: [galaxy-dev] Opening Galaxy with a specified History Name

2015-09-10 Thread rbrown1422
Message -From: John Chilton <jmchil...@gmail.com>To: rbrown1422@comcast.netCc: galaxy-dev@lists.galaxyproject.orgSent: Wed, 09 Sep 2015 15:32:39 - (UTC)Subject: Re: [galaxy-dev] Opening Galaxy with a specified History Name Can you please elaborate on what will be driving thi

Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-07 Thread rbrown1422
display my heatmap when the user clicks on the eyeball after creating the history output file from the HM creation tool. Similar to how one can display an image file or csv by clicking on the eyeball. Thanks again, bob - Original Message -From: rbrown1422@comcast.netTo: Bjrn Grning

[galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-04 Thread rbrown1422
Good afternoon, I am trying create a display module for a special binary datatype. When someone requests to view the output file in the History using the eyeball it will kick off my code to create an HTML display in the Galaxy center section. I am looking at binary.py but I am not sure if

[galaxy-dev] How does one run Javascript or HTML as a tool?

2015-12-07 Thread rbrown1422
Good evening Galaxy team, Is it possible to run JavaScript or HTML as a tool or a display module? I see support for URLs, e.g. UCSC Genome Browser, but I would like to process a specific datatype to allow it to be viewed in Galaxy -- but the application is a combination of HTML and

[galaxy-dev] AssertionError: ID tag is required for a Display Application

2015-12-10 Thread rbrown1422
Dear Galaxy Team, I am trying to create my own visualization for a unique datatype but I cannot get past this error in the load. Where is the ID tag assigned for my visualization? Thanks Bob galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading display application

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? Part 2

2015-12-14 Thread rbrown1422
Bjoern > - Original Message -From: Eric Rasche <e...@tamu.edu>To: > rbrown1422@comcast.netCc: galaxy-dev <galaxy-...@lists.bx.psu.edu>Sent: Tue, > 08 Dec 2015 02:34:47 - (UTC)Subject: Re: [galaxy-dev] How does one run > Javascript or HTML as a tool?> > >

Re: [galaxy-dev] How does one run Javascript or HTML as a tool?

2015-12-12 Thread rbrown1422
t;e...@tamu.edu>To: rbrown1422@comcast.netCc: galaxy-dev <galaxy-...@lists.bx.psu.edu>Sent: Tue, 08 Dec 2015 02:34:47 - (UTC)Subject: Re: [galaxy-dev] How does one run Javascript or HTML as a tool? Hi Bob, Yes, galaxy supports output formats of HTML+JS, though the tool producing th

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

2015-12-12 Thread rbrown1422
. By clicking the visualization icon. what does it call (hopefully 1or2 above) so i can add specific code to display my datatype internal "visualization?" (preferred) in galaxy? - Original Message -From: Eric Rasche <e...@tamu.edu>To: rbrown1422@comcast.netCc: ga

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? --success

2015-12-16 Thread rbrown1422
Good morning Carl, I had to go down to the last option -- but it WORKED MD_zip Thanks, Bob - Original Message -From: Carl Eberhard <carlfeberh...@gmail.com>To: rbrown1422@comcast.netCc: Eric Rasche <e...@tamu.edu>, galaxy-dev <galaxy-...@lists.bx.psu.edu>

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

2015-12-14 Thread rbrown1422
ds( "".join( dataset.readlines() )) """ def __init__( self, dataset, **kwards ): raise NotImplementedError() super( MDA_zipDataProvider, self ).__init__( dataset, **kwargs ) My tool in tools dir Display HeatMap generated by MDAnderson HeatMap tools MDAheatmap.py $input $out_file

[galaxy-dev] How to access current user's History Id within a Mako file?

2015-12-29 Thread rbrown1422
Good morning team Maybe it would be better, and easier to pass the History ID to a mako file to access a file in the current History. Is there a Galaxy predefined item for the History ID similar to the Dataset_id that can be passed? Thanks bob - Original Message -From: Martin Čech

[galaxy-dev] how to access current user's apikey

2015-12-26 Thread rbrown1422
Good morning team, Is there a way to access the current user's API Key similar to seeing their email address via a tool's xml parameter "$__user_email__" ? Thanks, Bob___ Please keep all replies on the list by using "reply all" in your

[galaxy-dev] how does .mako access the dataset for the file it is visualizing (under config/plugin/ from the History?

2015-12-19 Thread rbrown1422
_init__( dataset, **kwargs ) My tool in tools dir Display HeatMap generated by MDAnderson HeatMap tools MDAheatmap.py $input $out_file - Original Message -From: Carl Eberhard <carlfeberh...@gmail.com>To: rbrown1422@comcast.netCc: Eric Rasche <e...@tamu.edu>, gala

Re: [galaxy-dev] how to access current user's apikey

2015-12-27 Thread rbrown1422
Good morning, I am trying to pass this info to by plugin mako that will display an output file in their history. With that info and the history data file location I can pass a URL for the file location to the tool in the mako doing the display. Tools already have access to the user email etc.

Re: [galaxy-dev] how to access current user's apikey or History Id

2015-12-28 Thread rbrown1422
Good morning Martin, Then maybe it would be better, and easier?, to pass the History ID to a mako file. Is there a galaxy predefined item for the History ID similar to the Dataset_id that can be passed? Thanks bob - Original Message -From: Martin Čech To:

[galaxy-dev] required param history_id not found in URL

2015-12-28 Thread rbrown1422
n/plugins/resource_parser.py", line 88, in parse_parameter_dictionaryraise KeyError( 'required param %s not found in URL' % ( param_name ) )KeyError: 'required param history_id not found in URL' = - Original Message -From: Martin Čech <mar...@bx.psu.edu>To: rb

[galaxy-dev] SUCCESS Re: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

2016-02-05 Thread rbrown1422
gui...@sb-roscoff.fr>To: rbrown1422@comcast.netCc: John Chilton <jmchil...@gmail.com>, galaxy-dev@lists.galaxyproject.orgSent: Fri, 05 Feb 2016 08:27:07 - (UTC)Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size Hi, Beca

[galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

2016-02-04 Thread rbrown1422
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. Rscript --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 . Why

[galaxy-dev] CANCEL request I solved it Re: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

2016-02-04 Thread rbrown1422
thanks - Original Message -From: rbrown1422@comcast.netTo: galaxy-dev <galaxy-dev@lists.galaxyproject.org>Sent: Thu, 04 Feb 2016 19:05:06 - (UTC)Subject: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size Good morning team, I have an R

Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

2016-02-04 Thread rbrown1422
John, Thanks for the great info. I got the R to work not the Rscript. However, my data files return RED even though there is data in them I am still getting R warning but no errors During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_COLLATE failed, using

[galaxy-dev] Has anyone started defining a DataSource that connect to Google Big Query outputs?

2016-02-25 Thread rbrown1422
Dear team, Has anyone started defining a DataSource that connects to Google Big Query outputs? Thanks Bob___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other

[galaxy-dev] It would be nice to know that labels can only be lowercase in format tags

2016-02-18 Thread rbrown1422
Good evening, Having wasted multiple hours it would be helpful to see in the documentation that only LOWERCASE is allowed for defining unique file extensions to link specific files output by one tool as a particular input to another tool. outgoing tool's xml Accepting tool's xml

[galaxy-dev] Galaxy drops my tenth xml tool parameter

2016-03-20 Thread rbrown1422
Good afternoon, It appears my Galaxy updated overnight and has caused issues that I am fairly certain I didn't introduce. Did something change or what did I do? 1 the Parameter $GALAXY_ROOT_DIR/tools/Heatmaps/' is not showing up see bottom where I dump parameters. 2. The repeat seems to

[galaxy-dev] Sandbox repository item says "This revision can be installed: False

2016-04-01 Thread rbrown1422
Good afternoon, I loaded a tool into the Galaxy https://testtoolshed.g2.bx.psu.edu/ toolshed. It is an xml and python module. It accepted the file fine but with the following output Sharable link to this