[galaxy-dev] tool form in remote mode
Hi, Galaxy Developers, I'm trying to integrate galaxy into another system and using its remote mode. While I still want to use the html of the tool form generated by galaxy. I know that I cannot get the html through the API. So I want to write some code to call the tool package code directly. But I can't find the documentation about the tool package and don't know where to start with. Can any one help me? Any help will be appreciated! Best, Yanbo ___ 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] workflow_execute_parameters.py
Dear Dannon,
when the parameter (that I need to fix) is 'set at runtime', the value
that it gets is: __lt__galaxy.tools.parameters.basic.RuntimeValue
python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db
'14=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test'
the parameter prefix needs to be set at the value test (I tried
without the quotes also)
---
Here is what you asked for:
{
id: f2db41e1fa331b3e,
inputs: {
14: {
label: input Dataset,
value:
}
},
model_class: StoredWorkflow,
name: export_WF,
published: false,
steps: {
14: {
id: 14,
input_steps: {},
tool_id: null,
type: data_input
},
15: {
id: 15,
input_steps: {
inputs_0|input: {
source_step: 14,
step_output: output
}
},
tool_id: export_sbw,
type: tool
}
},
tags: [],
url: /api/workflows/f2db41e1fa331b3e
}
as you can see, the parameter called prefix, is not there.
Thank you for your help
--
Olivia
Le 25/04/14 19:49, Dannon Baker a écrit :
Olivia,
Is the parameter set to 'set at runtime' when you view the workflow in
the editor? Could you send me the workflow json (just the
http://127.0.0.1:8080/api/workflows/workflow_id/ bit)?
-Dannon
On Fri, Apr 25, 2014 at 5:26 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr mailto:olivia.dopp...@pasteur.fr wrote:
Dear Dannon,
Thank you for your answer, it works better now that I know the
steps ID for my workflow.
I have another question though.
The second step of my WF uses a parameter input named prefix. I
really need to specify it when I launch the WF using the API.
When i display the WF using the url you gave me, the parameters
prefix, is not there and when I use this in my command line, the
specified Value is not read by Galaxy.
python workflow_execute_parameters.py
43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e
a799d38679e985db '10=hda=52ea4fd71e9f7c3f'
'param=export_sbw=prefix=test'
Could you help me on that ? How do I give a value to a parameter
if it does not appear in the WF description ??
Thanks in advance,
--
Olivia
Le 23/04/14 18:40, Dannon Baker a écrit :
Hi Olivia!
It's probably talking about the workflowstep object with
identifier 8. If you request the description of this workflow
via the API (http://yourgalaxyinstance.org/api/workflows/the id
of this workflow), you'll be given the exact step identifiers
to use. In other words, unless this is the first workflow ever
created on a brand new galaxy instance, your step ids will not be
0 and 1.
-Dannon
On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr mailto:olivia.dopp...@pasteur.fr wrote:
Dear developpers,
I'm trying to launch a small workflow using the api script
workflow_execute_parameters.py
I have 2 steps: the input data step and a second step which
needs a parameter called prefix.
The workflow is attached to this email.
I get an error on the parameters inputs which asks me to
specify information about an 8th step (which does not exist)
Is there a test case available to use this script ?
Please keep me informed on that.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
___
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/
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
___
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] an uploading problem
HI, I've been trying to upload a bigwig file for at least 2 days now, but it doesn't upload (no error message though). What to do? Would it help to delete some other heavy files? Thanks Dana -- Dana Avrahami-Tzfati, Ph.D. Postdoctoral Fellow Kaestner Lab Dept. of Genetics Institute of Diabetes, Obesity Metabolism University of Pennsylvania School of Medicine Philadelphia Phone: 484-343-7598 Fax: 215-573-2326 email: dan...@mail.med.upenn.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] disk space error
I hope this is the correct place to submit this problem. I'm using Galaxy main and there appears to be an error in the calculation of the disk space I'm using. I was using 7% of the allowed 250GB and then ran a series of jobs that produced files of ~200GB each. I deleted all of those jobs (most of which hadn't started execution), and then went back and deleted each one permanently, and my usage went back down to 7%. I requested a few jobs which should have produced smaller files, and they paused straight after starting. When I checked back, I was suddenly apparently using 597GB of disk space despite the size on disk of each of my histories adding up to 25GB. I've permanently deleted everything created since the initial problems and still my usage is recorded as 597GB. On Trello, there's a bug report that currently running jobs in deleted histories don't stop execution. Possibly my problem is due to the same bug, despite all the tasks being purged and not recoverable. I cannot do anything on Galaxy until my recorded disk space usage dips back under 100%. Can anyone help? Many thanks, Jessica Gaunt ___ 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 with get data function
Hello, I contact you because I need some help with my galaxy account. I can't use functionget data for 3 days. This number error appears : GURU MEDITATION: #18e5fee395824913a0f27ff2063a0ead The adress mail noemie.delr...@gustaveroussy.fr is used for log in on server. Thank you. Best regards, Noémie Delrieu ___ 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] Galaxy Error Message
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated. The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
___
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] Galaxy Error Message
Please keep all replies on the list by using reply all
well, what happens if you run
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running
as), replacing $genedata $pathwayid $species $output with meaningful
arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
command
interpreter=bashRscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
/command
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out now.
thanks,
Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in
the tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated. The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
_
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/
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] Galaxy Error Message
On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 04/28/2014 03:32 PM, Bradley Belfiore wrote: Thank you for your quick response, my command tag is: command interpreter=bashRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command So I believe Im calling R via the Rscript_wrapper.sh? There is a problem with the XML closing of the command tag. You appear to have a bash script calling an R script. Try: command interpreter=bashRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command Or, if you mark your shell script as executable and include the #!/bin/bash line, you don't need the interpreter setting: commandRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command Also, you should be able to use relative paths rather than that absolute path (which is not portable). 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] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?
Hi Dave, This problem persists (or has reoccured), This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Did you discover anymore last week? Sorry for the lag in my reply, I busy with other things. Thanks, Peter On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation. --Dave B. On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote: Hi all, This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration? http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 Regards, Peter On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a new wrapper for samtools depad (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency (status Error) event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtoolspackage 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies/- installation of these additional repositories is required/ Tool shed NameOwner Changeset revision testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939 ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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] Galaxy Error Message
The initial error now seems to be taken care of and now am getting this
message on attempting to run tool:
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 153, in prepare_job
job_wrapper.runner_command_line = self.build_command_line(
job_wrapper, include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs )
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 176, in build_command_line
return build_command( self, job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs )
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py,
line 19, in build_command
commands_builder = CommandsBuilder(job_wrapper.get_command_line())
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py,
line 109, in __init__
commands = initial_command.rstrip(; )
AttributeError: 'NoneType' object has no attribute 'rstrip'
On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Please keep all replies on the list by using reply all
well, what happens if you run
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running as),
replacing $genedata $pathwayid $species $output with meaningful arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
command
interpreter=bashRscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
/command
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out
now.
thanks,
Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in
the tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R
script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a
Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated.
The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
_
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/__search/mailinglists/
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Error Message
Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch - tryCatchList - tryCatchOne - Anonymous In addition: Warning message: In file(file, rt) : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On 04/28/2014 03:58 PM, Bradley Belfiore wrote: The initial error now seems to be taken care of and now am getting this message on attempting to run tool: File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 109, in __init__ commands = initial_command.rstrip(; ) AttributeError: 'NoneType' object has no attribute 'rstrip' This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Error Message
So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA' Error in grep(species, pathway.id) : argument pathway.id is missing, with no default Calls: pathview - grep Execution halted On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch - tryCatchList - tryCatchOne - Anonymous In addition: Warning message: In file(file, rt) : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: On 04/28/2014 03:58 PM, Bradley Belfiore wrote: The initial error now seems to be taken care of and now am getting this message on attempting to run tool: File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 109, in __init__ commands = initial_command.rstrip(; ) AttributeError: 'NoneType' object has no attribute 'rstrip' This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
