Hello Benoît,
I remember seeing projects trying to do something similar (store workflows
internally and execute on Galaxy), like http://refinery-platform.org/, so
it could be useful to take a look there too. I've been trying to do
something similar but with the Java interface to the Galaxy API
ht
Dear Benoît Meilhac,
In my plugin, I would have to import the workflow, then run it with inputs
> listed in the executable command line, and after a successful execution, I
> would have to retrieve the outputs generated, then delete the created
> workflow and any files related that exist.
The in
Dear Sir or Madam,
I am working for the University of Westminster on the ER-Flow project
(http://www.erflow.eu/home). I'm currently investigating a way to use the
galaxy workflow engine with a command line interface in order to support it
within our project.
The idea would be to develop a plugi
Sorry for the late response.
Thanks for your help.
On Wed, Jan 4, 2012 at 2:32 PM, Carlos Borroto wrote:
> On Wed, Jan 4, 2012 at 2:25 PM, Ryan wrote:
> > On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad
> wrote:
> >>
> >> Usha:
> >>
> >> Galaxy is essentially a wrapper around other command li
t; Brad Langhorst
> > New England Biolabs
> > langho...@neb.com
> >
> >
> >
> > From: Ryan
> > Date: Wed, 4 Jan 2012 14:25:44 -0500
> > To: Brad Langhorst
> > Cc: Usha Reddy , "galaxy-...@bx.psu.edu" <
> galaxy-...@bx.psu.edu>
>
Ryan
> Date: Wed, 4 Jan 2012 14:25:44 -0500
> To: Brad Langhorst
> Cc: Usha Reddy , "galaxy-...@bx.psu.edu"
>
> Subject: Re: [galaxy-dev] galaxy command line
>
> On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad wrote:
>> Usha:
>>
>> Galaxy is essenti
sha Reddy mailto:usha.reddy...@gmail.com>>,
"galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>"
mailto:galaxy-...@bx.psu.edu>>
Subject: Re: [galaxy-dev] galaxy command line
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad
mailto:langho...@neb.com>> wrote:
Ush
On Wed, Jan 4, 2012 at 2:25 PM, Ryan wrote:
> On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad wrote:
>>
>> Usha:
>>
>> Galaxy is essentially a wrapper around other command line tools.
>> So, while you could probably extract some of its pieces to run on the
>> command line, I don't know why you w
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad wrote:
> Usha:
>
> Galaxy is essentially a wrapper around other command line tools.
> So, while you could probably extract some of its pieces to run on the
> command line, I don't know why you would want to.
>
>
I would argue it would be benefic
reddy...@gmail.com>>
Date: Tue, 3 Jan 2012 13:07:25 -0500
To: mailto:galaxy-...@bx.psu.edu>>
Subject: [galaxy-dev] galaxy command line
Galaxy is a web based platform. Can Galaxy be run as a command line tool?
Thanks,
Usha ___ Please kee
Galaxy is a web based platform. Can Galaxy be run as a command line tool?
Thanks,
Usha
___
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Hi
Looks like the argument list should be longer.
Marina
I am forwarding your question to the Galaxy Dev list, which is the
best place to ask this type of question.
Dave C
On Tue, Dec 28, 2010 at 11:27 PM, wrote:
Hi,
I am trying to run locally the fastq_groomer.py
My command:
python /usr/l
Hi Gilgi,
If you read the beginning of the fastq_groomer.py file, you can see that
this script takes 5 mandatory arguments (input_filename, input_type,
output_filename, output_type, force_quality_encoding) and an optional
argument (summarize_input):
input_filename = sys.argv[1]
inpu
There are two more parameters that the fastq groomer requires,
force_quality_encoding and summarize_input.
Try this:
python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt
illumina seq_out.txt sanger None summarize_input
force_quality_encoding can be 'None', 'ascii', or 'deci
I am forwarding your question to the Galaxy Dev list, which is the
best place to ask this type of question.
Dave C
On Tue, Dec 28, 2010 at 11:27 PM, wrote:
>
> Hi,
>
> I am trying to run locally the fastq_groomer.py
>
> My command:
>
> python /usr/local/src/galaxy-central/tools/fastq/fastq_groo
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