Tool XML Question - using option/from_file name in 'label'
by Assaf Gordon
Hello,
I have a tool which has an <option> with 'from_file' attribute:
...
<param name="database" type="select" label="Mapping Database">
<options from_file="mapping_filter_databases.txt">
<column name="name" index="1"/>
<column name="value" index="0"/>
</options>
</param>
...
I want to use the database name in the label of the output dataset:
<outputs>
<data format="fasta"
name="output_mapped" label="Mappers of $input.name to $database" />
</outputs>
The '$database' variables is replaced with the database's filename (the
'value' column). I'd like it to be the 'name' column, but using
"$database.name" throws an runtime exception:
NotFound: cannot find 'name' while searching for 'database.name'
(full backtrace is listed below).
Is there a way to display the name instead of the value in an <option>
clause ?
Thanks!
Gordon.
URL: http://tango/tool_runner/index
File
'build/bdist.solaris-2.11-i86pc/egg/weberror/evalexception/middleware.py',
line 364 in respond
File 'build/bdist.solaris-2.11-i86pc/egg/paste/debug/prints.py', line 98
in __call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/wsgilib.py', line 539 in
intercept_output
File 'build/bdist.solaris-2.11-i86pc/egg/beaker/session.py', line 103 in
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/recursive.py', line 80 in
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/httpexceptions.py', line
632 in __call__
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/base.py',
line 126 in __call__
body = method( trans, **kwargs )
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/controllers/tool_runner.py',
line 45 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py',
line 708 in handle_input
out_data = self.execute( trans, incoming=params )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py',
line 915 in execute
return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid )
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/actions/__init__.py',
line 159 in execute
data.name = fill_template( output.label, context=params )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/util/template.py', line
9 in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File '<string>', line 28 in respond
NotFound: cannot find 'name' while searching for 'database.name'
13 years, 5 months
Workflow improvement requests (long)
by Assaf Gordon
Dear all,
Recently, users (of our local galaxy server) started using workflows,
and are very pleased. However, as workflows get more complicated, it
gets harder to track the input and output of the workflows.
I'd like to share an example, to illustrate the problems that we encounter.
The workflow (pictured in the attached 'workflow.jpg') takes 4 input
datasets, and produces 4 output datasets.
The first problem is that there's no way to differentiate between the
input datasets (They appear simply as "Step 1: Input dataset", "Step 2:
Input Dataset", etc). Since each dataset has a specific role, I've had
to print the workflow and give the users instructions as to which
dataset (in their history) goes into what dataset. (see attached
'crosstab_workflow_input_datasets.jpg').
The second problem is that whenever I change something in the workflow
and save it - the order of the dataset change!
So what was once dataset 1, can now be dataset 2,3 or 4.
Users have no way of knowing this... (keen users might notice the the
description of the first tool changed from "Output dataset 'output' from
step 2" to "Output dataset' output' from step 4" - but this is very
obscure...).
The third problem is that once the workflow completes, the resulting
dataset have cryptic names such as "Join two queries on Data 10 and Data
2". Since "Data 10" is "Awk on Data 8" and data-8 is "Generic
Annotations on Data 7 and Data 1" and data-7 is "Intersect data 1 and
data 6" - it gets a bit hard to know what's going on. (see attached
'crosstab_history.png').
For the meantime, I've simply gave written instructions on what each
dataset means (see attached 'crosstab_workflow_dataset_explnanations.jpg).
If I may suggest a feature - it would be great if I could name a dataset
inside the workflow. Instead of naming it "Input dataset" I could give
it a descriptive name, so even if the order of the input datasets
changes, users will know which dataset goes into which input.
Regarding the output dataset names, the 'label' option in the tools' XML
is a good start, but still creates very long, hard-to-understand names.
Another great feature would be the possibility to add an 'output label'
for each step in the workflow.
Regardless of the above, I'd like to say (once again) that Galaxy is a
great tool, and workflows are really cool - we have several long
workflows which do wonderful things.
Thanks for reading so far,
Gordon.
13 years, 5 months
Moving and processing large files: will a local installation help?
by Johannes Waage
Hi all,
I'm moving quite a lot of large files (>2 GB) between Galaxy and our local
network for processing (mainly sequence retrieval and interval processing).
This is a tad on the slow side; will a local installation of Galaxy help
improve the speed? Or will the gain in transfer speed be lost in increased
processing time (I do not plan on installing on a cluster)?
Thankyou in advance,
Johannes Waage,
Uni. of Copenhagen, Denmark
13 years, 5 months
prevent tool escaping input
by James Casbon
Hi,
how can I prevent a tool escaping the input to a tool's text field?
For example, if I put a [ in the text field, I see it in the console
as __ob__ on the command line?
thanks,
James
13 years, 5 months
Re: [galaxy-user] Workflow improvement requests
by Eric Schauberger
I second the request on sometype of labeling system for the workflow--at
least a numbering system. I made a workflow with many inputs, then when I
tried it out I realized that the first input that I was joining with the
second input was intermixed and unidentifable. Then I realized that the
inputs are ordered in their creation order and not anytype of order how they
are placed. Since I was making many, many, inputs I simply made a bunch of
them at once and didn't keep track of their order or where I put them.
Thank again for the sweet tool.
Eric
On Tue, Nov 25, 2008 at 12:00 PM, <galaxy-user-request(a)bx.psu.edu> wrote:
> Send galaxy-user mailing list submissions to
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> Today's Topics:
>
> 1. Re: Workflow improvement requests (long) (James Casbon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 25 Nov 2008 11:14:14 +0000
> From: "James Casbon" <casbon(a)gmail.com>
> Subject: Re: [galaxy-user] Workflow improvement requests (long)
> To: "Assaf Gordon" <gordon(a)cshl.edu>
> Cc: galaxy-user(a)bx.psu.edu
> Message-ID:
> <15d850bd0811250314h4075f1edld1ea2dc6b1a76fef(a)mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Everyone,
>
> Slightly off-topic, but I see you have awk in your workflows. Awk
> could work on text, tabular, and other formats but I'd rather not
> define a new tool for each input type.
>
> Is there a way to define a tool which accepts more any type of input?
> It should ideally preserve the format in the output as well.
>
> thanks,
> James
>
> 2008/11/14 Assaf Gordon <gordon(a)cshl.edu>:
> > Dear all,
> >
> > Recently, users (of our local galaxy server) started using workflows, and
> > are very pleased. However, as workflows get more complicated, it gets
> harder
> > to track the input and output of the workflows.
> >
> > I'd like to share an example, to illustrate the problems that we
> encounter.
> >
> > The workflow (pictured in the attached 'workflow.jpg') takes 4 input
> > datasets, and produces 4 output datasets.
> >
> > The first problem is that there's no way to differentiate between the
> input
> > datasets (They appear simply as "Step 1: Input dataset", "Step 2: Input
> > Dataset", etc). Since each dataset has a specific role, I've had to print
> > the workflow and give the users instructions as to which dataset (in
> their
> > history) goes into what dataset. (see attached
> > 'crosstab_workflow_input_datasets.jpg').
> >
> > The second problem is that whenever I change something in the workflow
> and
> > save it - the order of the dataset change!
> > So what was once dataset 1, can now be dataset 2,3 or 4.
> > Users have no way of knowing this... (keen users might notice the the
> > description of the first tool changed from "Output dataset 'output' from
> > step 2" to "Output dataset' output' from step 4" - but this is very
> > obscure...).
> >
> > The third problem is that once the workflow completes, the resulting
> dataset
> > have cryptic names such as "Join two queries on Data 10 and Data 2".
> Since
> > "Data 10" is "Awk on Data 8" and data-8 is "Generic Annotations on Data 7
> > and Data 1" and data-7 is "Intersect data 1 and data 6" - it gets a bit
> hard
> > to know what's going on. (see attached 'crosstab_history.png').
> >
> > For the meantime, I've simply gave written instructions on what each
> dataset
> > means (see attached 'crosstab_workflow_dataset_explnanations.jpg).
> >
> >
> > If I may suggest a feature - it would be great if I could name a dataset
> > inside the workflow. Instead of naming it "Input dataset" I could give it
> a
> > descriptive name, so even if the order of the input datasets changes,
> users
> > will know which dataset goes into which input.
> >
> > Regarding the output dataset names, the 'label' option in the tools' XML
> is
> > a good start, but still creates very long, hard-to-understand names.
> > Another great feature would be the possibility to add an 'output label'
> > for each step in the workflow.
> >
> >
> > Regardless of the above, I'd like to say (once again) that Galaxy is a
> great
> > tool, and workflows are really cool - we have several long workflows
> which
> > do wonderful things.
> >
> >
> > Thanks for reading so far,
> > Gordon.
> >
> >
> > _______________________________________________
> > galaxy-user mailing list
> > galaxy-user(a)bx.psu.edu
> > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
> >
> >
>
>
> ------------------------------
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user(a)bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
>
> End of galaxy-user Digest, Vol 29, Issue 16
> *******************************************
>
--
________________________________________________________
Eric M Schauberger
Physician Scientist Training Program (DO/PhD)
Genetics Program
Ewart Lab
MSU College of Osteopathic Medicine (MSUCOM)
Email: Schaube2(a)msu.edu
Skype: Emschaub
See my availability: http://www.timebridge.com/mytime/eschauberger
__________________________________________________________
13 years, 5 months
Re: [galaxy-user] galaxy-user Digest, Vol 29, Issue 13
by Ross
AFAIK, both $userId (the user numeric id) and $userEmail are added to
the parameters in jobs/__init__.py, so should work...
On Thu, Nov 20, 2008 at 12:00 PM, <galaxy-user-request(a)bx.psu.edu> wrote:
> Date: Wed, 19 Nov 2008 13:45:24 -0500
> From: Assaf Gordon <gordon(a)cshl.edu>
> Subject: [galaxy-user] Using user name in a tool's XML
> To: galaxy-user(a)bx.psu.edu
> Message-ID: <49245EC4.7020402(a)cshl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
> Is it possible to access the user name inside a tool's XML configuration
> file ?
>
> I want to pass the user name (the user who executed the job) as an
> argument to the tool. Is there such a variable?
>
> Something like:
>
> <tool id="mytool" name="foobar">
> <command>mytool.sh --file $input --title $input.name --user
> $galaxy_user</command>
> ...
> ...
--
Ross Lazarus, Associate Professor, DACP, Harvard Medical School.
Director of Bioinformatics, Channing Laboratory, BWH
181 Longwood Ave., Boston MA 02115, USA.
13 years, 6 months
Using user name in a tool's XML
by Assaf Gordon
Hello,
Is it possible to access the user name inside a tool's XML configuration
file ?
I want to pass the user name (the user who executed the job) as an
argument to the tool. Is there such a variable?
Something like:
<tool id="mytool" name="foobar">
<command>mytool.sh --file $input --title $input.name --user
$galaxy_user</command>
...
...
Thanks,
Gordon
13 years, 6 months
file conversion for viewing
by James D Cavalcoli
This is probably a 'newbie' question, but after many years, I'm getting
caught up in sequence assembly analysis again.
I've been looking around for a way to view *.ace file in a genome browser
such as the UCSC or IGV? Is there any straightforward way to view
assemblies from Illumina or 454 reads which are in *.ace format in the .bed
or .wig formats?
Thanks in advance!
Jim Cavalcoli
Center for Computational Medicine and Biology,
University of Michigan
13 years, 6 months
Running development and live servers side-by-side
by Chris Cole
What is the best way to work with development and live versions of
Galaxy concurrently and being able to have access to the same data (e.g.
user histories)?
Currently, I'm trying to run two instances of galaxy at the same time
using the same MySQL database back-end and pointing to the same user
files (via softlinks). Does this way madness lie? Although, it does seem
to be working...
I'm asking this because if we do go down the route of deploying Galaxy
here, we'd like to be able to be able to test new tools without
constantly having to restart the server and annoy the users.
Cheers,
Chris
13 years, 6 months
Megablast wrapper
by Henrikki Almusa
Hi,
Just wanted to let you know that I had some problems with using the
Megablast wrapper in the 'tools/metag' directory. I put the tool to run
a sge cluster, but ran into problem. Blast didn't create any output at
all but reported successful run in galaxy website. The output and error
files were empty (outside of output file having the commandline to be
executed).
The problem was that megablast kept on segfaulting in the cluster. After
testing the blast command manually (from which I removed the '-a 8'
option without thinking about that) it run without problems. Finally I
realised this and removed the option '-a 8' from the wrapper and got a
correct result into galaxy as well. The cluster that I use here has 2
cores on each node.
Regards,
--
Henrikki Almusa
13 years, 6 months
