This is likely fixed in templates/library/common/browse_library.mako in the
development source:
https://bitbucket.org/galaxy/galaxy-central/changeset/5f5dae7e7ccc
___
Please keep all replies on the list by using reply all
in your
We're getting a segfault from csamtool.so when the tracks controller is invoked:
Mar 21 17:12:14 bat4 kernel: [4080861.873724] python[14319]: segfault at
45cfb1e8 ip 7f1559865444 sp 7f155192d1b0 error 4 in
csamtools.so[7f1559837000+55000]
Anyone have advice on where to start
It went into galaxy-central:
$ hg log -pr 5082
changeset: 5082:a86e1fa82a89
user:Kanwei Li kan...@gmail.com
date:Thu Feb 17 15:35:07 2011 -0500
summary: Add a format_source attribute to the ToolConfig output data
element [JJ Johnson]. Closes #470
diff -r 885f04ae671e -r
I added an example taken from trim.seqs.xml in the Mothur metagenomics
tool_suite to:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
The following will create datasets in the history panel, setting the output data type to
be the same as that of an input dataset named by
to work on.
ed
On Fri, Jul 15, 2011 at 1:09 PM, Jim Johnson johns...@umn.edu
mailto:johns...@umn.edu wrote:
I haven't had time to work on it for a couple months.
I remember getting stuck on the output of some scripts being a HTML with a
file hierarchy underneath.
I proposed setting
...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Jim Johnson [j...@umn.edu]
Sent: Friday, October 07, 2011 2:06 PM
To: galaxy-dev@lists.bx.psu.edu
Cc: Greg Von Kuster
Subject: Re: [galaxy-dev] Tool shed and datatypes
Greg,
It would be great if there were a way to expand upon
I get them I'll add
this new feature set to my development list.
Thanks everyone for all the input on this!
Greg Von Kuster
On Oct 7, 2011, at 2:05 PM, Jim Johnson wrote:
Greg,
It would be great if there were a way to expand upon the core datatypes using
the ToolShed.
Would it be possible
Kuster wrote:
Jim,
Sounds great - this will be very helpful!
Greg
On Oct 18, 2011, at 11:03 AM, Jim Johnson wrote:
Greg,
The mothur_toolsuite in the ToolShed contains a file with added datatypes for
metagenomics (used by mothur and some by qiime):
mothur_toolsuite/mothur/lib/galaxy/datatypes
On 10/21/11 12:29 PM, James Taylor wrote:
Excerpts from Jim Johnson's message of 2011-10-21 17:13:02 +:
I put the gmap tool suite in the galaxy Tool Shed, let me know if there is
more I should do.
Awesome!
I added a requirement tag for the datatypes to the tool-configs:
% grep
Hi,
I'm seeing the same behavior. Galaxy is returning a web page rather than the
requested .bai index file for the BAM file.
In class WebApplication ( lib/galaxy/web/framework/base.py ) in __call__( self,
environ, start_response ) line 133
# Setup the transaction
trans =
them up on the
toolshed.
She will be in touch as soon as the scripts are validated a couple of times
with different datasets.
cheers...
Pat
On Dec 29, 2011, at 3:02 PM, Jim Johnson wrote:
It is easiest to generate tools for galaxy when the applications or scripts can
take arbitrarily
Nate,
John Chilton got that fixed for us. As you suggest, it involved a fix in our
proxy configuration.
JJ
On 2/1/12 9:01 AM, Nate Coraor wrote:
On Dec 19, 2011, at 12:24 PM, Jim Johnson wrote:
Hi,
I'm seeing the same behavior. Galaxy is returning a web page rather than the
requested
I put a samtools_filter tool in the toolshed that uses samtools view command. I
called the samtools view command from the command section of the tool_config and
redirected stderr to stdout to avoid having galaxy interpret it as an error. Jim
Johnson Minnesota Supercomputing Institute
The VCF format (
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
)
specifies . to represent missing values.
lib/galaxy/visualization/tracks/data_providers.py throws an float conversion error when
the qual field of a vcf file has the
Greg, Pablo,
I'm using a SnpEffect repository 'snpeff_with_dep' in
http://testtoolshed.g2.bx.psu.edu/
to test using tool_dependencies.xml with the set_environment tag.
( You both write access, if you want to use this for correcting my errors or
debugging. )
I'm getting an error in
${tool_dependency_readme_text}/pre/td/tr
+%endif
%endif
%endif
%endfor
On 9/16/12 8:48 AM, Jim Johnson wrote:
Greg, Pablo,
I'm using a SnpEffect repository 'snpeff_with_dep
The filter on the tophat2 fusions output wasn't being evaluated correctly when
settingsType is preSet since the param dict wouldn't then have an entry for
'fusion_search'
$ hg diff tools/ngs_rna/tophat2_wrapper.xml
diff -r 3f12146d6d81 tools/ngs_rna/tophat2_wrapper.xml
---
I believe you have to tag with optional=true when omitting the value:
param name=x type=integer optional=true help=the x param/
Hi,
If I have a tool wrapper with this:
param name=x type=integer help=the x param/
I get an error when I start Galaxy:
galaxy.tools ERROR 2012-09-19
Checking to see if there is any interest in including a parameter option to
select outputs for cuffdiff,
potentially including a composite output and a cummeRbund sqlite database.
Issues:
cuffdiff produces 21 output files, which is a little unwieldy in a galaxy
history.
cummeRbund
A user encountered a KeyError when clicking the View Details icon from an
older Cuffdiff history item:
File '/galaxy/PRODUCTION/database/compiled_templates/show_params.mako.py', line
106 in render_body
__M_writer(unicode( inputs_recursive(tool.inputs, params_objects, depth=1) ))
File
Ilya,
Could you send me a failing input file, and I'll try to find out what is
failing?
Thanks,
JJ
--
Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +
From: Sytchev, Ilya isytc...@hsph.harvard.edu
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
appreciate any pointers.
Thanks,
Ilya
On 11/27/12 3:57 PM, Jim Johnson johns...@umn.edu wrote:
Ilya,
Could you send me a failing input file, and I'll try to find out what is
failing?
Thanks,
JJ
--
Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +
From: Sytchev, Ilya
Fix for SelectToolParameter rerun,workflow when multiple=true
The following change allows multiple select values to be set on rerun and in
workflows. I checked that DrillDownSelectToolParameter and
ColumnListParameter stiil worked.
$ hg diff lib/galaxy/tools/parameters/basic.py
diff -r
File
'/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/base/base_panels.mako.py',
line 68 in render_body
__M_writer(unicode(self.javascripts()))
File
'/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/webapps/reports/index.mako.py',
line 104 in
I was using the quotas api to update a quota amount and got the error:
galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File /Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py, line 189, in
decorator
rval
I've had occasion to use some of the samtools misc utilities in galaxy tools.
Should those also be copied to the $INSTALL_DIR/bin when package_samtools is
installed?
Thanks,
JJ
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
On 9/17/13 7:08 AM, Bjoern Gruening wrote:
Hi JJ,
I've had occasion to use some of the samtools misc utilities in galaxy
tools.
Should those also be copied to the $INSTALL_DIR/bin when
package_samtools is installed?
Sorry, I do not get the question :(
Are you asking to enhance the existing
I pushed a copy of GATK2 from the testtoolshed to bitbucket:
https://bitbucket.org/jjohnson/gatk2
The existing tool dependency no longer makes sense with the current licensing
and access policies by Broad.
Also, much of the duplication in the individual tool wrappers could be moved to
Bjoern,
Looks good.
This page also had some info on per tool use of -nt and -nct
http://www.broadinstitute.org/gatk/guide/tagged?tag=nct
If remember correctly, GATK doesn't ignore options that don't apply, it just
does an ungraceful exit.
I not sure if I had that sorted out when I last
Peter,
It's good news that the description field is available in tabular format.
That has been the primary reason for using the xml format. The tabular format
allows use of the task parallel feature.
I think you have good default options for output format.
But, I would think we should
lib/galaxy/webapps/galaxy/api/provenance.py
throws an exception when an optional dataset parameter is None
Traceback (most recent call last):
File /Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py, line 199, in
decorator
rval = func( self, trans, *args, **kwargs)
File
On 12/2/13, 7:03 AM, Nicola Soranzo wrote:
Il 2013-12-02 13:08 Peter Cock ha scritto:
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning wrote:
Peter wrote:
But, I would think we should offer the option to get all available result
information. The multi-select checkboxes could serve that
On 12/4/13, 10:21 AM, Peter Cock wrote:
On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Sun, Dec 1, 2013 at 7:10 PM, Bjrn Grning
I now have 2 versions of snpeff installed from the toolshed on my galaxy server.
Each snpeff version includes an identical datatypes_conf.xml
The galaxy server is setting metadata externally.
When any job runs, (in may case I was running a picard tool), the following
message is written to the
On 2/13/14, 10:22 AM, Greg Von Kuster wrote:
Hi JJ,
On Feb 13, 2014, at 11:00 AM, Jim Johnson johns...@umn.edu wrote:
I now have 2 versions of snpeff installed from the toolshed on my galaxy server.
Each snpeff version includes an identical datatypes_conf.xml
The galaxy server is setting
I suggested augmenting the tool_conf syntax as part of the DataCollection
development.
To replace the need for the the multiple output determined at runtime,
I suggest being able to declare data collections within the outputs tags, and
being able to use regular expressions in the
Attempting to run a workflow with the tool XY_Plot_1 results in an error when
trying to display the workflow steps. The local dep_value variable is
undefined.
The XY_Plot_1 tool has contains a repeat with a DataToolParameter input and 2
ColumnListParameter xcol, ycol dependent on the
The current code in: lib/galaxy/tools/parameters/dynamic_options.py
only searches the top layer of the dict to find the dependency value.
A fix is provide in pull request:
#343: Need to traverse the other_value dict to find dependencies for ParamValueFilter
- can you
confirm? Any chance this also solves your other problem with the XY
plotting tool (Pull Request #336)?
-John
On Fri, Feb 28, 2014 at 12:12 PM, Jim Johnson johns...@umn.edu wrote:
The current code in: lib/galaxy/tools/parameters/dynamic_options.py
only searches the top layer of the dict
Ira,
Thanks for getting a sqlite datatype into galaxy. I was wanting to subclass a
sqlite datatype for another application: cistrome CEAS
I had made a sqlite datatype that captured a little metadata that I thought
could be useful for the display peek, and perhaps for filtering.
Is this worth
Andrew,
Thanks for investigating this. I changed the subject and sent to the galaxy dev
list.
I've had a number of tools quit working recently. Particularly tools that
inspect the extra_files_path when setting metadata, Defuse, Rsem, SnpEff.
I think there was a change in the galaxy
to you.
-John
On Tue, Oct 14, 2014 at 6:04 AM, Jim Johnson johns...@umn.edu wrote:
Andrew,
Thanks for investigating this. I changed the subject and sent to the galaxy
dev list.
I've had a number of tools quit working recently. Particularly tools that
inspect the extra_files_path when setting
with this
approach ($input.extra_files_path for inputs and $output.files_path
for outputs) as the best practices for how to reference these
directories.
-John
On Wed, Oct 15, 2014 at 11:44 AM, Jim Johnson johns...@umn.edu wrote:
I agree with you about the inadvisable use of: input.dataset
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