Re: [galaxy-dev] snpeff tool for Galaxy extra_files_path

$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 wrote: I agree with you about the inadvisable use of: input.dataset.*. I'm looking at: lib/galaxy/model/__init__.py class Dataset( o

Re: [galaxy-dev] snpeff tool for Galaxy extra_files_path

more research and get back to you. -John On Tue, Oct 14, 2014 at 6:04 AM, Jim Johnson 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_pa

[galaxy-dev] snpeff tool for Galaxy extra_files_path

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 framewor

[galaxy-dev] sqlite galaxy datatype metadata

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

Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

me locally - 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 wrote: The current code in: lib/galaxy/tools/parameters/dynamic_options.py only searches the top layer of the dict t

[galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

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 in

[galaxy-dev] Fix for need_late_validation error when running workflow with XY_Plot_1 tool

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

Re: [galaxy-dev] Tools with multiple input files, and multiple output files

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 from_work_di

Re: [galaxy-dev] WARNING:galaxy.datatypes.registry:Overriding conflicting datatype

On 2/13/14, 10:22 AM, Greg Von Kuster wrote: Hi JJ, On Feb 13, 2014, at 11:00 AM, Jim Johnson 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 metadata externally

[galaxy-dev] WARNING:galaxy.datatypes.registry:Overriding conflicting datatype

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 jo

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

On 12/4/13, 10:21 AM, Peter Cock wrote: On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock wrote: > On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning >

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

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 purp

[galaxy-dev] Patch for lib/galaxy/webapps/galaxy/api/provenance.py for optional dataset parameters

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 "/Users/jj/g

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

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 offe

Re: [galaxy-dev] Status of GATK in Galaxy

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 work

Re: [galaxy-dev] Status of GATK in Galaxy

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 ma

Re: [galaxy-dev] [galaxy-iuc] package_samtools_0_1_19 - bcftools and misc utilities

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 sam

[galaxy-dev] package_samtools_0_1_19 - bcftools and misc utilities

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 ___

[galaxy-dev] ActionInputError undefined

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

[galaxy-dev] report server failing - lib/galaxy/webapps/reports/config.py does not have attribute sentry_dsn

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 render_javascripts

Re: [galaxy-dev] igvtools

Jorge, I think that I omitted the igvtools index command because galaxy implicitly manages indexes for datasets as as defined in the datatypes_conf.xml configuration file. I could add the igvtools index command if the galaxy implicit indexing is not sufficient. Thanks, JJ On 1/24/13 9:49 AM

[galaxy-dev] Fix for SelectToolParameter rerun, workflow when multiple="true"

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 0

Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31

p I'd appreciate any pointers. Thanks, Ilya On 11/27/12 3:57 PM, "Jim Johnson" 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: &qu

Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31

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" To: "galaxy-dev@lists.bx.psu.edu" Subject: [galaxy-dev] No output from IGVtools tile M

[galaxy-dev] Fix for KeyError in templates/show_params.mako

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 '/gala

[galaxy-dev] Composite datatype output for Cuffdiff

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 generates

Re: [galaxy-dev] Error when has no value and type is float or integer

I believe you have to tag with optional="true" when omitting the value: Hi, If I have a tool wrapper with this: I get an error when I start Galaxy: galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from path: RGalaxy_test_tool/foo.xml Traceback (most recent call las

[galaxy-dev] Fix for tophat2 output filter on fusions

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 --- a/tools/ngs_rna/toph

Re: [galaxy-dev] environment variables and paths for toolshed tools

%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' in http://testtoolshed.g2.bx.psu

Re: [galaxy-dev] environment variables and paths for toolshed tools

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 tag. ( You both write access, if you want to use this for correcting my errors or debugging. ) I'm getting an error in prepare_for_install: Modu

[galaxy-dev] patch for vcf QUAL field with missing value "." in lib/galaxy/visualization/tracks/data_providers.py

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 missi

Re: [galaxy-dev] samtools view region

Jaap, I put a tool: "samtools_filter" into the galaxy toolshed http://toolshed.g2.bx.psu.edu/ that uses samtools view to filter regions. It creates symbolic links as Peter suggests. (The symbolic links are created in the job_working directory which is automatically deleted when the job i

Re: [galaxy-dev] About an additional tool

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

Re: [galaxy-dev] Error viewing BAM files in IGV

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 requ

Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?

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

Re: [galaxy-dev] Error viewing BAM files in IGV

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 = self

[galaxy-dev] HTTP Error 404 pushing to toolshed.g2.bx.psu.edu

I successfully pushed updates to my gmap and mothur toolshed repositories yesterday, but got an error when I tried to push changes to defuse. % hg push pushing to http://jjohn...@toolshed.g2.bx.psu.edu/repos/jjohnson/defuse searching for changes abort: HTTP Error 404: Not Found I also tried u

Re: [galaxy-dev] Tool shed and 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 're

Re: [galaxy-dev] Tool shed and datatypes

iit_store.xml: splicesites.iit iit_store.xml: introns.iit iit_store.xml: snps.iit snpindex.xml: gmapsnpindex snpindex.xml: gmapdb snpindex.xml: gmap_snps snpindex.xml: snps.iit Thanks, JJ On 10/18/11 10:18 AM, Greg Von Kuster wrote: Jim, Sounds great - this will be very he

Re: [galaxy-dev] Tool shed and datatypes

class would be ideal ). When 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

Re: [galaxy-dev] Tool shed and datatypes

7;t occurred to me yet? What would be the benefits and potential pitfalls? Best, Eric ________ From: galaxy-dev-boun...@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: gala

Re: [galaxy-dev] Tool shed and datatypes

Greg, It would be great if there were a way to expand upon the core datatypes using the ToolShed. Would it be possible to have a separate datatype repository within the ToolShed? Datatype name="" description="" datatype_dependencies=[] definition= The tool config could be expanded

[galaxy-dev] DeFuse gene fusion detection tool added to toolshed

I added a defuse galaxy tool to the toolshed: http://toolshed.g2.bx.psu.edu/ DeFuse is software developed by Andrew McPherson for gene fusion discovery using RNA-Seq data. http://sourceforge.net/projects/defuse/ ___ Please keep all

Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?

you can find me something to work on. ed On Fri, Jul 15, 2011 at 1:09 PM, Jim Johnson 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 underneat

Re: [galaxy-dev] galaxy-dev] format="input"

the "format_source" attribute. Note that a conditional name is not included, so 2 separate conditional blocks should not contain parameters with the same name. no yes (qual['add'] == 'yes') On 6/9/11 2:39 AM, Peter Cock wrote: On Wed, Jun 8

Re: [galaxy-dev] galaxy-dev] format="input"

ut an example in: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax On 6/8/11 3:32 PM, Peter Cock wrote: On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnson wrote: I added an attribute "format_source" (analogous to metadata_source) to the tag to deal with that kind of

Re: [galaxy-dev] galaxy-dev] format="input"

I added an attribute "format_source" (analogous to metadata_source) to the tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax qual_file != None JJ Hi everyone, I'm facing a little problem ... I have the fo

[galaxy-dev] galaxy python crash with segfault in csamtools.so when using tracks

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 investiga

Re: [galaxy-dev] importing into history from library

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

[galaxy-dev] Support for subdirs in dataset extra_files_path

Request is issue#494 https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch I'm finding that some qiime metagenomics applications build HTML results with an inherent directory structure. For some other applications, e.g. FastQC, I've been able to f

[galaxy-dev] Proposal to add a "format_source" attribute to the ToolConfig output data element

I would like to propose adding a "format_source" attribute to the tool_config output data element. This would be a backward compatible change. It is analogous to the "metadata_source" attribute. Motivation: It is often convenient to have an output dataset inherit the format of an input dat

[galaxy-dev] Barcode Splitter - added param to add selected barcode splits as datasets to history

s: tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.py Would you be interested in those changes for the main codebase? Jim Johnson University of Minnesota Supercomputing Institute 117 Pleasant St. SE Minneapolis, MN 55455 Email: j...@umn.edu ___ galaxy-dev mailing list galaxy-

Re: [galaxy-dev] histogram tool not working

I had to change the matrix to a one dimensional array: $ hg diff histogram.py diff -r ea364eb4375f tools/plotting/histogram.py --- a/tools/plotting/histogram.py Tue Feb 01 13:35:46 2011 -0500 +++ b/tools/plotting/histogram.py Tue Feb 01 16:05:42 2011 -0600 @@ -69,7 +69,8 @@