galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

Dan Fornika

@dfornika

@bgruening Using the same tools, or simple tools that just create the same topology of collections?

(I guess that's not a smart question.... I can't install tools on those servers....)

Freddie Pengfei Li

@FreddieLPF

thanks for the info

So another issue here --our lab tried to install a tool from "test tool shed”, but it was cloning forever, and we checked all the parameters in the galaxy.yml, still not working. any idea?

Björn Grüning

@bgruening

use tools from the main tool shed ;)

Not sure the test tool shed contains good data.

@dfornika yeah just check the topology

Freddie Pengfei Li

@FreddieLPF

got it, thx

Dan Fornika

@dfornika

@bgruening I've created a couple tabular datasets. Can you think of any tools that take tabular data and produce a collection? I don't see any.

I'm working on usegalaxy.org.

Ajit Singh

@AjitPS

Hi, we are using the hmmalign IUC tool (to align sequences to a profile HMM) - Galaxy Version 0.1.0 in GalaxyEU and also on our own internal Galaxy instance (at Rothamsted). We (David Hughes and I) have a user who wants to use 1 of the advanced options in the tool: http://www.csb.yale.edu/userguides/seq/hmmer/docs/node18.html
Would it please be possible to modify the galaxy tool wrapper/conda to include this? David informed me that it needs:
• a dropdown to select “advanced/expert options”; a second dropdown to choose between “mapali” and “withali”,
• input box to select an alignment file from the history; and then use that to launch the job with either parameter.
thanks.

Björn Grüning

@bgruening

@AjitPS sure this is possible. Do you want to work on this? Not sure when we have time.

I think the tool in question is here: https://github.com/galaxyproject/tools-iuc/blob/master/tools/hmmer3/hmmalign.xml

Ajit Singh

@AjitPS

thanks @bgruening , I'll have a look :)

Freddie Pengfei Li

@FreddieLPF

Hi, is it possible that we have database(web) to trigger Galaxy?

and how does our database know where the tools&workflows are?

Simon BENATEAU

@sbenateau

Dear all,

I am trying to combine sections, repeat and conditional and I am a bit lost with my variables.
Here is a "simplified" version of my code.
And here the full version:
https://github.com/65MO/Galaxy-Bricks/blob/master/tools/ggplot2/ggplot_all.xml

macro.xml

<inputs>
    <section name="mainOps" title="Main graph options" expanded="true">
        <repeat name="primaryLayer" title="Primary layer">
            <conditional name="primaryLayerType">
                <param name="layerType" type="select" label="Type of layer to plot" >
                    <option value="points">Points (default)</option>
                    <option value="errorbars">Error bars</option>
                </param>
                <when value="errorbars">
                    <param name="yminErr" label="Mininum value for error" type="data_column" data_ref="input1"/>
                </when>
            </conditional>
        </repeat>
    </section>
</inputs>

I get the "layerType" like this:

#for $i, $primaryLayerNb in enumerate($mainOps.primaryLayer)
#set $layerTypeR = $primaryLayerNb.primaryLayerType.layerType

But how do I get the value of "yminErr"?

I am not sure if it is the rigth place to ask this question, please excuse me if it isn't appropriate.
Thank you very much!

Björn Grüning

@bgruening

Not tested but something like

#for $layer in $mainOPs.primaryLayer:
    #if $layer.primaryLayerType.layerType == 'errorbars'
         --yminErr   $layer.primtaryLayerType.yminErr
    #end if
#end for

Simon BENATEAU

@sbenateau

Thank you Björn for your answer! I can get the value this way but cannot assign the value to the variable.

pvanheus

@pvanheus

hello Galaxy cognescenti :) minimap2 cookbook lists a combination of options for generating a self-homology map (https://github.com/lh3/minimap2/blob/master/cookbook.md#hom-map) that includes options (-D and -P) that are not used elsewhere. I'd like to add it to the minimap2 wrapper... is it appropriate to add it as a "mode" (like the -x modes)? or should it be under advanced options?

Björn Grüning

@bgruening

@pvanheus please feel encouraged to do whatever you think is best :)

pvanheus

@pvanheus

could someone please review: galaxyproject/tools-iuc#2620

Björn Grüning

@bgruening

can we trade @pvanheus ... galaxyproject/tools-iuc#2611

@/all we need urgently help with some reviews :(

Jennifer Hillman-Jackson

@jennaj

Could anyone share the status of updating GATK (version 4?). The question was asked at Galaxy Help, I checked server, toolshed, tools-iuc repos, etc but cannot figure it out or missed it. https://help.galaxyproject.org/t/galaxy-gatk-tool/2239

Alex Ostrovsky

@astrovsky01

Could I get a review on galaxyproject/tools-iuc#2622 please?

Björn Grüning

@bgruening

@astrovsky01 done. Please also help reviewing if you have some time.

@jennaj .... @davebx knows this

pvanheus

@pvanheus

@bgruening I'll look through the PRs this morning

pvanheus

@pvanheus

looking forward to an update from @davebx on that question

Freddie Pengfei Li

@FreddieLPF

https://www.biostars.org/p/94305/

does anyone know how to find the WORKFLOW_ID and TOOL_ID_IN_GALAXY?

Dan Fornika

@dfornika

I've updated the abricate tool. Review please? galaxyproject/tools-iuc#2624

Björn Grüning

@bgruening

Done and thanks!

Nicola Soranzo

@nsoranzo

@erasche Can you add a webhook for RTD to https://github.com/galaxy-iuc/standards/settings/hooks as explained in https://docs.readthedocs.io/en/stable/webhooks.html#webhook-creation ?

The repo was still set up to use the old deprecated GitHub integration which does not work any more for RTD.

Dan Fornika

@dfornika

I'm a contributor to the IRIDA project (http://irida.ca). IRIDA uses Galaxy as a workflow engine. One of the design goals of IRIDA is to use ontologies to organize data to maximize interoperability with other systems.

I noticed that it's possible to tag galaxy tools with EDAM topic & operation terms. Would anyone be opposed to me submitting a series of pull-requests to add those tags to several tools-iuc tools?

Björn Grüning

@bgruening

@dfornika you could start with this or take it furhter

https://github.com/galaxyproject/tools-iuc/pulls?utf8=%E2%9C%93&q=is%3Apr+is%3Aopen+edam

I would :heart: to merge it!

Dan Fornika

@dfornika

Ok, I'll take a closer look at those issues and see if it would be feasible for me to contribute to them. My short-term goal is to just make sure that all of the tools used by IRIDA's core set of pipelines are tagged with EDAM terms.

But if we could have a simple way to automatically tag all tools-iuc tools, that would be a better community-wide contribution.

Björn Grüning

@bgruening

:+1:

btw. there is also now a FF plugin somewhere that translates EDAM to some readable terms

you might want to use this for reviewing

Dan Fornika

@dfornika

I had one other idea. I've searched the issues on the galaxy GitHub repo and didn't find any existing issues. Would it be possible/sensible to add EDAM tags to tool inputs and outputs?

Björn Grüning

@bgruening

This is already implicitly given

we added EDAM terms to Galaxy datasets

so FASTQ is mapping to edam_1234

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