galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

Marius van den Beek

@mvdbeek

looks like there are some issues with missing certificates on that installation

mblue9

@mblue9

official python https://www.python.org/downloads/

Marius van den Beek

@mvdbeek

I see. In that case open /Applications/Python\ 3.8/Install\ Certificates.command should install the certificates, I think

alternatively pip install --upgrade certifi may help

mblue9

@mblue9

oh brill.. /Applications/Python\ 3.8/Install\ Certificates.command fixed it ..thanks a lot @mvdbeek !

Marius van den Beek

@mvdbeek

cool!

Björn Grüning

@bgruening

Hi IUC, can we have your opinion here: galaxy-iuc/standards#58

John Chilton

@jmchilton

I'm planning to remove a bunch of older, experimental commands from Planemo - I think they are all unused. bioc_conda_recipe_init, bioc_tool_init, brew, brew_env, brew_init, cwl_script, dependency_script, tool_factory - let me know if there any objections to any of these being removed.

galaxyproject/planemo#1043

Nicola Soranzo

@nsoranzo

:+1: to a cleanup

Björn Grüning

@bgruening

Please, aggressive cleanup is good. Maybe also hide a few commands from the default help and offer an extendes help?

John Chilton

@jmchilton

I do want to hide more commands from help also - that has been on my todo list for a while.

It is meant to be useful - not overwhelming :)

Björn Grüning

@bgruening

:+1:

jhl667

@jhl667

#for $num, $txt in enumerate($optional.partition_type_rpt)
#if $txt.partition_type
--partition-type '$txt.partition_type'
#end if
#end for

Have this Cheetah code for a repeat element with one param
I am trying to provide a filter on an output element, based on the string that is contained within partition_type
This is what I'm doing now:

<filter>'sample' in [str(x[1].partition_type) for x in list(enumerate(optional['partition_type_rpt']))]</filter>

I've tried lots of things, nothing seems to be doing what I want

jhl667

@jhl667

nvm, the above should be

<filter>'sample' in [x[1]['partition_type'] for x in list(enumerate(optional['partition_type_rpt']))]</filter>

too much coding today I think :-/

pvanheus

@pvanheus

Hi there - I am trying to do a conda install of planemo 0.70 but it seems to be stuck on Python 2.7 - does anyone have a python 3 + planemo 0.70 environment working? and if so how did you get it working?

Björn Grüning

@bgruening

I use pip for planemo.

And I run it under py3k

pvanheus

@pvanheus

ok I'll try that

John Chilton

@jmchilton

In the next couple days I’m going to do a release of the first Python 3 only Planemo - that might make the conda recipe simpler - not sure

pvanheus

@pvanheus

@jmchilton thanks, I will take a look at it when it is out. One part of the conda problem is not coming from planemo but rather old builds of e.g. cwltool

Nicola Soranzo

@nsoranzo

The new Planemo release should be usable with recent cwltool.

thanks to dropping Py2

pvanheus

@pvanheus

+1 to that thanks.

pvanheus

@pvanheus

@bernt-matthias hey - I think you wrote the idba_tran wrapper. I'm having an odd problem with it - the tool tests work but when I run actually run it it gets a zero-length dataset.

as far as I can tell this is because idba tran produces a contig.fa whereas the wrapper looks for scaffold.fa

I don't understand why the tests are passing though

pvanheus

@pvanheus

ooooooh.... DEFAULT_DELTA is 10000 so sim_size is true if datasets are within 10000 bytes of each other?

next oddness - I thought that if an output was from_work_dir="blah" than it was an error if blah does not exist in the working directory. seems that is not the case

pvanheus

@pvanheus

I see @blankenberg was worrying about the opposite case: galaxyproject/galaxy#8743

pvanheus

@pvanheus

anyway, fix for idba_tran: galaxyproject/tools-iuc#3150

Robert Leach

@hepcat72

I'm stumped. Why doesn't this change the format to fasta when the when condition is met?:

      <discover_datasets pattern="__designation__" ext="txt" format="txt" directory="downloads">
        <change_format>
          <when input="output_format" value="fasta-text" attribute="ext" format="fasta" />
        </change_format>
      </discover_datasets>

John Chilton

@jmchilton

I'm pretty sure change_format is for regular outputs - not discovered datasets. You've got to either use discover_datasets and setup the extension to be detected for the file name (e.g. extension) or use normal fixed outputs with change_format

pvanheus

@pvanheus

can someone please merge: galaxyproject/tools-iuc#3150 - it has been reviewed already

Björn Grüning

@bgruening

done

thanks @pvanheus

pvanheus

@pvanheus

thanks @bgruening

question for IUC folks: metaeuk uses an odd version numbering system, so its current version is 2.ddf2742

this results in a planemo lint error because the version number of the tool (2.ddf2742+galaxy0) is not PEP 440 compliant

should I come up with a PEP440-compliant tool version or is it more important to include the underlying dependency version? I personally tend towards #2

Björn Grüning

@bgruening

I think we should switch to a pep8 compliant version

the problem is that with the next version it is no guarenteed that the new version is larger than the new one, so you might end with the old version as top-Galaxy version

John Chilton

@jmchilton

in re: bioconda/bioconda-recipes#23718 - anything I can bribe someone with to publish galaxy-tool-util-20.9.0.dev2 ? Will that work with bioconda or are dev releases not really supported? Any thoughts on whether it would be a good idea to publish Galaxy packages between releases - like 20.6.0 which will be a sort of experimental release branch until 20.9 is branched?

Robert Leach

@hepcat72

I'm pretty sure change_format is for regular outputs - not discovered datasets. You've got to either use discover_datasets and setup the extension to be detected for the file name (e.g. extension) or use normal fixed outputs with change_format

Ah. That would explain it. Unfortunately, I don't have the ability to control the extensions and they change based on input selections. I guess I'll just have to manipulate the extensions in subsequent code in <command> because the underlying tool doesn't use recognized extensions in all cases.

@jmchilton - Is this code in hicExplorer a viable work-around?

    <outputs>
        <data format='cool' name="normalize_matrix">
            <discover_datasets pattern="__name_and_ext__" directory="output"  visible="true"/>
            <change_format>
                <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
            </change_format>
        </data>
    </outputs>

Marius van den Beek

@mvdbeek

if it works, sure, that’d be fine

Björn Grüning

@bgruening

@jmchilton dev releases are an edge case. We do not encourage them in Bioconda. But if needed we can do it. The problem is that if you have not pinned planemo for example to galaxy-tool-util <=20.05 you will get the latest dev release.

Robert Leach

@hepcat72

@mvdbeek - nah, didn't work

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