galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

M Bernt

@bernt-matthias

I guess implementing something that allows something like

        <test>
            <param name="sel" >
                <value>o,1</value>
                <value>o,2</value>
             </param>
            <data format="txt" name="sample"/>
        </test>

within galaxyproject/galaxy#9079 might be an option.

An alternative might be a sanitizer+mapping and to use the mapped value in the test, right?

Björn Grüning

@bgruening

@bernt-matthias you can alway put something like o_1 in the value and handle the substitution elsewhere

M Bernt

@bernt-matthias

You are right, but in the context of my "little" CTD -> tool converter .. its a wee bit more tricky :)

Marius van den Beek

@mvdbeek

There’s a new samtools version out with lots of nice new things: https://github.com/samtools/samtools/releases/tag/1.10

Can write index files during sort, sam.gz seems recommended for huge contigs, no longer considers a zero-length file to be a valid SAM file,

Nicola Soranzo

@nsoranzo

Yeah, I saw the release notes.

Marius van den Beek

@mvdbeek

Making good progress:

list of failing test is at https://mvdbeek.github.io/iuc-tool-test-results/, as usual

we also have some regressions (this is testing against the current dev, which will probably become 20.01 pretty soon), so that’s good to see as well

Dan Fornika

@dfornika

Does anyone know of a simple (one-step) way to concatenate tabular files that contain a header? (while preserving a single header line at the top but removing all others)

Aaron Petkau

@apetkau

@dfornika https://toolshed.g2.bx.psu.edu/repository?repository_id=3c30cec7c6c119ff

Dan Fornika

@dfornika

Ahhh..... I've seen that one before but forgot about it. Thanks!

Björn Grüning

@bgruening

Can we not extend the cut tool to ignore headers?

Dan Fornika

@dfornika

Which tool exactly? Is it a shed tool, or is it built-in to the main galaxy codebase?

Dan Fornika

@dfornika

Could I request a review on this PR that extends the tetyper tool to allow users to load variant profiles from tool data tables? galaxyproject/tools-iuc#2772

Lucille Delisle

@lldelisle

Dear iuc,
Is there a galaxy datatype that would be close to bedpe: https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format

M Bernt

@bernt-matthias

@lldelisle BED I guess could be easily extended https://github.com/galaxyproject/galaxy/blob/47613021c6dbe4bd4a95f1c9c10ae6dbe37e14d5/lib/galaxy/datatypes/interval.py#L378

Lucille Delisle

@lldelisle

Thx @bernt-matthias

Dan Fornika

@dfornika

Sorry to ask again, but could someone please review this PR that adds support to tetyper for loading variant profiles from tool data tables? Thanks! galaxyproject/tools-iuc#2772

Björn Grüning

@bgruening

on it @dfornika !

Greg Von Kuster

@gregvonkuster

I'm working with a lab doing research with bacterial genomes and I'm working on introducing their pipeline into Galaxy. In many cases the bacterial data consists of a combination of species, so mapping to a specific genome is tricky.

Mapping bacterial data to a referencce genome has 3 options:

the genome is known, so is selected from local cache as is often done in Galaxy
a custom reference is selected - these custom references are a composition of files, and I'm not aware if/how this is currently handled in Galaxy. For example, for the custom reference for Brucella_abortus1 consists of the following 7 files:
- Bab1_define_filter.xlsx
- Bab1_remove_from_analysis.xlsx
- NC_006932-NC_006933.fasta
- NC_006932-NC_006933.gbk
- NC_006932-NC_006933.genome
- NC_006932-NC_006933.gff
The input data is inspected to determine the optimal genome to be mapped.

Does anyone know if this is currently being done in Galaxy? I've done some searching and only found this so far https://help.galaxyproject.org/t/mapping-rna-seq-data-to-a-composite-build-of-bacterial-genomes/1443.

I can wrap the tool for Galaxy that the lab is using, but I want to make sure I'm not re-inventing the wheel.

Jennifer Hillman-Jackson

@jennaj

Could someone who knows more about the status of GATK4 wrapper dev reply to this post? I see a few in done, some in progress, but didn't find a master ticket summary -- maybe missed it? Thx! https://help.galaxyproject.org/t/galaxy-tool-wrappers-for-gatk-4/2798

M Bernt

@bernt-matthias

Do you think its good practice to list the allowed data types in a data input in the label or the help?

e.g. select tsv data sets(s)

Nicola Soranzo

@nsoranzo

:+1:

M Bernt

@bernt-matthias

Maybe the Galaxy web UI should just do this? similar to -argument.

Nicola Soranzo

@nsoranzo

That's a very good idea!

M Bernt

@bernt-matthias

galaxyproject/galaxy#9218

Anton Nekrutenko

@nekrut

Someone removed interleaved fastq input option from bwa (0.7.17) This is not good. Previous version (0.7.15) does have it

.... wait ... I think I'm crazy = its there, sorry

Björn Grüning

@bgruening

We all now that you love the interleaved format and would never remove this option ;)

M Bernt

@bernt-matthias

fancy tool dev question regarding the command cheetah code: how could one get a dictionary containing the parameter names as keys and the parameter values as values?

Wolfgang Maier

@wm75

Would https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-configfiles-inputs work for you?

M Bernt

@bernt-matthias

fancy :) might work .. I guess the json file contains the structure implied by sections and conditionals?

Wolfgang Maier

@wm75

I guess so, but I've never tried it myself

Slugger70

@Slugger70

Is there any reason that linting is taking so long on Travis? PR#2795 (Build #10920) linting has been running for over 20 minutes. Even though the output say that the build exited with 0.

Björn Grüning

@bgruening

mh, testing is finished already

Nicola Soranzo

@nsoranzo

I think it's a refresh issue on Travis, the build is green now.

I've seen the same today on another unrelated project using TravisCI.

Björn Grüning

@bgruening

@Slugger70 you should remove the parameter completey I guess if they do not exist anymore

Slugger70

@Slugger70

Thanks

Greg Von Kuster

@gregvonkuster

Does anyone know a quick proper fix for this galaxyproject/tools-iuc#2783 Could this be caused by a recent change in the data manager framework?

M Bernt

@bernt-matthias

Maybe you can test this galaxyproject/galaxy#9243

John Chilton

@jmchilton

Does anyone have an examples of "real world" workflow reports?

Wolfgang Maier

@wm75

Already generated with Galaxy or with something else?

John Chilton

@jmchilton

With Galaxy

I want to generate or find some more real world screenshots

Nolan Woods

@innovate-invent

Hey guys, I need a category added to the main tool shed for generic math algorithms. A tool that calculates sha256 and a tool that does clustering of distance matrices are what I have in mind

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