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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
pvanheusden
@pvanheusden:matrix.org
[m]
on ivar variants ? yes
pvanheusden
@pvanheusden:matrix.org
[m]
just want to get this all resolved by the end of the week so that it can got into next weekend's .eu update
bgruening
@bgruening:matrix.org
[m]
pvanheusden: could you maybe look at this?
“BTW, it doesn’t bother me, but I think there is a problem with the column names in the NextClade tables: https://galaxy.hpc.ut.ee/datasets/8fb1cd32e9c26adb/display/?preview=True. There is a mismatch between column name and content from some point (and in total one less column name than there are columns), I think the column name “insertionsmissing” should actually be two column names “insertions” and “missing”"
Thanks!
pvanheusden
@pvanheusden:matrix.org
[m]
ok! will get onto that!
and they got the error exactly... there was a typo
pvanheusden
@pvanheusden:matrix.org
[m]
btw bioconda/bioconda-recipes#28845 - might as well do the version update and this bugfix at the same time
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
pvanheusden: just catching up with everything that has happened over my holidays.
In the latest version of the Pangolin tool, what exactly is the consequence of choosing to use the UShER model?
Does that imply that the pangoLEARN source will be ignored no matter what you choose there, or are these different things?
pvanheusden
@pvanheusden:matrix.org
[m]
no, the pangoLEARN DB contains the data used in the UShER model.
Let me see if they have release notes on this - there is a bunch of new stuff I don't quite understand - Scorpio being the other part
pvanheusden
@pvanheusden:matrix.org
[m]
ok so scorpio seems to specifically related to identifying VOCs based on constellations of mutations.
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Seems so, yes. I have yet to understand what exactly this adds to the existing pangolin functionality.
pvanheusden
@pvanheusden:matrix.org
[m]
yep. it would be good to have a better description & a changelog
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Definitely, though it's always easy to complain about other projects' documentation ;)
wm75
@wm75:matrix.org
[m]
Ok, so it seems that if you run pangolin in --usher mode, it will use lineageTree.pb from the paangoLEARN data as the model (tree) - https://github.com/cov-lineages/pangolin/blob/4a4f5ec390efba89524ac6f4365981199607c1cb/pangolin/command.py#L295
Makes sense, but the command line help is really confusing.
pvanheusden
@pvanheusden:matrix.org
[m]
wm75
@wm75:matrix.org
[m]
Thanks, I'll take one last look at it later today.
pvanheusden
@pvanheusden:matrix.org
[m]
wm75 (Wolfgang Maier): I checked with the ivar_variants_to_vcf.py authors and there was no compelling reason to format things the way they did it, so I implemented a change to move the info to the INFO block. So I think galaxyproject/tools-iuc#3716 is now done
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Supercool - thanks for investigating!
I'm busy with two talks this morning but will review and merge early in the afternoon
From a quick first look: Can you eliminate the genotype and FORMAT column altogether then?
GT is not worth keeping it seems to me.
Another improvement could be to rename ALT_FREQ to the much more common AF to enhance interoperability with other tools.
pvanheusden
@pvanheusden:matrix.org
[m]
yeah I can remove GT and FORMAT... since its not really being used.
pvanheusden
@pvanheusden:matrix.org
[m]
ok made those changes, let's wait for the tests to run
M Bernt
@bernt-matthias
Can someone explain the difference between the mothur.seq.taxonomy and mothur.ref.taxonomy datatypes. In the tests I found the same test file is used? I'm asking because I would like to add a test for the converter that is built into the Galaxy sources.
Björn Grüning
@bgruening
Maybe @shiltemann knows?
Saskia Hiltemann
@shiltemann
yes, iirc there is a optional column in one of them but not the other, hang on I'll try to find you a link/example
Saskia Hiltemann
@shiltemann
so, it's been a while, but constaxonomy is 3-column, name, taxonomy and number of OTUs, see here. And the reference taxonomy is just the names and the taxonomy (without the counts). You could probably get exaples for both from the GTN tutorial, a ref taxonomy files is used as reference, and a cons.taxonomy is generated for our samples along the way.
M Bernt
@bernt-matthias
Hi @shiltemann mothur.cons.taxonomy seems to be another datatype. Question was about mothur.seq.taxonomy and mothur.ref.taxonomy ...
Saskia Hiltemann
@shiltemann
oh oops, umm
Saskia Hiltemann
@shiltemann
I think those might be the same file format (the 2-column format), but called differently in mothur to distinguish between whether its a reference file or a result generated by analysis, but I guess we don't need to treat it as two separate datatypes in Galaxy
(but not 100% sure here)
they don't seem to distinguish between the filetypes on their wiki: https://mothur.org/wiki/tags/#file_types
3 replies
Björn Grüning
@bgruening
Could anyone please review and merge: galaxyproject/tools-iuc#3738
Marius
@mvdbeek:matrix.org
[m]
@bgruening left some minor comments
1 reply
Marius
@mvdbeek:matrix.org
[m]
no problem, I just merged it
Björn Grüning
@bgruening
Merci
pvanheus
@pvanheus
I'm working on different approaches to plotting amplicon depth... a report that's quite useful from a SARS-CoV-2 analysis point of view. I've got 2 different tools that do similar but not the same thing - i.e. they present slightly different information... not sure how to deal with this from an IUC point of view: I know there has been some reluctance in the past to have too many similar tools?
Marius
@mvdbeek:matrix.org
[m]
I guess that question is difficult to answer. I personally prefer separate tools over many options within a tool, but if you're in control of both scripts a single tool might make sense ?
2 tools within a repo might be fine too ?
Peter Cock
@peterjc

Got a fun one here for workflow version pinning breaking because the version of Python was not specified: peterjc/pico_galaxy#37

What I think is happening is my old workflow (on the Tool Shed) is pointing at an old Python-2-only version of my RXLR tool, which breaks under a modern Python-3 based Galaxy. The RXLR tool itself was updated for Python 3, but the workflow was not updated to point at this.

Another question, do people still share workflows on the Tool Shed? There isn't a category for them, and the newest search result for "workflow" is from 2020, second and third newest from 2019.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
https://workflowhub.eu/ is better solution for sharing workflows going forward.
Peter Cock
@peterjc
Looks like https://www.myexperiment.org/ is pretty quiet nowadays too.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
WorkflowHub it's myExperiment 2.0, it's from the same people.
Peter Cock
@peterjc
Oh - I hadn't heard of it till now. It sounds promising.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
It's been developed as part of the EOSC-Life project led by ELIXIR.