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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
Nicola Soranzo
@nsoranzo
We use it for a few Earlham tools
I'm not sure I understand what the problem is, is it just a change of name?
mblue9
@mblue9
@jennaj I've created an issue for discussion of wrapping HOMER here galaxyproject/tools-iuc#1892
Jennifer Hillman-Jackson
@jennaj
@mblue9 nice! thank you
pvanheus
@pvanheus
Hiya there... I'm working on a tool that merges BLAST XML outputs... this tool takes either multiple datasets as input or a list collection, and outputs a single output (i.e. it is a "reduce" step) - is there any way to unify this or must I just use a conditional for switching between the two input modes?
John Chilton
@jmchilton
If you use a data parameter with multiple=true you will be able to run it on individual datasets or a collection. You’d need a conditional if you wanted to either (1) have more control of the order of the datasets (use a repeat) or (2) you want to be able to map over a collection instead of reduce it (less likely in this case it sounds like)
pvanheus
@pvanheus
Thanks @jmchilton - the tool is done then, #1893 - just waiting on the checks to complete. Thanks for the CWL work on planemo btw - I have yet to use it because of the messiness of the CWLs I've been working with lately but it is nice to see that ecosystem get some attention
Greg Von Kuster
@gregvonkuster
@nsoranzo @bgruening I think @nekrut just wants to change the "nhx" extension defined by Galaxy to be "newick". This came up because I have been trying to get the PlantTribes tools installed on Galaxy main and this tool https://toolshed.g2.bx.psu.edu/view/greg/plant_tribes_gene_family_phylogeny_builder/c088c185f63f produces outputs that have the "nhx" extension.
pvanheus
@pvanheus
@gregvonkuster interesting in this new visualisation - is it in the codebase anywhere yet?
Greg Von Kuster
@gregvonkuster
Not yet, and I am not involved in developing it.
Nicola Soranzo
@nsoranzo
You can define newick as an alias for nhx in config/datatypes.conf.sample, I suppose
Greg Von Kuster
@gregvonkuster
Ah, @nekrut was hoping we could do this. But how does that work? Is there now support for multiple file extensions per datatype class where I can add another extension here https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/data.py#L935? Or is there another way?
Nicola Soranzo
@nsoranzo
Not really, you need to use subclass in config/datatypes.conf
Greg Von Kuster
@gregvonkuster
I've been away from this long enough that I'm a bit rusty, so bear with me ;). Would it be as simple as <datatype extension="newick" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> <datatype extension="nhx" type="galaxy.datatypes.data:Newick" subclass="true" display_in_upload="true"/>
Nicola Soranzo
@nsoranzo
I'd think so
Greg Von Kuster
@gregvonkuster
ok, thanks @nsoranzo I'll do some testing and submit a PR.
Nicola Soranzo
@nsoranzo
Cool!
pvanheus
@pvanheus
@peterjc so what to do with the travis problems? Seems you've fixed the tigrfams URL problem but that galaxyproject/galaxy#6180 remains...
Peter Cock
@peterjc
I'm hoping the yarn vs nodejs thing with the Galaxy master branch gets fixed shortly, but for the moment am ignoring that failure and relying on the Galaxy dev branch tests only. Rebasing your pull request branch ought to trigger a re-test with the URL problem fixed.
Nicola Soranzo
@nsoranzo
@peterjc I would have less problems using the latest official release branch (18.01) instead of master
Peter Cock
@peterjc
@nsoranzo I have wondered about dropping testing against master in place of testing on a couple of release branches (which would require periodic updating when a new release happens). I had been assuming master would be a reasonable substitute for the latest release branch, but that does not seem to be quite the case?
pvanheus
@pvanheus
@peterjc - rebasing... I'm not such a git expert...
Nicola Soranzo
@nsoranzo
@peterjc Most of the times master is updated when a new release is tagged, but not kept in sync with the corresponding release_XX.XX branch until someone asks for it. We could do a better job here (e.g. automate syncing), but for the time being my suggestion above should give you a smoother experience.
pvanheus
@pvanheus
@peterjc in the absence of deep git understanding I just added a little commentary to trigger a commit to trigger a re-test
Peter Cock
@peterjc
@pvanheus sometimes there is a simple solution :thumbsup:
Björn Grüning
@bgruening
@nickeener the error is usually above this.
can you provide more data?
@/all any idea how we can review this: galaxyproject/tools-iuc#1905 galaxyproject/tools-iuc#1897
I have ask the EDAM people and ELIXIR people and hope they will help as well.
Martin Cech
@martenson
I only skimmed through the collab notebook but probably with proper tests?
Björn Grüning
@bgruening
How would you design tests? In the end the edam terms needs to match the tools I guess.
Martin Cech
@martenson
given there is not really easy way to externally validate (or is there?) I would start with unit tests
how does it fare with edam-hand-annotated tools?
Björn Grüning
@bgruening
I do not know. In the end all of this is hand annotated.
Would it be enough if everyone of us takes 5 tools and checks if they are coorect.
Random tools?
Martin Cech
@martenson
It would be something, hard to say if it would be enough.
What is the risk if it is wrongly annotated? It has no impact on Galaxy's functionality now, does it?
Björn Grüning
@bgruening
No impact on Galaxy.
Jennifer Hillman-Jackson
@jennaj
Problem report when installing samtools from MTS with certain versions of ubunto as the OS. Known? Could someone help troubleshoot? https://biostar.usegalaxy.org/p/28213/
Nicola Soranzo
@nsoranzo
Would need to know exactly which Tool Shed package this "samtools" is
Jennifer Hillman-Jackson
@jennaj
I'll add a comment asking for more details .. the post has very few details
Nicola Soranzo
@nsoranzo
Thanks!
Jennifer Hillman-Jackson
@jennaj
@nsoranzo The user replied at https://biostar.usegalaxy.org/p/28213/. They are trying to install an older version that is required by other tools as a dependency. Would you be able to help with a reply?
Nicola Soranzo
@nsoranzo
The easiest solution is to update the tool to use conda dependencies by default. In the mean time it should be possible to uninstall package_samtools_1_2 and install samtools 1.2 from conda
nickeener
@nickeener
I'm running the test command on a tool I've been working on but it fails each time saying "History item different than expected, difference (using diff):". My output when I execute the command myself appears to have an extra space at the beginning of each line so I'm fairly certain that's what's causing my issue. Is there a way I can tell the test to ignore the spaces?
Björn Grüning
@bgruening
you could use a different test
for example searching with a regex in your expected output
Dave B.
@davebx
@mblue9 I have an idea that could fix the filenames in diffbind while keeping the informative column headers, unless you're still working on this
Nicola Soranzo
@nsoranzo
@davebx Maybe galaxyproject/tools-iuc#1923 ?