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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
Jennifer Hillman-Jackson
@jennaj
@jj-umn reported problem using RSEM tool repo owned by you. Do you know what could be going wrong? Do these tools work for you in the 18.01 stable release? or the 18.05 pre-release? https://biostar.usegalaxy.org/p/28044/
mblue9
@mblue9
@jennaj I'll add info on the annotation to the featurecounts wrapper help section (as per your suggestion) after this featurecounts header PR galaxyproject/tools-iuc#1890 (assuming I should wait and make a separate PR)
there are also newer version of featurecounts 1.6.1 in bioconda and 1.6.2 not in bioconda, maybe would be good to update the wrapper
I'd also like to move the featurecounts stranded option up out of "Advanced options" to under "Alignment file" as another PR if noone objects
mblue9
@mblue9
btw how are people adding gene names to macs2 and diffbind peaks? I don't have a good method for that yet
Jennifer Hillman-Jackson
@jennaj
To get genes overlapping with peaks, you need to get a reference dataset with the gene bounds/coordinates and compare to the peaks by coordinate overlap. Don't think there is an easier way. This gets asked quite a bit, maybe we should build a tool for that ("annotate peaks")
Jennifer Hillman-Jackson
@jennaj
And I like the idea of putting the info in the help and moving the strand assignment up top on the form. Digging for it is not always obvious and it really matters. The alignment has to be stranded, too. Maybe mention that in the help under the option? eg: "Strand setting must be the same as the strand settings used to produce mapped BAM input(s)". Could be more specific.. or better worded .. or we can leave it out and hope for the best :)
Other IUC peeps should comment about which version of featurecounts to use. Not sure which is better, or easier, to incorporate.
mblue9
@mblue9
thanks @jennaj, we used to have the homer annotate peaks tool that worked well afaik, this tool https://toolshed.g2.bx.psu.edu/view/kevyin/homer/f0b5827b6051
but just tried to install it and it didn't work, (might be our setup) I get Conda False in the Manage Tool Dependencies
mblue9
@mblue9
it's an old wrapper though, hasn't been updated since 2012
pvanheus
@pvanheus
good morning @shiltemann - I'm trying to help colleagues here with mother Chimera.vsearch - in IUC as: https://github.com/galaxyproject/tools-iuc/blob/master/tools/mothur/chimera.vsearch.xml
They're hitting a problem with mothur and readline - but I wonder why the <requirements> state vsearch but the command line is | mothur ?
pvanheus
@pvanheus
oh I see the mothur is coming in via the macros.xml - that makes sense
Jennifer Hillman-Jackson
@jennaj
@mblue9 Homer probably needs an update or replacement...
Maybe create a ticket at IUC github for discussion? We'll have that large codefest in later June/early July at GCCBOSC, could put it out there as a potential project for hacks unless someone else picks it up first
Björn Grüning
@bgruening
we started a few years ago to integrate the HOMER suite, which is really a great tool collection, but never really got to it anymore
@davebx wanted to look at it if time allows
Dave B.
@davebx
won't be for a few weeks, though
Greg Von Kuster
@gregvonkuster
I've been in a discussion with @nekrut about the newick data format in Galaxy. Unfortunately, this format uses the nhx extension instead of just using newick. @nekrut would like me to submit a PR to the Galaxy core to change this extension to be newick. Although nhx is based on newick, it seems to have become deprecated, and phyloxml is advised, at least based on this link: https://sites.google.com/site/cmzmasek/home/software/forester/nhx. But changing the extension in Galaxy will affect tools in both the tools-devteam and tools-iuc repos. My understanding is that support for a new PhyloTree viz is soon coming to the Galaxy core. This viz will be used in the HIV research with which Galaxy is involved, and it will be using the newick format as well. What does the iuc advise here?
Björn Grüning
@bgruening
can someone of the admins grep in the TS if this extension is used in TS tools? At least to get an estimation of the problem?
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