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Johnny Li
@iamjli
This is using our own instance
John Chilton
@jmchilton
what version of Galaxy?
Johnny Li
@iamjli
sorry, how can I check?
John Chilton
@jmchilton
Go to /api/version under the URL to your instance I think (like https://usegalaxy.org/api/version)
Johnny Li
@iamjli
Thanks. 18.01
John Chilton
@jmchilton
Yeah - that should work then - I wonder if it reads dataset names and not collection names when building the variables that can be used as inputs :(
Johnny Li
@iamjli
In that case, wouldn't the collection name remain unchanged and the datasets within be renamed with the .fastq suffix?
John Chilton
@jmchilton
The output collections can be renamed - I'm just not sure they can be renamed based on input collections - seems like maybe not?
Johnny Li
@iamjli
Bummer. So the renaming tool is for datasets then?
Martin Cech
@martenson
export default {
    data() {
        return {
            test: null
        }
    }
}
data is a shorthand definiton of a function that returns object with property test in it, right?
therefore equal to?
export default {
    () =>  {
        return {
            test: null
        }
    }
}
Martin Cech
@martenson
(except the second example is an anonymous function)
Dannon
@dannon
Not sure of the full context of what you're trying to do, but those aren't equal. One exports an object with a data parameter, the other doesn't
I mean, the functions do the same thing, yes. But you won't be able to access the second one.
Dannon
@dannon
s/parameter/property
Jennifer Hillman-Jackson
@jennaj
Tophat has problems with collection inputs. Maybe try HISAT instead?
Details here and I am not sure if Tophat will be changed, or Galaxy changed, to address the issue: https://github.com/galaxyproject/usegalaxy-playbook/issues/155#issuecomment-417509888
(if either done -- Tophat is considered deprecated by many)
galaxybot
@galaxybot
[dannon] @jen Do you mind if I impersonate you on main to see what's up with a particular page of yours from 2012?
Jennifer Hillman-Jackson
@jennaj
no problem :)
galaxybot
@galaxybot
[dannon] Cool, thanks
Jennifer Hillman-Jackson
@jennaj
anytime is ok, for any reason :)
Nicola Soranzo
@nsoranzo
@selten The link to cluster in https://docs.galaxyproject.org/en/latest/admin/production.html (and many more links in the docs) have been fixed, thanks for reporting!
angela1995angela
@angela1995angela
hey guys. I am totally new in galaxy. I have just made a new workflow in order to convert FastQ files to VCF but in the "get data" section i cannot upload a file from my computer. The only available option is import file from GenomeSpace. Can anyone help me?
Marius van den Beek
@mvdbeek
@angela1995angela this describes how to upload files to galaxy: https://galaxyproject.org/tutorials/upload/
Nicola Soranzo
@nsoranzo
@jmchilton If you want I can open a backport PR, I still have the 18.05 branch
John Chilton
@jmchilton
I already just pushed it
The rules allow for it.
Nicola Soranzo
@nsoranzo
John Chilton
@jmchilton
It is very black and white in my mind, but I'm admittedly biased :D
Nicola Soranzo
@nsoranzo
E.g.: I open a PR for dev, someone merges it (no other approvals), then I can cherry-pick it to a release branch without a second approval.
While a PR targeting a release branch requires 2 approvals.
John Chilton
@jmchilton
You can call it a silly compromise, but that was the intent and that is how it reads - so it isn't a gray area in mind.
I think it is silly we slow down the smallest, most important and urgent PRs by requiring 2 approvals while we let huge API changes in dev through with just one approval - the fix is switching that to 1 but it would be vetoed so it won't be fixed.
Micropathology
@Micropathology
simple question but as far as galaxy is concerned if I want to to increase the maximum number of concurrent jobs run by galaxy do i just need to modify galaxy.ini threadpool workers for each of the handlers or have i got his wrong?
Marius van den Beek
@mvdbeek
Ashok Varadharajan
@ashvark
For some reasion, "import files from path" in data libraries does not accept filenames having '+' character in it. Is it known already?
Martin Cech
@martenson

jmchilton: but it would be vetoed so it won't be fixed.

wanna try?

John Chilton
@jmchilton
Procedure PRs that fail seem to hurt team morale - I'd rather only open ones that are going pass.
Ashok Varadharajan
@ashvark
For some reasion, "import files from path" in data libraries does not accept filenames having '+' character in it. Is it known already?
Actually I am not getting any error message. It is simply ignoring/skipping the files containting '+' character. I would like to know what are all the other characters that would not work.
Martin Cech
@martenson
@ashvark anything that is not alphanumeric could fail would be my assumption
Ashok Varadharajan
@ashvark
filename with characters like '_' and '-' are working fine
Martin Cech
@martenson
yeah, those are generally safe
Ashok Varadharajan
@ashvark
okay. '@' character is also working.
galaxybot
@galaxybot
[dan] seems like a bug though, libraries should accept any valid file, especially when not symlinking
Nicola Soranzo
@nsoranzo
@ashvark Do you have any error message? Where is this happening, e.g. usegalaxy.org or some local server?
Micropathology
@Micropathology
@mvdbeek so "workers ='x'" in LocaljobRunner runner handles the maximum concurrent jobs?
Nate Coraor
@natefoo
@Micropathology: if you're not using a cluster, that's correct
Marius van den Beek
@mvdbeek
If you're not connected to a cluster, yes