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Lon Blauvelt
@DailyDreaming
I could try to run it from my end if you have a reproducible workflow that you wanted to make an issue for: https://github.com/DataBiosphere/toil/issues
Vijay Lakhujani
@vlakhujani
the clusterStats option does not produce a json output, am I missing something ?
Lon Blauvelt
@DailyDreaming
@vlakhujani That option could be worded better, as it only works with mesos (and therefore AWS). If using a different cluster, try the --stats option. If using mesos/aws, then let me know because then that's a bug we need to fix.
1 reply
I'll go ahead and change the wording on the option to explain that it only works on mesos/aws.
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] Should we throw if we're trying to use it not on Mesos/AWS?
Lon Blauvelt
@DailyDreaming
That's probably a good idea Adam. I'll add that in too.
Douglas Lowe
@douglowe
should the cwltool:overrides: notation work when using toil-cwl-runner? I have an input file containing this, which does what I expect when I try running it with cwltool, but does not when I try using toil-cwl-runner
Peter Amstutz
@tetron
I don't think so, I think that's still a cwltool specific feature. it might show up in a future CWL spec revision
Douglas Lowe
@douglowe
ahh, okay
I'll stop trying to fix my syntax then :-/
Lon Blauvelt
@DailyDreaming
[Lon Blauvelt, UCSC GI] @douglowe We have an issue for this, so it's on the roadmap, but not currently being worked on.
karma29
@karma29:matrix.org
[m]
hi! i'm new to CWL & Toil. can i discuss this issue DataBiosphere/toil#3469 in this channel?
Peter Amstutz
@tetron
@karma29:matrix.org yes that would be appropriate. also https://gitter.im/common-workflow-language/common-workflow-language
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] Uh-oh, does the Matrix bridge not talk to the Slack bridge?
Lon Blauvelt
@DailyDreaming
@karma29:matrix.org What's the issue? @adamnovak D:
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] Oh, looks like it works.
karma29
@karma29:matrix.org
[m]

hello! just curious about the code here : https://github.com/DataBiosphere/toil/blob/master/src/toil/cwl/cwltoil.py#L736

mutable is by default set to false, which means that there is no downloaded copy of the file (and a link to it is created instead). in the function call examples, there wasn't any explicit declaration of mutable to true, so do they exhibit "streamable" properties? what more changes should we make here?

karma29
@karma29:matrix.org
[m]
actually i'm a gsoc'21 applicant so i wasn't sure if it would be more suitable to reply to the comment threads on github or join the irc. what's recommended though? i'm fine with either! 😃
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] We watch Github issues, and the chat here, but not really Github code comments. Either there or here is fine; here is maybe better fro questions that are not themselves bugs.
[Adam Novak, UCSC GI] I think the idea behind CWL streamable is that you will get a pipe (a FIFO) presented to the tool instead of a normal file? I'm not really sure.
Peter Amstutz
@tetron
yes
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] Anyway, readGlobalFile produces an ordinary file, with a filename and all the data on disk. It might be given via a symlink, and the lack of mutable means the user code isn't allowed to modify it, as other jobs may be using the same copy.
Peter Amstutz
@tetron
and if the data is coming from a remote location, it can be streamed incrementally instead of waiting for a full download
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] Toil already has a file_store.readGlobalFileStream function, but that returns a Python file object, and doesn't currently produce a FIFO on disk. So I think getting CWL streamable support would involve handling streamable requests from CWL by using file_store.readGlobalFileStream and producing a FIFO and a thread to fill it with data.
Michael R. Crusoe
@mr-c
Or by using a third party utility to achieve the same thing, given the s3 url
karma29
@karma29:matrix.org
[m]

okay, i see! thank you 👍️ so we need to implement a FIFO process for

  1. a sequence of files (irrespective of whether they're downloaded or not, because i think right now it waits for all the input files to be processed to release the outputs?)
  2. a sequence of data within the file, in case the file comes from a remote location or s3 url (so we don't need to download it)
  3. combination of the above two, if there are more files from a remote location or s3 url in the pipe

is that correct?

Lon Blauvelt
@DailyDreaming
@karma29:matrix.org I'm sorry, it seems the matrix.org connection doesn't sync to our slack channel, so your message was missed. In general, this will need to be one FIFO per file. I would focus on the AWS s3 functionality alone first.
I'll try to check the gitter manually more often.
Michael R. Crusoe
@mr-c
@DailyDreaming does your slack connection sync via gitter? Maybe switch to directly syncing your slack channel with the matrix version?
Lon Blauvelt
@DailyDreaming
I'll try that.
Thanks!
karma29
@karma29:matrix.org
[m]
Okay! Is there a link to the slack group i can join?
1 reply
I'd be grateful if you could give feedback on it! I'm a bit confused regarding how we would actually implement streamable properties, except for the part where we change file_store.readGlobalFileStream so any inputs regarding that would be much appreciated
karma29
@karma29:matrix.org
[m]
Also is a "job class" a Python class? I have heard of text files getting pickled. So does a job class getting pickled mean that the job class is being implemented as an object and then their contents being pickled to a file?
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] The jobs in Toil are instances of various "job classes", like CWLJob and JobFunctionWrappingJob. We do indeed instantiate these classes and then pickle the resulting objects into files.
karma29
@karma29:matrix.org
[m]

Okay, thank you for the feedback!

I've made some changes - if it looks good, may I go ahead and submit the proposal?

karma29
@karma29:matrix.org
[m]

Hello!

Just a follow-up to my previous message, since there's ~ 2 hours for the submission to end 😃 crusoe @DailyDreaming

1 reply
karma29
@karma29:matrix.org
[m]
Thank you, just updated with another query. Can you please check the doc? Thank you crusoe @DailyDreaming
Dennis R Kennetz
@drkennetz
Is it appropriate to post job openings in here? We have a more senior position open that is CWL/toil related for bioinformatics.
Michael Milton
@multimeric
Is there any interest in my suggestion here: https://github.com/DataBiosphere/toil/issues/1768#issuecomment-818475173 ? I'd be happy to give it a go if it's okayed by a maintainer
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] It sounds like a good idea to me!
Lon Blauvelt
@DailyDreaming
@drkennetz That's fine by me.
crusoe
@mr-c:matrix.org
[m]
Google just "alerted" me to this 11 month old toil-cwl-runner question on biostars https://www.biostars.org/p/448085
Lon Blauvelt
@DailyDreaming
@mr-c:matrix.org Thanks for the link! Good work around hack, I agree. We should definitely make it less hacky. I'll create a Toil-side issue.
mareq
@mareq
hello, i am not sure if this is the correct place to ask but anyway: i would like to run cwl workflows in azure cloud and toil seems like one of the good ways to go. the k8s option looks quite good (based on the documentation i have read), except it says that it requires aws for job store. hence the question: is there some other way (possibly without even k8s: it would be great to do it in a way independent of particular cloud, but it is not hard requirement) to use toil for running cwl workflows on azure and azure only?
Lon Blauvelt
@DailyDreaming
[Adam Novak, UCSC GI] @mareq, we used to have an Azure job store and an Azure template for stamping out clusters, but we dropped them. The AWS job store is not able to run on top of just any S3-compatible storage system; we currently also need SimpleDB, and we're swapping that out for DynamoDB which also isn't part of S3.
[Adam Novak, UCSC GI] In the future to run on Azure we would use the Kubernetes batch system, because everybody has a good way to provide Kubernetes, but there's still the need for a job store. The only one that isn't tied to a cloud provider is the one that requires a shared filesystem.
[Adam Novak, UCSC GI] We might be able to get the file job store working with Kubernetes if you can get all your nodes a shared strongly-consistent filesystem (which NFS sort of isn't) and we can get it exposed to the Toil kubernetes pods, maybe with some kind of extra host path volume.