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Created by James Eddy jaeddy
Correct. Probably a week later (1/6) for submission reports/wikis. I'll send out an announcement about both deadlines.
Ok, thanks. To be clear, are you saying you're moving the deadline for workflow validation back to 12/31 and then later for submission reports and Wikis?
Hi @bernest ? I plan to keep the evaluation queues for workflow submissions open through **12/31**. After that, I'll leave some lag time for folks to finalize submission reports.   We'll push pause on workflow submissions at the start of 2018 ? hopefully for not much longer than a few weeks ? so that we can regroup and implement any changes prior to the next round of testing. I'll be sure to update everyone on these plans as they become more concrete.   Thanks! James
Will we be able to access the workflows and submit results (not counting toward the challenge of course) after the deadline of December 22?
Hi @james, Thank you for taking care of this request! I am happy with the team name appearing at the submission and overall stats page. This is perfect. Regards, Vipin
Hi @vipin ? the issue has been resolved! See this thread for more info: https://www.synapse.org/#!Synapse:syn8507133/discussion/threadId=2967
Hi @vipin,   This question came up in another thread recently. The short answer is that there's technically no way to retroactively associate a submission with a team (without deleting and resubmitting ? which would be a pain). However, because there are only a couple of these cases for this challenge, I should be able to update how the team _appears_ for submissions (e.g., in the overall stats and leaderboards). I'll take a look at that and let you know what I find!   One thing I won't be able to change is how the challenge infrastructure checks for "eligibility" when submitting. In other words, if you've already submitted for a particular workflow as an individual, you won't be eligible to then submit new results as part of a team (and vice versa). Just something to pay attention to when setting your parameters for the `synapse-submit` tool.   Best, James
Dear James, I have recently created a team called "ETH Zurich NEXUS Workflow Handler" from our institute for participating in GA4GH/DREAM Workflow Execution Challenge. I have been participating in this challenge for past months and I submitted results of the workflow run to the result tracking system with complete documentations. The previous submissions are are under my name (Vipin T Sreedharan). Now my question is that will it be possible to link the old results submissions (which are already in the synapse page under my account) to the newly created team? Please let me know whether this will be possible? I am happy to provide more details if you want. Thank you for considering, Vipin
Dear @vipin My apologies for not spotting your request sooner! I just created a thread for the **knoweng_gene_prioritization** workflow, which you can find here: https://www.synapse.org/#!Synapse:syn8507133/discussion/threadId=2619 Best, James
Hi @stevetsa , We sent out an email to participants last Thursday announcing that the challenge will be extended till **December 22nd.** We posted some additional notes on the [news & updates page](https://www.synapse.org/#!Synapse:syn8507133/wiki/451397) as well, if you're curious. Thanks! James
Is there a decision whether this challenge (or phase) will be extended? Thanks.
Hi @jaeddy, Can you create a discussion thread for **knoweng_gene_prioritization** workflow help. I have found an issue with running this workflow using `rabix` runner. Thanks! Vipin
Is this helpful? https://gist.github.com/OliPelz/4cf1ea585fe0a8a3c24ba711d5bccb89
Hi @benstory, Sorry for not getting back to you sooner! I've tested on Ubuntu and macOS and haven't run into this particular issue yet (though I did have to mess with the Docker daemon config to avoid containers maxing out my scratch space..). We've had a couple questions come up now that are beyond my Docker expertise; I'll raise these again to the group on our Tuesday call next week and see if anyone has suggestions. In the meantime, cc'ing @briandoconnor, @denis.yuen, and @jeremiahsavage, in case they have a better answer. Will hopefully follow up with you soon.
I'm having significant problems with inherent limits to docker container sizes in CentOS 6 (it might be OS specific). Mainly tried adding this to my docker config: --storage-opt dm.basesize=100G. I followed a tutorial on https://www.projectatomic.io/blog/2016/03/daemon_option_basedevicesize/ to allocate more space to the container but despite that the container never changed its rootfs size. This is a problem for two of the pipelines where I need to download large images that fill up my entire container. Anybody else encounter similar problem and overcome it?
Thanks James! Turns out an upgrade of Synapse was enough to fix the problem. Best, Trevor
Hi @tcickovs,   Which version of the Synapse client are you using? I found a thread in the Synapse help forums that discusses a similar error: https://www.synapse.org/#!Synapse:syn5637528/discussion/threadId=1423   The JIRA issue related to the error is still open, but I can add details from your case to help with debugging. Please share any other information about your environment that you think might be relevant.   In the meantime, I suggest trying to download the folders for each workflow using the process described [**here*](https://www.synapse.org/#!Synapse:syn8507133/wiki/451410) for `dockstore-tool-synapse-get` along with the corresponding JSON file for the workflow you want. Because this CWL tool is based on a Docker image with a fixed version of the Synapse client, behavior should hopefully be more consistent ? but obviously, we'd like to resolve issues with the actual client as well. :)   Let me know if you have further questions.   Thanks! James
Hi: I am attempting to use 'synapse' to download files for the challenge, but keep getting an error that is something like this: > synapse get -r syn9630939 SynapseHTTPError: 416 Client Error: Requested Range Not Satisfiable InvalidRangeThe requested range is not satisfiablebytes=6-6CB1451537B5DA9BFoLNF/Kh6wRyQVR4kvoAbBTwoMQjQi6rIHxHWNk7AQsWrawAvZHf1X5r4B9MfW+sFrV4r01iKU1M= That is a download from the root directory, I've tried subdirectories as well and sometimes get slightly different ones, though they all resemble the above. Anyone else have this problem, any suggestions? Thanks, Trevor
For this particular challenge, yes ? Docker is required.   The goal of these challenges is to evaluate standards and tools for sharing and running reproducible analytical workflows. We're currently focusing on those conventions put forth and described by the [**GA4GH Containers and Workflows**](https://genomicsandhealth.org/working-groups/our-work/containers-and-workflows) group. These conventions are based on distributing tools/dependencies as Docker images and describing the execution and parameterization of the resulting Docker containers through CWL or WDL.   As such, all of the workflows provided for the **Workflow Execution Challenge** are based in one or more Docker images hosted in [**Docker Hub**](https://hub.docker.com/) or [**QUAY**](https://quay.io/).   Docker is the only containerization technology with stable support in CWL and WDL platforms right now. However, we expect that other types of containers (e.g., Singularity or Linux Containers) might become more relevant in the future. At that point, it would certainly be interesting to reevaluate some of the workflows in this challenge using alternative container technologies!
Is it required to use docker?

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