Difference between revisions of "21th Discussion-6 Nov 2018"

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(Comments on points to clarify before talk (by Alex Peltzer))
 
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Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.  
 
Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.  
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UPDATE:  Here are the  [https://t.co/FecFUcOzDk slides from the talk]
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and the [http://bifx-core.bio.ed.ac.uk/Bioinf-Core/zoom_1.mp4 full video]
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After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core.  This will be on November 6th, 3 PM GMT.  Details on how this will occur are being finalized but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it.   
 
After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core.  This will be on November 6th, 3 PM GMT.  Details on how this will occur are being finalized but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it.   
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* How to convert Docker pipelines to singularity (with and without AWS)?  
 
* How to convert Docker pipelines to singularity (with and without AWS)?  
 
* Easiest pipelines to create from scratch
 
* Easiest pipelines to create from scratch
a What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?  
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** What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
* Resources per pipeline language?  Such as YAML files for each tool?
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*** Are there tools, or existing configuration files, that would make the job easier?
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*** Any good GUIs such as can be found in Galaxy?
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** Resources per pipeline language?  Such as YAML files for each tool?
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*** Yes
 
b Not sure what you mean with this - do you mean how we define dependencies per pipeline?   
 
b Not sure what you mean with this - do you mean how we define dependencies per pipeline?   
 
* Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?
 
* Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?

Latest revision as of 06:59, 13 November 2018

Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.

UPDATE: Here are the slides from the talk and the full video


After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core. This will be on November 6th, 3 PM GMT. Details on how this will occur are being finalized but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it.

Please add your questions below:

  • How to configure a pipeline for all users?
  • How/where is the best location to store pipelines and make them accessible for users?
  • How bad are the docker vulnerabilities?
  • How to configure Dockerized pipelines properly?
  • How to convert Docker pipelines to singularity (with and without AWS)?
  • Easiest pipelines to create from scratch
    • What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
      • Are there tools, or existing configuration files, that would make the job easier?
      • Any good GUIs such as can be found in Galaxy?
    • Resources per pipeline language? Such as YAML files for each tool?
      • Yes

b Not sure what you mean with this - do you mean how we define dependencies per pipeline?

  • Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?