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

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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.  
  
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 finalised 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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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.   
  
 
Please add your questions below:
 
Please add your questions below:
  
* How to configure a pipeline for all users  
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* How to configure a pipeline for all users?
* How/where is best to store pipelines and make accessible for users  
+
* How/where is the best location to store pipelines and make them accessible for users?
* How bad are the docker vulnerabilities  
+
* How bad are the docker vulnerabilities
* How to configure dockerised pipelines properly
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* How to configure Dockerized pipelines properly?
* 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
* Resources per pipeline language?  Such as yaml files for each tool?  
+
** 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?
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*** Yes
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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?