21th Discussion-6 Nov 2018 - Revision history

Alastair.kerr at 11:59, 13 November 2018

2018-11-13T11:59:07Z

Alastair.kerr at 10:36, 7 November 2018

2018-11-07T10:36:00Z

Alastair.kerr at 12:53, 5 November 2018

2018-11-05T12:53:41Z

Apeltzer: Comments on points to clarify before talk (by Alex Peltzer)

2018-11-03T18:33:30Z

Comments on points to clarify before talk (by Alex Peltzer)

Mcm at 21:15, 29 October 2018

2018-10-29T21:15:44Z

Alastair.kerr: Created page with "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 bioi..."

2018-10-26T08:52:43Z

Created page with "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 bioi..."

New page

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. I plan to schedule this on November 1st, late afternoon in the GMT timezone. 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.

Please add your questions below:

* How to configure a pipeline for all users
* How/where is best to store pipelines and make accessible for users
* How bad are the docker vulnerabilities
* How to configure dockerised pipelines properly
* How to convert docker pipelines to singularity (with and without AWS)
* Easiest pipelines to create from scratch
* Resources per pipeline language? Such as yaml files for each tool?
* Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?

← Older revision		Revision as of 11:59, 13 November 2018
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	UPDATE: Here are the [https://t.co/FecFUcOzDk slides from the talk]		UPDATE: Here are the [https://t.co/FecFUcOzDk slides from the talk]
−	~~Video will be added pending Alex's approval~~ and ~~a suitable server~~.	+	and the [http://bifx-core.bio.ed.ac.uk/Bioinf-Core/zoom_1.mp4 full video]

← Older revision		Revision as of 10:36, 7 November 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.
		+
		+	UPDATE: Here are the [https://t.co/FecFUcOzDk slides from the talk]
		+	Video will be added pending Alex's approval and a suitable server.
		+
		+

	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.

@@ Line 11: / Line 11: @@
 * How to convert Docker pipelines to singularity (with and without AWS)?
 * 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?
+** 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?
+*** Are there tools, or existing configuration files, that would make the job easier?
 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?

@@ Line 1: / Line 1: @@
 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.
+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 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
+* 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
-* Resources per pipeline language?  Such as yaml files for each tool?
+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?
 * Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?