Running Qiime2 using Docker


#1

Hi!
I recently shifted from Ubuntu to Windows10 in a new laptop and installed qiime2-2018.8 using Docker. Earlier working on natively installed qiime2 in ubuntu. I am new to the use of Docker and not sure how to run qiime2 in the windows power shell with docker activated. I am sure there are people here also running qiime2 using docker. Can someone help me out with the basic commands, how to run qiime2 commands, how to set the directory for qiime2 commands to access the input file and save the qiime2 outputs? Docker is completely new to me and I am not sure what actually is going on, how input files are accessed, where outputs get saved etc. I am sure someone can share their experience with Docker and how they use it for running qiime2. It would be great if someone can share some tutorial on using docker for qiime2 similar to those in the moving tutorials. I apologize if I am missing out some petty things on docker usage. Thanks!


#2

Thanks for the update! Would it be possible to also include the ITSxpress plugin in the core distribution of qiime2-2018.11, so that we can access it using Docker. I am not sure how to install this plugin through docker in Windows10 unless it is packed in the core distribution. I am totally new to using qiime2 in docker. Thanks!


QIIME 2 2018.11 release is now live!
(Nicholas Bokulich) #4

(Matthew Ryan Dillon) #5

Hey there @bsen2018 — I am planning on writing up two Community Tutorials in the next week on both of these topics — please stay tuned. In the meantime, there is a lot of material on Docker, generally speaking, online. Sorry, that is a crummy answer, but please stay tuned for new tutorials!
:t_rex:


(Matthew Ryan Dillon) #6