Dock image for transcriptomics assembly

Question

[judhenaosa]

Dear all.

I need to do the assembly by reference of a raw illumina transcriptomics. However, the server I use needs to upload all the needed platforms as a docker image. Before to trying to create my own image (it could take some time). I want to ask if you know about public repos with docker images with the necessary features to run those kind of analysis.

Thanks in advance.

Kind regards,

Juan

[lieven.sterck]

Does it need to be via docker? and/or something local?

Otherwise you can (should?) look into galaxy. It has all available tools to run transcript assembly with it.

[ATpoint]

Depends on the pipeline. For a single tool you probably want to search Quay, and for anything custom it is actually simple to build your own container even on a local machine. Just install software with conda into an existing base container which you can pull from Dockerhub. Ping me if you need instructions for that.

[judhenaosa]

Hi!

Thanks for your reply. If you can provide me hints about how to do it I will really appreciate it. I tried to create docker images for my own in the past. However, I have no idea why never works.

Kind regards,

Juan

[cpad0112]

try in searching for rnaseq or transcriptomics in dockerhub. Here are the results for dockerhub search on rnaseq: https://hub.docker.com/search?q=RNAseq&type=image

Answer 1

[ATpoint]

I made a tutorial here: Building Docker images