Dock image for transcriptomics assembly
1
0
Entering edit mode
4 months ago
judhenaosa ▴ 10

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

transcriptomics docker • 341 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4 months ago
ATpoint 54k

I made a tutorial here: Building Docker images

ADD COMMENT

Login before adding your answer.

Traffic: 2468 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6