ABSOLUTE not anymore on the GenePattern

Question

[francois.virard]

Hi everyone,

I want to use ABSOLUTE for but I can find any documentation, the module seems to have disappeared from Genepattern and the link https://www.genepattern.org/modules/docs/ABSOLUTE doesn't work anymore.

I found the repository from getzlab https://github.com/getzlab/ABSOLUTE/ but I don't know how to proceed for the installation.

Thanks for your help

Answer 1

[Ram]

It's got a Docker file. You can either use that to make your own image or use the older docker image from https://hub.docker.com/r/kv3vk/getzlab-github-absolute

[francois.virard]

Thank you Ram for your reply. I managed to build the docker image, as you suggest.

I suppose I need to run one of the scripts in the folder:

/xchip/tcga/Tools/absolute/releases/v1.5/run

However, there are 8 scripts in the directory and I'm not sure who does what and which one to start with

For example:

Rscript "/xchip/tcga/Tools/absolute/releases/v1.5/run/ABSOLUTE_cli_start.R" --help

remains rather limited in its documentation

[Ram]

I don't know how to use ABSOLUTE. I was just able to figure out how you might get it installed. Using it is a different problem and is an offshoot of your original problem so it warrants its own thread. Please accept my answer to provide closure to this post then open a new post referencing this post.