I'm trying to set up the GeoMXAnalysis Workflow, Documented here. The way it works is I need to install a bunch of packages, download the github repo, and then use docker to view an R markdown file which walks you through the workflow. My problem is that following all the steps, on both a galaxy server and my local Windows laptop, is impossible.
#@ Title: GeoMX workflow Intro
## INSTALL PACKAGES from Bioconductor:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("standR","edgeR","limma","msigdb","GSEABase","igraph","vissE","SpatialExperiment","scater"), force = TRUE)
#install geomx workflow package
remotes::install_github("DavisLaboratory/GeoMXAnalysisWorkflow", build_vignettes = FALSE, force=TRUE)
#build and load docker image
system("cmd.exe", input="docker run -e PASSWORD=pass -p 8787:8787 ghcr.io/ningbioinfo/geomxanalysisworkflow:latest")
This is my script that I'm using to download and install the packages. My problem is with the docker command. First I didn't have it installed, but now that I have I'm receiving the following error:
> #build and load docker image
> system("cmd.exe", input="docker run -e PASSWORD=pass -p 8787:8787 ghcr.io/ningbioinfo/geomxanalysisworkflow:latest")
Microsoft Windows [Version 10.0.19044.2486]
(c) Microsoft Corporation. All rights reserved.
C:\Users\a\Documents>docker run -e PASSWORD=pass -p 8787:8787 ghcr.io/ningbioinfo/geomxanalysisworkflow:latest
Unable to find image 'ghcr.io/ningbioinfo/geomxanalysisworkflow:latest' locally
docker: Error response from daemon: Head "https://ghcr.io/v2/ningbioinfo/geomxanalysisworkflow/manifests/latest": denied.
See 'docker run --help'.
C:\Users\a\Documents>[1] 0
Do I need to switch the Daemon somehow, or is this a problem with the github repo not existing? pasting it into my browser doesn't lead me anywhere concrete. Any thoughts on how to resolve this much appreciated.
