tpall/geo-rnaseq:latest
$ singularity pull shub://tpall/geo-rnaseq:latest
Singularity Recipe
BootStrap: shub
From: tpall/singularity-tidyverse
%labels
Maintainer tpall
%help
This container will run geo-rnaseq workflow R scripts. Includes Rstudio server.
%post
# Install dependencies
apt-get update
apt-get install -y \
unzip \
xorg \
libx11-dev \
libglu1-mesa-dev \
libfreetype6-dev
# Install CRAN packages
Rscript -e "install.packages(c('bookdown','XML','formattable','gridExtra','gridBase','viridis','knitr','ape','data.table','kableExtra','sparkline','evaluate','hexbin','broom','digest'), repos = 'https://cloud.r-project.org', dependencies = TRUE)"
# Install Bioconductor packages
Rscript -e "BiocManager::install(update = FALSE, ask = FALSE)"
Rscript -e "BiocManager::install(c('GEOquery', 'Biobase', 'limma', 'ggtree'), update = FALSE, ask = FALSE)"
# Install Github packages
Rscript -e "devtools::install_github('tpall/SRP')"
Rscript -e "devtools::install_github('tpall/entrezquery')"
# Install gridDiagram
Rscript -e "install.packages('https://www.stat.auckland.ac.nz/~paul/R/Diagram/gridDiagram_0.2-1.tar.gz', repos = NULL, type = 'source')"
# Clean up
rm -rf /var/lib/apt/lists/*
Collection
- Name: tpall/geo-rnaseq
- License: Other
View on Datalad
Metrics
key | value |
---|---|
id | /containers/tpall-geo-rnaseq-latest |
collection name | tpall/geo-rnaseq |
branch | master |
tag | latest |
commit | cbbb4555249e6953a318dc068d95b21fdf2e1e50 |
version (container hash) | 80210c381b28932a0140aee78450a34e |
build date | 2020-01-17T08:29:05.425Z |
size (MB) | 3104.0 |
size (bytes) | 1029046303 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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