phelelani/transcriptomics:r
$ singularity pull shub://phelelani/transcriptomics:r
Singularity Recipe
Bootstrap:shub
From:singularityhub/ubuntu
%labels
Maintainer Phelelani.Mpangase@wits.ac.za
%post
## Updates and essentials
apt-get update
apt-get install -y build-essential
apt-get install -y wget git curl gfortran zlib1g-dev libbz2-dev liblzma-dev libpcre3-dev libcurl4-gnutls-dev
apt-get install -y libxml2-dev libssl-dev libopenblas-dev libmagick++-dev libudunits2-dev libcairo2-dev libxt-dev
## Install R
cd /opt \
&& wget https://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz \
&& tar -vxf R-3.5.1.tar.gz \
&& cd R-3.5.1 \
&& ./configure --with-x=no --with-readline=no \
&& make \
&& make install \
&& rm /opt/R-3.5.1.tar.gz
## Install basic CRAN R packages
R -e 'install.packages(c("tidyverse","data.table","dtplyr","devtools","roxygen2", "Cairo"), repos="http://cloud.r-project.org/", dependencies=TRUE)'
## Install CRAN R packages
R -e 'install.packages(c("ggplot2", "gridExtra", "ggrepel", "xtable", "gplots", "kableExtra", "grid", "pheatmap", "enrichR", "BiocManager", "UpSetR", "PoiClaClu"), repos="http://cloud.r-project.org/", dependencies=TRUE)'
## Install Bioconductor R packages
R -e 'BiocManager::install(c("DESeq2", "biomaRt", "genefilter", "AnnotationDbi", "org.Hs.eg.db", "pathview", "gage", "gageData", "PROPER"), version = "3.8")'
Collection
- Name: phelelani/transcriptomics
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/phelelani-transcriptomics-r |
collection name | phelelani/transcriptomics |
branch | master |
tag | r |
commit | 2727089b11ee4cc02389edffc42a55d20429d7d5 |
version (container hash) | d7f8bba7d0a1902f846eca9c8d0875da |
build date | 2020-02-12T21:23:08.125Z |
size (MB) | 2287 |
size (bytes) | 880869407 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.