dfernandezperez/bioinformatics-singularity:seurat_monocle2
$ singularity pull shub://dfernandezperez/bioinformatics-singularity:seurat_monocle2
Singularity Recipe
Bootstrap: docker
From: bioconductor/release_core2
%apprun R
exec R --vanilla "$@"
%apprun Rscript
exec Rscript --vanilla "$@"
%runscript
exec R --vanilla "$@"
%post
apt-get update
# Basic dependencies for Seurat and most R packages
apt-get install -y apt-transport-https apt-utils software-properties-common
apt-get install -y curl wget nano libboost-all-dev libudunits2-dev gawk
apt-get install -y libblas3 libblas-dev liblapack-dev liblapack3 curl
apt-get install -y gcc fort77 aptitude
apt-get install -y g++
apt-get install -y xorg-dev
apt-get install -y libreadline-dev
apt-get install -y gfortran
gfortran --version
apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev
apt-get install -y libhdf5-dev hdf5-helpers libmariadb-client-lgpl-dev python-pip python-virtualenv
# Dependencies for rgl package
apt-get install -y xorg libglu1-mesa-dev libx11-dev libfreetype6-dev
# Dependencies for umap and monocle
pip install umap-learn
pip install louvain
# installing packages from cran
R --slave -e 'install.packages("devtools",repos="https://cran.rstudio.com/")'
R --slave -e 'install.packages("dplyr",repos="https://cran.rstudio.com/")'
R --slave -e 'install.packages("Seurat",repos="https://cran.rstudio.com/")'
R --slave -e 'install.packages("reticulate",repos="https://cran.rstudio.com/")'
R --slave -e 'install.packages("rgl",repos="https://cran.rstudio.com/")'
R --slave -e 'install.packages("shinythemes",repos="https://cran.rstudio.com/")'
# installing from bioc
R --slave -e 'source("https://bioconductor.org/biocLite.R"); biocLite("monocle")'
R --slave -e 'source("https://bioconductor.org/biocLite.R"); biocLite("scran")'
R --slave -e 'source("http://cf.10xgenomics.com/supp/cell-exp/rkit-install-2.0.0.R")'
# Packages from github
R --slave -e 'devtools::install_github("ggjlab/scMCA")'
Collection
- Name: dfernandezperez/bioinformatics-singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dfernandezperez-bioinformatics-singularity-seurat_monocle2 |
collection name | dfernandezperez/bioinformatics-singularity |
branch | master |
tag | seurat_monocle2 |
commit | e9d7c85e3e4407372736a8af77e819b4cff9a719 |
version (container hash) | 20a85b874f573f58aa96ca3243718821 |
build date | 2018-11-07T20:20:33.155Z |
size (MB) | 3205 |
size (bytes) | 1169301535 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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