nrachman/reproducibility:latest
$ singularity pull shub://nrachman/reproducibility:latest
Singularity Recipe
Bootstrap: shub
From: singularity-hub.org/ii-bioinfo/R3.5.1_Bioc3.8_rstudio1.1.463:latest
##the shub:// tag should not be included
##see https://github.com/sylabs/singularity/issues/2847
%post
sudo apt-get update
sudo apt-get -y install libcairo2-dev #for arrayQualityMetrics
sudo apt-get -y install libxt-dev #for arrayQualityMetrics
sudo apt-get -y install libudunits2-dev #for ggraph
R -e "install.packages('gridSVG')" #required by arrayQualityMetrics
R -e "BiocManager::install('limma')"
R -e "BiocManager::install('variancePartition')"
R -e "BiocManager::install('oligo')"
R -e "BiocManager::install('preprocessCore')" #needed for metaintegrator
R -e "BiocManager::install('arrayQualityMetrics')"
R -e "BiocManager::install('GEOquery')"
R -e "BiocManager::install('sva')"
R -e "BiocManager::install('impute')"
R -e "BiocManager::install('GO.db')" #needed for WGCNA
R -e "BiocManager::install('multtest')" #needed for metaintegrator
R -e "BiocManager::install('GEOmetadb')" #needed for metaintegrator
R -e "install.packages('knitr')"
R -e "install.packages('tidyverse')"
R -e "install.packages('plyr')" #used in pick probeset code
R -e "install.packages('r.jive')"
R -e "install.packages('ComplexHeatmap')"
R -e "install.packages('pheatmap')"
R -e "install.packages('tidygraph')"
R -e "install.packages('units')"
R -e "install.packages('ggraph')"
R -e "install.packages('igraph')"
R -e "install.packages('randomForest')"
R -e "install.packages('reshape2')"
R -e "install.packages('fpc')"
R -e "install.packages('glmnet')"
R -e "install.packages('WGCNA')"
R -e "install.packages('ggpubr')"
R -e "install.packages('ggrepel')"
R -e "install.packages('cowplot')"
R -e "install.packages('gridExtra')"
R -e "install.packages('MetaIntegrator')"
R -e "install.packages('ROCR')"
R -e "install.packages('pROC')"
Collection
- Name: nrachman/reproducibility
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/nrachman-reproducibility-latest |
collection name | nrachman/reproducibility |
branch | master |
tag | latest |
commit | 6bf29a4259ecbb3ff3e75413f6f680810bf4ceb3 |
version (container hash) | c8c83a5357bbd5f2ddfba2366ba14823 |
build date | 2019-06-13T14:46:44.406Z |
size (MB) | 3094 |
size (bytes) | 1032818719 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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