brucemoran/Singularity:ucs_ucec_rnaseq.analysis

$ singularity pull shub://brucemoran/Singularity:ucs_ucec_rnaseq.analysis

Singularity Recipe

Bootstrap:shub
From:brucemoran/Singularity:centos7-r_3.5.1_jupyter

%post

    R --slave -e 'library("devtools"); devtools::install_github(c("renozao/rngtools", "renozao/NMF"), build_vignettes = FALSE); library("BiocManager"); BiocManager::install(c("CellMix"), site_repository="http://web.cbio.uct.ac.za/~renaud/CRAN")'

    #BiocManager to install packages
    R --slave -e 'library("BiocManager"); BiocManager::install(c("rngtools", "NMF", "CAMERA", "DEFormats", "apeglm", "ggpubr",  "roots", "viper", "mixtools", "bcellViper", "aracne.networks", "rgexf", "fgsea", "PoiClaClu", "GSVA"),  dependencies=c("Depends", "Imports", "LinkingTo"), update=TRUE, ask=FALSE, build_vignettes=FALSE, clean=TRUE)'
    
    cd /usr/local

    yum install -y java-1.8.0-openjdk ant

    git clone https://github.com/califano-lab/ARACNe-AP
    cd ARACNe-AP
    ant main

    echo -e "#! /bin/bash\njavamem=""\nif [[ \$1 =~ "-Xmx" ]];then javamem=\$1; shift 1; fi\nexec java \$javamem -jar /usr/local/src/ARACNe-AP/dist/aracne.jar "\$@"" > /usr/local/bin/ARACNe-AP

Collection


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Metrics

key value
id /containers/brucemoran-Singularity-ucs_ucec_rnaseq.analysis
collection name brucemoran/Singularity
branch master
tag ucs_ucec_rnaseq.analysis
commit c574a3f18e7b1c408721d7a5d0d3bf4add0cc641
version (container hash) 0fc1799f49674dddc5c26203f84de264
build date 2019-06-21T13:53:24.552Z
size (MB) 3484
size (bytes) 1427677215
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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