asafpr/singularity:latest

$ singularity pull shub://asafpr/singularity:latest

Singularity Recipe

Bootstrap: docker
from: bioconductor/bioconductor_docker:RELEASE_3_10

%post
    apt-get update
    apt-get install -y sqlite3 wget libxml2-dev libgit2-dev
    
    # Install INRICH
    wget https://bitbucket.org/statgen/inrich/get/30c7f7e93e2a.zip
    unzip 30c7f7e93e2a.zip
    cd statgen-inrich-30c7f7e93e2a && make
    cp inrich /usr/local/bin
    # Install mousegwas
    Rscript -e 'install.packages("XML", repos = "http://www.omegahat.net/R")'
    Rscript -e 'install.packages("devtools", repos="http://cran.us.r-project.org")'
    Rscript -e 'library(devtools); local({r <- getOption("repos"); r["CRAN"] <- "http://cran.us.r-project.org"; options(repos=r)}); install_github("TheJacksonLaboratory/mousegwas")'
    # Install GEMMA
    curl -L https://github.com/genetics-statistics/GEMMA/releases/download/0.98.1/gemma-0.98.1-linux-static.gz |zcat - > /usr/local/bin/gemma
    chmod a+x /usr/local/bin/gemma
    # Install pyLMM
    pip install numpy
    pip install scipy
    wget https://github.com/brielin/pylmm/archive/master.zip
    unzip master.zip
    cp pylmm-master/pylmmGWAS.py /usr/local/bin
    cp pylmm-master/pylmmKinship.py /usr/local/bin
    chmod a+x /usr/local/bin/pylmmGWAS.py
    chmod a+x /usr/local/bin/pylmmKinship.py
    apt-get clean

%apprun run_GWAS
    Rscript -e 'source(file=system.file("exec/run_GWAS.R", package="mousegwas"))' "$@"

%apprun postprocess_mv
    Rscript -e 'source(file=system.file("exec/postprocess_mv.R", package="mousegwas"))' "$@"

Collection

• Name: asafpr/singularity
• License: None

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