base.recipe 1.46 KB
Newer Older
mmassaviol's avatar
mmassaviol committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Bootstrap: docker
From: rocker/r-ver:3.5.3

%environment
	export PATH=/opt/biotools/bin:$PATH
	export ROOTSYS=/opt/biotools/root
	export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'

%post

    if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
	if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi

    apt-get update
    apt-get install -y curl wget git nano
    apt-get install -y build-essential checkinstall make cmake software-properties-common
    apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev liblzma-dev
    apt-get install -y libxml2-dev libcurl4-openssl-dev

    # Python and Snakemake


    apt-get install -y python3-pip
    cd /usr/bin && ln python3 python && cd -
    pip3 install snakemake==5.4.0 oyaml

    pip3 install multiqc==1.7
    fic=$(find /usr/ -name stacks.py) && sed -i 's/out_dict\[s_name\] = cdict/out_dict\[content\[0\]\] = cdict/' $fic

    apt install -y fastqc=0.11.5+dfsg-6

    apt-get install -y graphviz pandoc

    Rscript -e 'install.packages("BiocManager",Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'
    Rscript -e 'install.packages("devtools",Ncpus=8, clean=TRUE)'
    Rscript -e 'install.packages(c("shiny","shinydashboard","shinyjs","shinyFiles"),Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'
    Rscript -e 'install.packages(c("DT","yaml","tidyverse","gplots"),Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'