ModelArray/Apptainer.def at ee53de69d07fdeed187f70625b947d408db87882 · PennLINC/ModelArray · GitHub

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
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
Bootstrap: docker
From: rocker/r2u:jammy

%help
    ModelArray - an R package for statistical analysis of fixel-wise data and beyond

%labels
    org.label-schema.name "modelarray_confixel"
    org.label-schema.description "ModelArray - an R package for statistical analysis of fixel-wise data and beyond"
    org.label-schema.url "https://pennlinc.github.io/ModelArray/"
    org.label-schema.vcs-url "https://github.com/PennLINC/ModelArray"
    org.label-schema.schema-version "1.0"

%environment
    export DEBIAN_FRONTEND=noninteractive

%post
    set -e
    apt-get update \
        && apt-get install -y --no-install-recommends \
            less \
            python3 \
            python3-pip \
            r-bioc-delayedarray \
            r-bioc-hdf5array \
            r-cran-broom \
            r-cran-crayon \
            r-cran-devtools \
            r-cran-doparallel \
            r-cran-dplyr \
            r-cran-glue \
            r-cran-gratia \
            r-cran-hdf5r \
            r-cran-hdf5r.extra \
            r-cran-magrittr \
            r-cran-mgcv \
            r-cran-pbapply \
            r-cran-pbmcapply \
            r-bioc-rhdf5 \
            r-cran-tibble \
            r-cran-tidyr \
            r-cran-tidyverse \
            r-cran-tiledb \
        && apt-get clean \
        && echo 'options(bspm.sudo = TRUE)' >> /etc/R/Rprofile.site \
        && rm -rf /var/lib/apt/lists/* \
        && pip3 install radian

    # Create .Rprofile in root home to silence bspm warning
    mkdir -p /root
    echo 'options(bspm.sudo = TRUE)' >> /root/.Rprofile

    # Install TileDBArray from Bioconductor (not available as r-bioc- package)
    R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("TileDBArray", update = FALSE, ask = FALSE)'

    cd /ModelArray
    R -e 'devtools::install()'

%files
    . /ModelArray

%runscript
    echo "ModelArray container"
    echo "R version: $(R --version | head -n 1)"
    if [ $# -gt 0 ]; then
        exec "$@"
    else
        exec radian
    fi