Skip to content

Commit cb098bb

Browse files
martabicamartabica
authored
Update Dockerfile
1 parent 31819c5 commit cb098bb

1 file changed

Lines changed: 31 additions & 30 deletions

File tree

‎fea/Dockerfile‎

Lines changed: 31 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
FROM rocker/r-ver:4.1.2
1+
FROM rocker/r-ver:4.5.2
22
MAINTAINER Marta Bica <mbica.compbio@gmail.com>
33

44
RUN apt-get update && apt-get -y upgrade && apt-get -y autoremove
@@ -17,44 +17,45 @@ RUN apt-get install -y libglpk40 libglpk-dev
1717

1818

1919
# Install R packages
20-
RUN R -e 'install.packages("cowplot", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
21-
RUN R -e 'install.packages("data.table", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
22-
RUN R -e 'install.packages("dplyr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
23-
RUN R -e 'install.packages("DT", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
24-
RUN R -e 'install.packages("ff", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
25-
RUN R -e 'install.packages("ggfun", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-27")'
26-
RUN R -e 'install.packages("ggplot2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
27-
RUN R -e 'install.packages("ggplotify", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
28-
RUN R -e 'install.packages("ggpubr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-09-19")'
29-
RUN R -e 'install.packages("ggrepel", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
30-
RUN R -e 'install.packages("ggridges", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
31-
RUN R -e 'install.packages("gridExtra", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
32-
RUN R -e 'install.packages("magrittr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
33-
RUN R -e 'install.packages("Matrix", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-01-20")'
34-
RUN R -e 'install.packages("matrixStats", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
35-
RUN R -e 'install.packages("msigdbr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-07")'
36-
RUN R -e 'install.packages("patchwork", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
37-
RUN R -e 'install.packages("plotly", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
38-
RUN R -e 'install.packages("reshape2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
39-
RUN R -e 'install.packages("Seurat", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2022-05-20")'
40-
RUN R -e 'install.packages("shiny", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
41-
RUN R -e 'install.packages("shinycssloaders", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
42-
RUN R -e 'install.packages("shinydashboard", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
43-
RUN R -e 'install.packages("shinyjs", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
44-
RUN R -e 'install.packages("shinythemes", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
45-
RUN R -e 'install.packages("stringi", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
46-
RUN R -e 'install.packages("stringr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
47-
RUN R -e 'install.packages("tidytree", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
20+
RUN R -e 'install.packages("cowplot", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-29")'
21+
RUN R -e 'install.packages("data.table", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
22+
RUN R -e 'install.packages("dplyr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
23+
RUN R -e 'install.packages("DT", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
24+
RUN R -e 'install.packages("ff", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
25+
RUN R -e 'install.packages("ggfun", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
26+
RUN R -e 'install.packages("ggplot2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
27+
RUN R -e 'install.packages("ggplotify", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
28+
RUN R -e 'install.packages("ggpubr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
29+
RUN R -e 'install.packages("ggrepel", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
30+
RUN R -e 'install.packages("ggridges", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
31+
RUN R -e 'install.packages("gridExtra", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
32+
RUN R -e 'install.packages("magrittr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
33+
RUN R -e 'install.packages("Matrix", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
34+
RUN R -e 'install.packages("matrixStats", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
35+
RUN R -e 'install.packages("msigdbr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
36+
RUN R -e 'install.packages("patchwork", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
37+
RUN R -e 'install.packages("plotly", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
38+
RUN R -e 'install.packages("reshape2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
39+
RUN R -e 'install.packages("Seurat", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
40+
RUN R -e 'install.packages("shiny", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
41+
RUN R -e 'install.packages("shinycssloaders", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
42+
RUN R -e 'install.packages("shinydashboard", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
43+
RUN R -e 'install.packages("shinyjs", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
44+
RUN R -e 'install.packages("shinythemes", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
45+
RUN R -e 'install.packages("stringi", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
46+
RUN R -e 'install.packages("stringr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
47+
RUN R -e 'install.packages("tidytree", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
4848

4949
RUN R -e 'install.packages("BiocManager")'
5050
RUN R -e 'BiocManager::install("scuttle")'
5151
RUN R -e 'BiocManager::install("BiocSingular")'
5252
RUN R -e 'BiocManager::install("fgsea")'
53+
RUN R -e 'BiocManager::install("markeR")'
5354

5455
RUN R -e 'install.packages("devtools")'
5556
RUN R -e 'remotes::install_github("YuLab-SMU/ggtree")'
5657
RUN R -e 'devtools::install_github("XiaoLuo-boy/ggheatmap")'
57-
RUN R -e 'install.packages("gplots", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
58+
RUN R -e 'install.packages("gplots", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
5859

5960
# Set the working directory
6061
WORKDIR /home/app

0 commit comments

Comments
 (0)