rstudio docker reduction

.gitignore

@@ -6,3 +6,8 @@ Docker/graphdb-free*
 graphdb-free
 P_*
 Docker/graphdb/graphdb-free*
+notebooks/.cache
+notebooks/.config
+notebooks/.ipython
+notebooks/.jupyter
+notebooks/.local

Docker/rstudio/Dockerfile

@@ -12,17 +12,14 @@ LABEL documentation="https://m-unlock.gitlab.io"
 LABEL license="NA"
 LABEL tags="Notebook"
 
-RUN install2.r ape gridExtra picante data.table RColorBrewer DT reshape reshape2 magrittr markdown ggpubr tibble pheatmap dplyr viridis devtools rmdformats intergraph network igraph ggplot2 gridExtra knitr plyr vegan dplyr ggrepel ggnetwork ade4 rmarkdown formatR caTools plotly rio ggfortify GGally
-# phyloseq microbiome phangorn genefilter 
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages(c('DT', 'reshape', 'reshape2', 'magrittr', 'markdown', 'ggpubr'))"
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages(c('tibble', 'pheatmap', 'dplyr', 'viridis', 'devtools', 'rmdformats'))"
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages(c('intergraph', 'network', 'igraph', 'ggplot2', 'gridExtra', 'knitr'))"
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages(c('plyr', 'vegan', 'dplyr', 'ggrepel', 'ggnetwork', 'ade4', 'rmarkdown'))"
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages(c('formatR', 'caTools', 'plotly', 'rio', 'ggfortify', 'GGally'))"
-RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages('BiocManager'); BiocManager::install(version = '3.12')"
-RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); BiocManager::install(c('phyloseq', 'microbiome', 'phangorn', 'genefilter'))"
+RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.12')"
+RUN R -e "BiocManager::install(c('phyloseq'))"
+
+RUN install2.r phangorn ape gridExtra picante data.table RColorBrewer DT reshape reshape2 magrittr markdown ggpubr tibble pheatmap dplyr viridis devtools rmdformats intergraph network igraph ggplot2 gridExtra knitr plyr vegan dplyr ggrepel ggnetwork ade4 rmarkdown formatR caTools plotly rio ggfortify GGally
+
+##########################################
+# microbiome genefilter
 # RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); require(devtools); install_version('foreign', version = '0.8-76', repos = 'http://cran.us.r-project.org')"
-# RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); install.packages('rio')"
 # # RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); devtools::install_github('microsud/microbiomeutilities')"
 # # RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); devtools::install_github('zdk123/SpiecEasi')"
 # RUN R -e "options(repos = list(CRAN = 'http://cran.r-project.org')); devtools::install_github('briatte/ggnet')"
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