diff --git a/.gitignore b/.gitignore
index 99e70dae5d25157ea9d85931c9feb41849e344b4..63e24325bd0aa1b252639a6d5c4f7398278787d5 100644
--- a/.gitignore
+++ b/.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
diff --git a/Docker/rstudio/Dockerfile b/Docker/rstudio/Dockerfile
index fb780b4a662f09e9d979d8ce5c6dbc9130331a8d..5accdd1019ec15aaf07f28f7ddf14bc5e0e8dd7a 100644
--- a/Docker/rstudio/Dockerfile
+++ b/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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