Fixed Dockerfiles

Some strange errors there.
MarcSaric · May 1, 2019 · 588c4d4 · 588c4d4
1 parent c218c5b
commit 588c4d4
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Showing 2 changed files with 36 additions and 17 deletions.
diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile
@@ -16,11 +16,13 @@ RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     fonts-dejavu \
     gfortran \
-    gcc && \
+    gcc \
+    unzip && \
     rm -rf /var/lib/apt/lists/*
 
 # Fix a bug in some R-packages, which want /bin/gtar instead of /bin/tar
-RUN ln -s /bin/tar /bin/gtar
+# And try to fix https://github.com/r-lib/devtools/issues/1722
+RUN ln -s /bin/tar /bin/gtar && export TAR=/bin/tar
 
 USER $NB_UID
 
@@ -52,18 +54,30 @@ RUN conda config --system --append channels r && \
     'r-sparklyr=0.9*' \
     'r-htmlwidgets=1.2*' \
     'r-hexbin=1.27*' && \
-    conda clean -tipsy && \
     fix-permissions $CONDA_DIR && \
+    conda clean -tipsy && \
     fix-permissions /home/$NB_USER
 
+# Add devtools set some options and go
 RUN R -e 'library("devtools");\
+          options(unzip = "internal");\
           install_github(c("jrnold/ggthemes"))'
 
 
+# Add the Bioconductor installer and install the base packages
+RUN R -e 'options(repos=structure(c(CRAN="https://cloud.r-project.org" )));\
+          if (!requireNamespace("BiocManager")) {install.packages("BiocManager")};\
+          BiocManager::install()'
+
+# And we still have to install BiocInstaller to install TCGABiolinks. Yay!
+RUN R -e 'source("https://bioconductor.org/biocLite.R");\
+	      biocLite("BiocInstaller")'
+
+# Need to install some dependencies for TCGAbiolinks explicitly
+RUN R -e 'BiocManager::install(c("sesame", "EDASeq", "GenomicFeatures"))'
+
 # Install TCGAbiolinks from dev
-RUN R -e 'if (!requireNamespace("BiocManager"))\
-             install.packages("BiocManager")\
-          BiocManager::install();'
 RUN R -e 'library("devtools");\
+          options(unzip = "internal");\
           install_github("BioinformaticsFMRP/TCGAbiolinks")'
 
diff --git a/deseq2-biocparallel-notebook/Dockerfile b/deseq2-biocparallel-notebook/Dockerfile
@@ -14,16 +14,21 @@ USER $NB_UID
 RUN  conda install --quiet --yes \
     'r-gplots' \
     'r-ape' 
-
-
-# Add DESeq2 dependencies from Bioconductor
-RUN R -e 'install.packages(c("pheatmap", "fastcluster"), repo = "https://cloud.r-project.org/")'
-
-# Add DESeq2 from Bioconductor
-RUN R -e 'BiocManager::install(c("DESeq2"))'
-
-# For historic reasons DESeq2 is already in the datascience-notebook
-RUN R -e 'BiocManager::install(c("apeglm", "BiocParallel", "DEGreport", "vsn", "goseq", "EnsDb.Hsapiens.v79", "org.Hs.eg.db"))'
-
 
+# Add the Bioconductor installer and install the base packages
+RUN R -e 'if (!requireNamespace("BiocManager")) {install.packages("BiocManager")};\
+          BiocManager::install()'
 
+# Add DESeq2 dependencies from Bioconductor
+RUN R -e 'install.packages(c("pheatmap", "fastcluster"), repo = "https://cloud.r-project.org")'
+
+# # Add DESeq2 from Bioconductor and other packages
+RUN R -e 'BiocManager::install(c("apeglm", \
+                                 "BiocParallel", \
+                                 "DESeq2", \
+                                 "DEGreport", \
+                                 "vsn", \
+                                 "goseq", \
+                                 "EnsDb.Hsapiens.v86", \
+                                 "org.Hs.eg.db")\
+                               )'