Raked the new changes to proteomics and metabolmics repos.

idot · Apr 2, 2019 · 6ab6a88 · 6ab6a88
1 parent 21ca11c
commit 6ab6a88
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/out/devel_metabolomics/Dockerfile b/out/devel_metabolomics/Dockerfile
@@ -31,7 +31,8 @@ RUN apt-get update -qq && \
     liblapack-dev \
     cmake \
     default-jdk \
-    libnetcdf-dev libpng-dev libbz2-dev liblzma-dev libpcre3-dev libicu-dev
+    libnetcdf-dev libpng-dev libbz2-dev liblzma-dev libpcre3-dev libicu-dev \
+    libudunits2-dev libgdal-dev
 
 RUN bash -i -c 'wget -O libSBML-5.10.2-core-src.tar.gz https://downloads.sourceforge.net/project/sbml/libsbml/5.10.2/stable/libSBML-5.10.2-core-src.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsbml%2Ffiles%2Flibsbml%2F5.10.2%2Fstable%2F && tar xzvf libSBML-5.10.2-core-src.tar.gz ; cd libsbml-5.10.2 && CXXFLAGS=-fPIC CFLAGS=-fPIC ./configure --prefix=/usr && make && make install && ldconfig'
 

diff --git a/out/devel_proteomics/install.R b/out/devel_proteomics/install.R
@@ -41,6 +41,8 @@ pkgs_to_install <- setdiff(pkgs_to_install, rownames(installed.packages()))
 
 # https://github.com/Bioconductor/bioc_docker/issues/58
 pkgs_to_install <- pkgs_to_install[!grepl("prot2D", pkgs_to_install)]
+# https://github.com/Bioconductor/bioc_docker/issues/55
+pkgs_to_install <- pkgs_to_install[!grepl("spliceSites", pkgs_to_install)]
 
 ## Start the actual installation:
 ok <- BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE) %in% rownames(installed.packages())

diff --git a/out/release_metabolomics/Dockerfile b/out/release_metabolomics/Dockerfile
@@ -31,7 +31,8 @@ RUN apt-get update -qq && \
     liblapack-dev \
     cmake \
     default-jdk \
-    libnetcdf-dev libpng-dev libbz2-dev liblzma-dev libpcre3-dev libicu-dev
+    libnetcdf-dev libpng-dev libbz2-dev liblzma-dev libpcre3-dev libicu-dev \
+    libudunits2-dev libgdal-dev
 
 RUN bash -i -c 'wget -O libSBML-5.10.2-core-src.tar.gz https://downloads.sourceforge.net/project/sbml/libsbml/5.10.2/stable/libSBML-5.10.2-core-src.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsbml%2Ffiles%2Flibsbml%2F5.10.2%2Fstable%2F && tar xzvf libSBML-5.10.2-core-src.tar.gz ; cd libsbml-5.10.2 && CXXFLAGS=-fPIC CFLAGS=-fPIC ./configure --prefix=/usr && make && make install && ldconfig'
 

diff --git a/out/release_proteomics/install.R b/out/release_proteomics/install.R
@@ -41,6 +41,8 @@ pkgs_to_install <- setdiff(pkgs_to_install, rownames(installed.packages()))
 
 # https://github.com/Bioconductor/bioc_docker/issues/58
 pkgs_to_install <- pkgs_to_install[!grepl("prot2D", pkgs_to_install)]
+# https://github.com/Bioconductor/bioc_docker/issues/55
+pkgs_to_install <- pkgs_to_install[!grepl("spliceSites", pkgs_to_install)]
 
 ## Start the actual installation:
 ok <- BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE) %in% rownames(installed.packages())