Merge pull request #19 from rachelicr/ra-r-script

Ra r script

.devcontainer/Dockerfile

@@ -6,53 +6,77 @@
 ### USE IMAGE
 # ctrl-sh-p in vscode and select the image
 
+### TAG IMAGE
+# docker tag rachelicr/env-pisca-v1 rachelicr/env-pisca-v1:v04
+
 ### PUSH IMAGE
+# docker push rachelicr/env-pisca-v1:v01
 # docker push rachelicr/env-pisca-v1
 
 #################################################################################
 # Image downloaded with advice from: # https://stackoverflow.com/questions/54437030/how-can-i-create-a-docker-image-to-run-both-python-and-r
+###########################################################################
+###################### THEN INSTALL PYTHON ################################
+###########################################################################
 FROM ubuntu:latest
-#FROM r-base:4.0.3
+#FROM r-base:4.3.2
+COPY . /app
 ENV DEBIAN_FRONTEND=noninteractive
-RUN apt-get update && apt-get install -y --no-install-recommends build-essential r-base r-cran-randomforest python3.10 python3-pip python3-setuptools python3-dev
-#RUN apt-get update && apt-get install -y --no-install-recommends build-essential libpq-dev python3.10 python3-pip python3-setuptools python3-dev
-#RUN pip3 install --upgrade pip
-WORKDIR /app
+#RUN apt-get update && apt-get install -y --no-install-recommends build-essential r-base r-cran-randomforest python3.10 python3-pip python3-setuptools python3-dev
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential python3.10 python3-pip python3-setuptools python3-dev
+###########################################################################
+############# # installing python libraries  ##############################
+###########################################################################
 ADD requirements.txt .
-ADD requirements.r .
-# installing python libraries
-#RUN python3 -m venv .cont_env
-#RUN source .cont_env/bin/activate
+ADD requirements.R .
 RUN pip3 install -r requirements.txt
-# installing r libraries
-RUN Rscript requirements.r
-COPY . /app
-#######################################################################################
-# The pisca special additions needed
+###########################################################################
 WORKDIR /project
 COPY . /project
 # Install software 
 RUN apt-get update -y
 RUN apt-get install -y openssh-client
 RUN apt-get install -y wget
+###########################################################################
+###################### INSTALL R ################################
+###########################################################################
+RUN apt-get install -y gdebi-core
+RUN apt-get install -y libcairo2-dev libxt-dev
+RUN wget -O r-4.3.2_1_amd64.deb https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-4.3.2_1_amd64.deb
+RUN gdebi -n r-4.3.2_1_amd64.deb
+ENV PATH=/opt/R/4.3.2/bin:$PATH
+# install required R libraries
+RUN R -e "install.packages('ape',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('jsonlite',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('data.table',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('ggplot2',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('cowplot',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('HDInterval',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('lubridate',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('svglite',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+# And from BIOCMANAGER
+RUN R -e "install.packages('BiocManager',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "BiocManager::install('treeio')"
+RUN R -e "BiocManager::install('ggtree')"
+###########################################################################
+###################### THEN INSTALL BEAST/PISCA ###########################
+###########################################################################
+RUN apt-get update -y
 ENV JAVA_HOME=/project/jdk-20.0.2
 ENV PATH=$JAVA_HOME/bin:$PATH
 ENV PATH=/project/BEASTv1.8.4/bin:$PATH
-# install the correct version of java!!!!!
-#RUN wget -O jdk.tar.gz https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.tar.gz
-# it looks like that version has been moved to the archive between 10/10/23 and 17/10/23
+# install the correct version of java!!!!!  - makes directory jdk-20.0.2
 RUN wget -O jdk.tar.gz https://download.oracle.com/java/20/archive/jdk-20.0.2_linux-x64_bin.tar.gz
 RUN tar zxvf jdk.tar.gz
-## makes directory jdk-20.0.2
-# Install beast
+# Install beast - makes directory BEASTv1.8.4
 RUN wget -O beast.tgz https://github.com/beast-dev/beast-mcmc/releases/download/v1.8.4/BEASTv1.8.4.tgz
 RUN tar -xvzf beast.tgz
-## makes directory BEASTv1.8.4
-# Install pisca
+# Install pisca - ## makes directory PISCAv1.1 ## note that cd has to be inline with other commands
 RUN wget -O pisca.tgz https://github.com/adamallo/PISCA/releases/download/v1.1/PISCAv1.1.tgz
 RUN tar -xvzf pisca.tgz
-## makes directory PISCAv1.1 ## note that cd has to be inline with other commands
 RUN chmod +x /project/PISCAv1.1/install.sh
 RUN cd /project/PISCAv1.1/ && ./install.sh /project/BEASTv1.8.4/
 # make a dir for the tmp files
 RUN mkdir /project/xml
+
+

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
     // Build development container from pre-existing image
-    "image": "rachelicr/env-pisca-v1",
+    "image": "rachelicr/env-pisca-v1:latest",
 
     // Set *default* container specific settings.json values on container create.
     "settings": {},

.gitignore

@@ -176,4 +176,6 @@ cython_debug/
 *.Zone.Identifier
 .ds_store
 *.svg
+/pisca-box-vue/temp/*
+!/pisca-box-vue/temp/make.txt