From c20826e50689b9fc5aba0e402e62255b61023051 Mon Sep 17 00:00:00 2001
From: gobikrishnan-s3141
 <139465475+gobikrishnan-s3141@users.noreply.github.com>
Date: Tue, 7 Jan 2025 21:34:12 +0000
Subject: [PATCH] Add files via upload

---
 Py.dockerfile  |  6 +++---
 R.dockerfile   | 18 +++++++++++++-----
 bsh.dockerfile |  6 +++---
 sh.dockerfile  |  2 +-
 4 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/Py.dockerfile b/Py.dockerfile
index a13e2ca..01c2b55 100644
--- a/Py.dockerfile
+++ b/Py.dockerfile
@@ -15,15 +15,15 @@ RUN apt-get update &&  apt-get install -y --no-install-recommends \
 	python3 \
 	python3-dev \
 	python3-pip \
-	vim \
 	wget \
 	curl \
 	git \
 	libopenblas-dev \
 	gfortran \
 	pkg-config \
+	zlib1g-dev \
 	libhdf5-dev\
-	&& rm -rf /var/lib/apt/lists/*
+	&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # user (for better security, don't run as root)
 RUN groupadd bioinfo && useradd -m -G bioinfo pymonk
@@ -43,7 +43,7 @@ WORKDIR ~/analysis && chown -R bioinfo:pymonk ~/analysis
 #        jupyter
 
 # python
-CMD ["python3"]
+ENTRYPOINT ["python3"]
 # (or, if you want to use jupyter notebook)
 # jupyter notebook
 #EXPOSE 8888
diff --git a/R.dockerfile b/R.dockerfile
index b9092f5..8e40698 100644
--- a/R.dockerfile
+++ b/R.dockerfile
@@ -2,12 +2,19 @@
 FROM ubuntu:latest
 # FROM r-base:latest [debian based R-image by rocker community]
 
+# avoids prompting during installation
+ENV DEBIAN_FRONTEND=noninteractive
+
 # install system dep
 RUN apt-get update && apt-get install -y --no-install-recommends \
 	build-essential\
 	cmake \
 	clang \
-	llvm \
+	clang-tools \
+	lldb \
+	lld \
+	libomp-dev \
+	curl \
 	r-base \
 	r-base-dev \
 	libcurl4-openssl-dev \
@@ -22,11 +29,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 	libpng-dev \
 	libtiff5-dev \
 	libjpeg-dev \
-	&& rm -rf /var/lib/apt/lists/*
+	zlib1g-dev \
+	&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ## set up env to use clang (experimental)
-#ENV CC=clang
-#ENV CXX=clang++
+ENV CC=clang
+ENV CXX=clang++
 
 # install core & required R pkgs
 RUN R -e "install.packages(c( \
@@ -57,7 +65,7 @@ RUN mkdir -p ~/analysis
 WORKDIR ~/analysis && chown -R rmonk:bioinfo ~/analysis
 
 # R
-CMD ["R"]
+ENTRYPOINT ["R"]
 
 #(or)
 # rserver
diff --git a/bsh.dockerfile b/bsh.dockerfile
index 3e527bd..f06cdd1 100644
--- a/bsh.dockerfile
+++ b/bsh.dockerfile
@@ -14,8 +14,8 @@ RUN apt-get update &&  apt-get install -y --no-install-recommends \
         libopenblas-dev \
         gfortran \
         pkg-config \
-        libhdf5-dev\
-        && rm -rf /var/lib/apt/lists/*
+        zlib1g-dev \
+	&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # user
 RUN groupadd bioinfo && useradd -m -G bioinfo bmonk
@@ -26,4 +26,4 @@ RUN mkdir -p ~/analysis
 WORKDIR ~/analysis && chown -R bmonk:bioinfo ~/analysis
 
 # launch a shell
-CMD ["sh"]
+ENTRYPOINT ["sh"]
diff --git a/sh.dockerfile b/sh.dockerfile
index 3e31548..8ead427 100644
--- a/sh.dockerfile
+++ b/sh.dockerfile
@@ -22,4 +22,4 @@ RUN mkdir ~/scripts
 WORKDIR ~/scripts
 
 #shell
-CMD ["sh"]
+ENTRYPOINT ["sh"]