add Reproducible checkpoint library

docker/Dockerfile

@@ -9,16 +9,21 @@ MAINTAINER yohan.jarosz@uni.lu
 ################
 # dependencies #
 ################
-RUN apt-get update && apt-get -yq upgrade \
-    && apt-get install -yq libboost-dev \
-    && apt-get install -yq make cmake wget build-essential unzip \
-    && apt-get install -yq openjdk-7-jdk ant git tig vim \
+RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty main restricted universe multiverse" > /etc/apt/sources.list
+RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty-security main restricted universe" >> /etc/apt/sources.list
+RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty-updates main restricted universe multiverse">> /etc/apt/sources.list
+RUN apt-get update \
+    && apt-get install -yq python-software-properties software-properties-common \
+    && add-apt-repository "deb http://cran.stat.ucla.edu/bin/linux/ubuntu trusty/" \
+    && gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 \
+    && gpg -a --export E084DAB9 | apt-key add - \
+    && apt-get update \
+    && apt-get -yq upgrade \
+    && apt-get install -yq make cmake wget build-essential unzip openjdk-7-jdk ant git tig vim \
     && apt-get install -yq libboost-filesystem1.54-dev libboost-program-options1.54-dev libboost-regex1.54-dev libboost-system1.54-dev libboost-thread1.54-dev libboost-system1.54-dev \
-    && apt-get install -yq bioperl=1.6.923-1 tabix=0.2.6-2 zlib1g zlib1g-dev \
-    && apt-get install -yq samtools gnuplot python3 \
+    && apt-get install -yq bioperl=1.6.923-1 tabix=0.2.6-2 zlib1g zlib1g-dev samtools gnuplot python3 \
     && apt-get install -yq r-base r-base-dev \
     && apt-get install -yq libncurses5 libncurses5-dev sudo libatlas-base-dev python2.7 gfortran python-dev \
-    && rm -rf /var/lib/apt/lists/* \
     && update-alternatives --set java /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java
 
 
@@ -34,17 +39,11 @@ RUN mkdir -p /home/imp/tmp /home/imp/lib \
     && pip install -Iv https://pypi.python.org/packages/source/b/bioservices/bioservices-1.3.5.tar.gz \
     && rm get-pip.py
 
-
-## R
+# R with checkpoint libraries
+ADD dependencies.R /home/imp/lib/
 RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile \
-    && Rscript -e "install.packages('ggplot2')" \
-    && Rscript -e "install.packages('gtools')" \
-    && Rscript -e "install.packages('data.table')" \
-    && Rscript -e "install.packages('reshape')" \
-    && Rscript -e "install.packages('stringr')" \
-    && Rscript -e "install.packages('xtable')" \
-    && Rscript -e "install.packages('psych')" \
-    && Rscript -e "install.packages('beanplot')" \
+    && Rscript -e "install.packages('checkpoint')" \
+    && Rscript -e "library(checkpoint);checkpoint('2015-04-27', project='/home/imp/lib')" \
     && Rscript -e "source('http://bioconductor.org/biocLite.R');biocLite('genomeIntervals')"
 
 

docker/dependencies.R

+require(ggplot2)
+require(gtools)
+require(data.table)
+require(reshape)
+require(grid)
+require(grDevices)
+require(genomeIntervals)
+require(stringr)
+require(xtable)
+require(beanplot)
+require(psych)

src/IMP_visualize_MGMT.R

@@ -3,6 +3,8 @@
 ###################################################################################################
 ## Load required packages
 ###################################################################################################
+library(checkpoint)
+checkpoint('2015-04-27')
 
 require(ggplot2)
 require(gtools)
@@ -682,11 +684,11 @@ print("Generating mapped reads plot")
 var1 <-log10(c(all.dat$MG_reads,all.dat$MT_reads))
 var1[is.infinite(var1)]=NA
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-mapped_reads<-data.frame(var1,var2) 
+mapped_reads<-data.frame(var1,var2)
 
 png(name_plot("IMP-reads_density.png"), width=350, height=700)
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= mapped_reads,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= mapped_reads,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 bw="nrd0", main="Mappable reads", ylab=expression(log[10]*~"count"))
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -697,11 +699,11 @@ print("Generating rpkm plot")
 var1 <-log10(c(all.dat$MG_rpkm,all.dat$MT_rpkm))
 var1[is.infinite(var1)]=NA
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-rpkm<-data.frame(var1,var2) 
+rpkm<-data.frame(var1,var2)
 
 png(name_plot("IMP-rpkm_density.png"), width=350, height=700)
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= rpkm,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= rpkm,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 bw="nrd0", main="RPKM", ylab=expression(log[10]*~"RPKM"))
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -711,11 +713,11 @@ dev.off()
 print("Generating coverage plot")
 var1 <-c(all.dat$MG_cov,all.dat$MT_cov)
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-coverage<-data.frame(var1,var2) 
+coverage<-data.frame(var1,var2)
 
 png(name_plot("IMP-coverage_density.png"), width=350, height=700)
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= coverage,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= coverage,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 bw="nrd0", main="Coverage", ylab="fraction")
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -725,11 +727,11 @@ dev.off()
 print("Generating depth density plot")
 var1 <-log10(c(all.dat$MG_depth,all.dat$MT_depth))
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-depth<-data.frame(var1,var2) 
+depth<-data.frame(var1,var2)
 
 png(name_plot("IMP-depth_density.png"), width=350, height=700)
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= depth,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= depth,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 bw="nrd0", main="Depth", ylab=expression(log[10]*~"avg. depth"))
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -786,13 +788,13 @@ dev.off()
 var1 <-log10(c(all.dat$MG_var,all.dat$MT_var))
 var1[is.infinite(var1)]=NA
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-variant_count<-data.frame(var1,var2) 
+variant_count<-data.frame(var1,var2)
 
 print("Generating variant count plots")
 png(name_plot("IMP-var_count.png") ,width=350, height=700)
 
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= variant_count,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= variant_count,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 main="Variant count", ylab=expression(log[10]*~count))
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -802,13 +804,13 @@ dev.off()
 var1 <-c(all.dat$MG_var_dens,all.dat$MT_var_dens)
 var1[is.infinite(var1)]=NA
 var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-variant_density<-data.frame(var1,var2) 
+variant_density<-data.frame(var1,var2)
 
 print("Generating variant density plots")
 png(name_plot("IMP-var_density.png") ,width=350, height=700)
 
 par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
-beanplot(var1 ~ var2, data= variant_density,  side = "both",log="auto", 
+beanplot(var1 ~ var2, data= variant_density,  side = "both",log="auto",
 what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
 main="Variant density", ylab="count / RPKM")
 legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
@@ -1000,3 +1002,4 @@ dev.off()
 save.image(name_plot("results.Rdat"))
 
 
+## Beanplot function