lrsim compiled inside the docker image

docker/Dockerfile

@@ -23,13 +23,14 @@ ARG CONTAINER_TIMEZONE=Europe/Amsterdam
 # Set locale
 #ENV LANG="en_US.UTF-8"
 
+
 RUN rm /bin/sh && \
     ln -s /bin/bash /bin/sh && \
     echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | tee -a /etc/apt/sources.list && \
     gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && \
     gpg -a --export E084DAB9 | apt-key add - && \
     apt-get update && \
-    apt-get install -y git python python-setuptools sudo wget curl bzip2 make unzip build-essential r-base r-base-dev openjdk-8-jre time && \
+    apt-get install -y git python python-setuptools sudo wget curl bzip2 make unzip build-essential r-base r-base-dev openjdk-8-jre cpanminus time && \
     echo "${CONTAINER_TIMEZONE}" > /etc/timezone && \
     ln -sf /usr/share/zoneinfo/${CONTAINER_TIMEZONE} /etc/localtime && \
     dpkg-reconfigure -f noninteractive tzdata && \
@@ -38,6 +39,12 @@ RUN rm /bin/sh && \
 
 ENV JAVA_HOME /usr/lib/jvm/java-7-openjdk-amd64
 
+#NEEDED BY LRSIM
+RUN cpanm -i Math::Random Inline Inline::C
+
+
+
+
 
 #
 # CREATE USER
@@ -60,45 +67,67 @@ USER tenx
 
 WORKDIR /home/tenx
 
-
+RUN mkdir /home/tenx/data && \
+    mkdir /home/tenx/bin
 
 #
 # INSTALL PROGRAMS
 #
 
-RUN curl $FILES_URL/files | tee files                                        && \
-    source ./files                                                           && \
-    wget $FILES_URL/$LONGRANGER  --progress=bar:force:noscroll -O- | tar axz && \
-    wget $FILES_URL/$LOUPE       --progress=bar:force:noscroll -O- | tar axz && \
-    wget $FILES_URL/$SUPERNOVA   --progress=bar:force:noscroll -O- | tar axz && \
-    wget $FILES_URL/$LRSIM       --progress=bar:force:noscroll -O- | tar axz && \
-    wget $FILES_URL/$JELLYFISH   --progress=bar:force:noscroll -O- | tar axz && \
-    ( mkdir kmc  && cd kmc  && \
-    wget $FILES_URL/$KMC         --progress=bar:force:noscroll -O- | tar axz    \
-    ) && \
-    ( mkdir GATK && cd GATK && \
-    wget $FILES_URL/$GATK        --progress=bar:force:noscroll -O- | tar axj    \
-    ) && \
-    wget $FILES_URL/$GENOMESCOPE --progress=bar:force:noscroll               && \
-    unzip -q $GENOMESCOPE                                                    && \
-    rm $GENOMESCOPE                                                          && \
-    mv longranger*  longranger                                               && \
-    mv loupe*       loupe                                                    && \
-    mv supernova*   supernova                                                && \
-    mv jellyfish*   jellyfish                                                && \
-    mv LRSIM*       LRSIM                                                    && \
-    mv genomescope* genoscope
+#RUN curl $FILES_URL/files | tee files
+
+#RUN curl $FILES_URL/files > files && source ./files                            && \
+#    wget $FILES_URL/$ANACONDA2   --progress=bar:force:noscroll -O anaconda2.sh && \
+#    bash anaconda2.sh -b                                                       && \
+#    rm anaconda2.sh                                                            && \
+#    echo 'export PATH=/home/tenx/anaconda/bin:$PATH' >> /home/tenx/.bashrc
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    wget $FILES_URL/$LONGRANGER  --progress=bar:force:noscroll -O- | tar axz   && \
+    mv longranger*  longranger
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    wget $FILES_URL/$LOUPE       --progress=bar:force:noscroll -O- | tar axz   && \
+    mv loupe*       loupe
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    wget $FILES_URL/$SUPERNOVA   --progress=bar:force:noscroll -O- | tar axz   && \
+    mv supernova*   supernova
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    wget $FILES_URL/$LRSIM       --progress=bar:force:noscroll -O- | tar axz   && \
+    cd LRSIM && ./make.sh && (perl simulateLinkedReads.pl -h || true)
+#NEEDED BY LRSIM
+#sudo apt-get install cpanminus
+#sudo cpanm -i Math::Random Inline Inline::C
+
+
+#RUN curl $FILES_URL/files > files && source ./files                            && \
+#    wget $FILES_URL/$JELLYFISH   --progress=bar:force:noscroll -O- | tar axz   && \
+#    mv jellyfish*   jellyfish                                                  && \
+#    cd jellyfish                                                               && \
+#    ./configure                                                                && \
+#    make
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    mkdir kmc  && cd kmc                                                       && \
+    wget $FILES_URL/$KMC         --progress=bar:force:noscroll -O- | tar axz
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    mkdir GATK && cd GATK                                                      && \
+    wget $FILES_URL/$GATK        --progress=bar:force:noscroll -O- | tar axj
+
+RUN curl $FILES_URL/files > files && source ./files                            && \
+    wget $FILES_URL/$GENOMESCOPE --progress=bar:force:noscroll                 && \
+    unzip -q $GENOMESCOPE                                                      && \
+    rm $GENOMESCOPE                                                            && \
+    mv genomescope* genoscope                                                  && \
+    echo -e '#!/bin/bash\nRscript /home/tenx/genoscope/genomescope.R $@\n' > /home/tenx/bin/genoscope && \
+    chmod +x /home/tenx/bin/genoscope
 
-ENV GATK_PATH /home/tenx/GATK/GenomeAnalysisTK.jar
 
-RUN cd jellyfish && \
-    ./configure  && \
-    make       
 
-RUN mkdir /home/tenx/data && \
-    mkdir /home/tenx/bin && \
-    echo -e '#!/bin/bash\nRscript /home/tenx/genoscope/genomescope.R $@\n' > /home/tenx/bin/genoscope && \
-    chmod +x /home/tenx/bin/genoscope
+ENV GATK_PATH /home/tenx/GATK/GenomeAnalysisTK.jar
 
 ADD activate           /home/tenx/activate