Merge pull request #3 from marissafujimoto/dependency-poc

Testing dependencies in Docker

inst/extdata/Dockerfile

@@ -20,12 +20,31 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3-pip \
     python3-dev 
 
+RUN apt-get update && apt-get -y upgrade && \
+	apt-get install -y build-essential wget \
+		libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev libcurl3-dev && \
+	apt-get clean && apt-get purge && \
+	rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 ## Put more python packages we need here 
+################### Install idemp ###################
+ENV FOLDER=idemp
+ENV DST=/usr/src
+
+WORKDIR $DST/
+
+RUN git clone https://github.com/yhwu/idemp.git
+
+WORKDIR $DST/$FOLDER
+
+RUN make && \
+    ln -s $DST/$FOLDER/idemp /usr/local/bin
+
 ################### Install Seqtk ###################
 ENV ZIP=seqtk-1.4.tar.gz
 ENV URL=https://github.com/lh3/seqtk/archive/refs/tags/v1.4.tar.gz
 ENV FOLDER=seqtk-1.4
-ENV DST=/home/seqtk
+ENV DST=/usr/src
 
 RUN mkdir -p $DST && \
     wget $URL -O $DST/$ZIP && \
@@ -34,15 +53,15 @@ RUN mkdir -p $DST && \
 
 WORKDIR $DST/$FOLDER
 
-RUN make
+RUN make && \
+    ln -s $DST/$FOLDER/seqtk /usr/local/bin
 
 ################## Install Bowtie2 ##################
 
 ENV ZIP=bowtie2-2.4.1-linux-x86_64.zip
 ENV URL=https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1
 ENV FOLDER=bowtie2-2.4.1-linux-x86_64
-ENV DST=/home/biodocker/bin
-ENV ULOCAL=/usr/local/bin
+ENV DST=/usr/local/bin
 
 RUN mkdir -p $DST && \
     wget $URL/$ZIP/download -O $DST/$ZIP && \
@@ -52,13 +71,6 @@ RUN mkdir -p $DST && \
     rmdir $DST/$FOLDER
 
 ################## Install Samtools ##################
-
-RUN apt-get update && apt-get -y upgrade && \
-	apt-get install -y build-essential wget \
-		libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev libcurl3-dev && \
-	apt-get clean && apt-get purge && \
-	rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 WORKDIR /usr/src
 
 # Samtools
@@ -67,11 +79,18 @@ RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9
 	rm samtools-1.9.tar.bz2 && \
 	cd samtools-1.9 && \
 	./configure --prefix $(pwd) && \
-	make
-
+	make && \
+    sudo ln -s /usr/src/samtools-1.9/samtools /usr/local/bin
 
 ################# COPY over config files 
-COPY config config/
+COPY config /home/config/
+
+#################### COPY scripts ###################
+COPY scripts /home/scripts/
+
+# TODO remove this once paths are not hard coded
+#################### COPY data ######################
+COPY data /home/data/
 
 WORKDIR /data