Add adaptive kmer selection

Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>

Dockerfile

@@ -5,12 +5,20 @@ RUN echo "deb http://http.debian.net/debian jessie main contrib non-free" > /etc
 RUN apt-get update -y
 RUN apt-get install -y libsparsehash-dev libboost-all-dev openmpi-bin gcc build-essential make autoconf bsdmainutils
 
-ADD https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz /tmp/
-RUN tar xzf /tmp/abyss-1.5.2.tar.gz
-WORKDIR /abyss-1.5.2
-RUN ./configure && make && make install
+RUN apt-get install -y r-base
 
-ADD run /
+ADD http://kmergenie.bx.psu.edu/kmergenie-1.6741.tar.gz /tmp/kmergenie.tar.gz
+RUN mkdir /tmp/kmergenie
+RUN tar xzf /tmp/kmergenie.tar.gz --directory /tmp/kmergenie --strip-components=1
+RUN cd /tmp/kmergenie && make && make install
+
+ADD https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz /tmp/abyss.tar.gz
+RUN mkdir /tmp/abyss
+RUN tar xzf /tmp/abyss.tar.gz --directory /tmp/abyss --strip-components=1
+RUN cd /tmp/abyss && ./configure && make && make install
+
+ADD run /usr/local/bin/
+ADD estimate_kmer /usr/local/bin/
 ADD Procfile /
 
-ENTRYPOINT ["/run"]
+ENTRYPOINT ["run"]

Procfile

@@ -1,3 +1,4 @@
-k-32: abyss-pe k=32 name=genome in=${READS}
 default: abyss-pe k=64 name=genome in=${READS}
+adaptive: abyss-pe k=$(estimate_kmer ${READS}) name=genome in=${READS}
+k-32: abyss-pe k=32 name=genome in=${READS}
 k-96: abyss-pe k=96 name=genome in=${READS}

estimate_kmer

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+kmergenie $1 2> /dev/null | tail -n 1 | cut -f 3 -d ' '