Merge pull request #220 from alneberg/installation_fix_0.4.1

Version 0.4.2

README.md

@@ -1,4 +1,4 @@
-## CONCOCT 0.4.1 [![Build Status](https://travis-ci.org/BinPro/CONCOCT.png?branch=master)](https://travis-ci.org/BinPro/CONCOCT)
+## CONCOCT 0.4.2 [![Build Status](https://travis-ci.org/BinPro/CONCOCT.png?branch=master)](https://travis-ci.org/BinPro/CONCOCT)
 
 A program for unsupervised binning of metagenomic contigs by using nucleotide composition, 
 coverage data in multiple samples and linkage data from paired end reads.

bin/concoct

@@ -7,7 +7,6 @@ import vbgmm
 
 from concoct.output import Output
 from concoct.parser import arguments
-from concoct.cluster import cluster
 from concoct.input import load_data
 from concoct.transform import perform_pca
 

doc/Dockerfile

@@ -1,12 +1,12 @@
-# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v0.4.1
-# VERSION 0.4.1
+# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v0.4.2
+# VERSION 0.4.2
 # 
 # This docker creates and sets up an Ubuntu environment with all
-# dependencies for CONCOCT v0.4.1 installed.
+# dependencies for CONCOCT v0.4.2 installed.
 #
 # To login to the docker with a shared directory from the host do:
 #
-# sudo docker run -v /my/host/shared/directory:/my/docker/location -i -t binnisb/concoct_0.4.1 /bin/bash
+# sudo docker run -v /my/host/shared/directory:/my/docker/location -i -t binnisb/concoct_0.4.2 /bin/bash
 #
 
 FROM ubuntu:13.10
@@ -83,16 +83,16 @@ RUN cd /opt;\
     printf "install.packages(\"ggplot2\", repo=$RREPO)\ninstall.packages(\"reshape\",repo=$RREPO)\ninstall.packages(\"gplots\",repo=$RREPO)\ninstall.packages(\"ellipse\",repo=$RREPO)\ninstall.packages(\"grid\",repo=$RREPO)\ninstall.packages(\"getopt\",repo=$RREPO)" > dep.R;\
     Rscript dep.R
 
-# Install python dependencies and fetch and install CONCOCT 0.4.1
+# Install python dependencies and fetch and install CONCOCT 0.4.2
 RUN cd /opt;\
     conda update --yes conda;\
     conda install --yes python=2.7 atlas cython numpy scipy biopython pandas pip scikit-learn pysam;\
     pip install bcbio-gff;\
-    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/0.4.1.tar.gz;\
-    tar xf 0.4.1.tar.gz;\
-    cd CONCOCT-0.4.1;\
+    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/0.4.2.tar.gz;\
+    tar xf 0.4.2.tar.gz;\
+    cd CONCOCT-0.4.2;\
     python setup.py install
 
-ENV CONCOCT /opt/CONCOCT-0.4.1
+ENV CONCOCT /opt/CONCOCT-0.4.2
 ENV CONCOCT_TEST /opt/Data/CONCOCT-test-data
 ENV CONCOCT_EXAMPLE /opt/Data/CONCOCT-complete-example