Merge pull request #83 from alneberg/develop

Bumped version number to 0.3.1

README.md

@@ -1,4 +1,4 @@
-#CONCOCT 0.3.0 [![Build Status](https://travis-ci.org/BinPro/CONCOCT.png?branch=master)](https://travis-ci.org/BinPro/CONCOCT)#
+#CONCOCT 0.3.1 [![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.
@@ -87,15 +87,15 @@ You need to [get Docker installed](https://www.docker.io/gettingstarted/) and sp
 
 We provide a Docker image:
 
-<b>binnisb/concoct_0.3.0</b> contains CONCOCT and all its dependencies for the [complete worklfow](doc/complete_example.md). Currently it does not do SCG evaluation.
+<b>binnisb/concoct_0.3.1</b> contains CONCOCT and all its dependencies for the [complete worklfow](doc/complete_example.md). Currently it does not do SCG evaluation.
 
 The following command will then download the image from the Docker image index, map the Data folder to the image and log you into the docker image.
 ```
-sudo docker run -v /home/USER/Data:/opt/Data -i -t binnisb/concoct_0.3.0 bash
+sudo docker run -v /home/USER/Data:/opt/Data -i -t binnisb/concoct_0.3.1 bash
 ```
 To test concoct you can then do:
 ```
-$ cd /opt/CONCOCT-0.3.0
+$ cd /opt/CONCOCT-0.3.1
 $ nosetests
 ```
 Which should execute all tests without errors.

doc/Dockerfile

@@ -1,12 +1,12 @@
-# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v0.3.0
-# VERSION 0.3.0
+# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v0.3.1
+# VERSION 0.3.1
 # 
 # This docker creates and sets up an Ubuntu environment with all
-# dependencies for CONCOCT v0.3.0 installed.
+# dependencies for CONCOCT v0.3.1 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_0.3.0 /bin/bash
+# sudo docker run -v /my/host/shared/directory:/my/docker/location -i -t binnisb/concoct_0.3.1 /bin/bash
 #
 
 FROM ubuntu:13.10
@@ -88,16 +88,16 @@ 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 0.3.0
+# Install python dependencies and fetch and install CONCOCT 0.3.1
 RUN cd /opt;\
     conda update --yes conda;\
     conda install --yes python=2.7 atlas cython numpy scipy biopython pandas pip scikit-learn pysam;\
-    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/0.3.0.tar.gz;\
-    tar xf 0.3.0.tar.gz;\
-    cd CONCOCT-0.3.0;\
+    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/0.3.1.tar.gz;\
+    tar xf 0.3.1.tar.gz;\
+    cd CONCOCT-0.3.1;\
     python setup.py install
 
-ENV CONCOCT /opt/CONCOCT-0.3.0
+ENV CONCOCT /opt/CONCOCT-0.3.1
 ENV CONCOCT_TEST /opt/Data/CONCOCT-test-data
 ENV CONCOCT_EXAMPLE /opt/Data/CONCOCT-complete-example
 

doc/complete_example.md

@@ -7,7 +7,7 @@ Required software
 ----------------------
 To run the entire example you need to install all dependencies as stated in the [README dependencies](../README.md#dependencies). This includes all the optional dependencies. You can also look at [doc/Dockerfile](Dockerfile) to help you install these packages on your server.
 
-Another way to get everything set up is to use our full Docker image (binnisb/concoct_0.3.0) as suggested in the [README docker](../README.md#using-docker).
+Another way to get everything set up is to use our full Docker image (binnisb/concoct_0.3.1) as suggested in the [README docker](../README.md#using-docker).
 
 It is not required to run all steps. The output files for each step are in the test data repository. At the end of this example the results should be the same as the results in the corresponding test data repository: https://github.com/BinPro/CONCOCT-test-data/releases. The version numbers listed above are the ones used to generate the results in that repository. Using newer versions will probably not be a problem, but your results may be different in that case.
 
@@ -32,11 +32,11 @@ Move the test data that was downloaded and extracted (CONCOCT-test-data) to the
 
 Now you want to execute the following command to log into our Docker image and to map the ```/HOST/path/to/Data``` to your image and the Data folder will be accessable in /opt/Data:
 
-    sudo docker run -v /HOST/path/to/Data:/opt/Data/ -i -t binnisb/concoct_0.3.0 bash
+    sudo docker run -v /HOST/path/to/Data:/opt/Data/ -i -t binnisb/concoct_0.3.1 bash
 
 This will download the 2G image to your machine and then leaves you in a BASH shell. In the Docker imgage, the following environmental variables have been set. So if you have your folders set up differently in the steps above you need to alter these variables accordingly:
 
-    CONCOCT=/opt/CONCOCT-0.3.0
+    CONCOCT=/opt/CONCOCT-0.3.1
     CONCOCT_TEST=/opt/Data/CONCOCT-test-data
     CONCOCT_EXAMPLE=/opt/Data/CONCOCT-complete-example
 

setup.py

@@ -3,7 +3,7 @@
 import sys, os
 from distutils.core import Extension
 
-version = '0.3.0'
+version = '0.3.1'
 
 module1 = Extension('vbgmm',
         libraries =['gsl',  'gslcblas'],