Merge pull request #223 from alneberg/develop

Merging master into develop and prepare for new release

Dockerfile

@@ -1,12 +1,12 @@
-# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v0.5.0
-# VERSION 0.5.0
+# Docker for CONCOCT (http://github.com/BinPro/CONCOCT) v1.0.0
+# VERSION 1.0.0
 #
 # This docker creates and sets up an Ubuntu environment with all
-# dependencies for CONCOCT v0.5.0 installed.
+# dependencies for CONCOCT v1.0.0 installed.
 #
 # To login to the docker with a shared directory from the host do:
 #
-# docker run -v /my/host/shared/directory:/my/docker/location -i -t alneberg/concoct_0.5.0 /bin/bash
+# docker run -v /my/host/shared/directory:/my/docker/location -i -t alneberg/concoct_1.0.0 /bin/bash
 #
 
 FROM ubuntu:18.04
@@ -18,13 +18,13 @@ RUN apt-get install -qq wget build-essential libgsl0-dev git zip unzip bedtools
 
 RUN pip install --upgrade pip
 
-# Install python dependencies and fetch and install CONCOCT 0.5.0
+# Install python dependencies and fetch and install CONCOCT 1.0.0
 RUN cd /opt/CONCOCT;\
     pip install -r requirements.txt;\
 
-#    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/0.5.0.tar.gz;\
-#    tar xf 0.5.0.tar.gz;\
-#    cd CONCOCT-0.5.0;\
+#    wget --no-check-certificate https://github.com/BinPro/CONCOCT/archive/1.0.0.tar.gz;\
+#    tar xf 1.0.0.tar.gz;\
+#    cd CONCOCT-1.0.0;\
 #    python setup.py install
 
 RUN cd /opt/CONCOCT/;\

README.md

@@ -1,4 +1,4 @@
-## CONCOCT 0.5.0 development version [![Build Status](https://travis-ci.org/BinPro/CONCOCT.png?branch=master)](https://travis-ci.org/BinPro/CONCOCT)
+## CONCOCT 1.0.0 [![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.
@@ -35,8 +35,8 @@ merge_cutup_clustering.py concoct_output/clustering_gt1000.csv > concoct_output/
 
 Extract bins as individual FASTA
 ```bash
-mkdir concoct_output/fata_bins
-extract_fasta_bins.py original_contigs.fa concoct_output/clustering_merge.csv --output_path concoct_output/fasta_bins
+mkdir concoct_output/fasta_bins
+extract_fasta_bins.py original_contigs.fa concoct_output/clustering_merged.csv --output_path concoct_output/fasta_bins
 ```
 
 ## Support ##

concoct/output.py

@@ -84,6 +84,7 @@ def write_pca(self, transform, threshold, index):
     @classmethod
     def write_assign(self, assign, threshold, index):
         transform_df = p.DataFrame(assign, index=index)
+        transform_df.columns=['cluster_id']
         transform_df.to_csv(
             self.ASSIGN_FILE_BASE.format(threshold),
             index_label="contig_id"