build: docker and conda with bugfix in createref

Dockerfile

@@ -0,0 +1,16 @@
+FROM continuumio/miniconda
+ARG app_version
+
+MAINTAINER Andrew McPherson <[email protected]>
+
+USER root
+RUN conda config --add channels https://conda.anaconda.org/dranew && conda config --add channels https://conda.anaconda.org/shahcompbio && conda config --add channels bioconda
+RUN conda install defuse==$app_version
+RUN conda install openssl=1.0
+RUN mkdir -p /root/.config/matplotlib
+RUN echo "backend : Agg" > /root/.config/matplotlib/matplotlibrc
+
+ENV NAME defuse
+
+ENTRYPOINT ["bash"]
+

README.md

@@ -116,6 +116,24 @@ The latest version of R can be downloaded from the [R project website](http://ww
 
 Install the ada package. Run R, then at the prompt type `install.packages("ada")`
 
+### Build with conda
+
+To build the latest version with conda inside docker run:
+
+```
+bash run_build_conda.sh
+```
+
+### Build with docker
+
+To build version 0.8.1 of defuse, use the following command:
+
+```
+docker build ./ --build-arg app_version=0.8.1 -t defuse:0.8.1
+```
+
+Note that the docker build installs inside a container via conda thus a conda package must be built first for the given version.
+
 ### Reference Dataset
 
 The reference dataset setup process has been simplified as of deFuse 0.6.0, and deFuse now automatically downloads all required files. 
@@ -355,4 +373,5 @@ You cannot run get_reads.pl if you have removed the temporary files from the out
   * reads.split.catalog
   * job/reads.*.improper.sam
   * job/reads.*.spanning.filelist
-  * job/reads.*.spanning/*
+  * job/reads.*.spanning/*
+

build_conda.sh

@@ -0,0 +1,11 @@
+
+yum install gcc-c++ git -y
+conda config --set always_yes true
+conda config --set anaconda_upload yes
+conda config --add channels https://conda.anaconda.org/dranew
+conda config --add channels https://conda.anaconda.org/shahcompbio
+conda config --add channels 'bioconda'
+conda install conda-build anaconda-client
+anaconda login --username dranew
+conda build conda/defuse
+

run_build_conda.sh

@@ -0,0 +1 @@
+docker run -v ${PWD}:/repo -w /repo -it conda/miniconda2-centos6 bash -e build_conda.sh

scripts/defuse_create_ref.pl

@@ -89,7 +89,7 @@
 
 
 # Create cmdrunner for running bowtie-build and samtools faidx
-my $log_directory = dirname($0)."/log";
+my $log_directory = $dataset_directory."/log";
 my $log_prefix = $log_directory."/create_reference_dataset";
 
 mkdir $log_directory if not -d $log_directory;