Add Dockerfile

Dockerfile

@@ -0,0 +1,30 @@
+FROM ubuntu:16.04
+MAINTAINER [email protected]
+
+# Install prerequisites
+RUN apt-get update && apt-get install -y build-essential wget unzip make gfortran libopenblas-dev liblapack-dev python2.7 python-dev git python-pip
+
+# Add files
+RUN mkdir /bin/deenurp
+ADD . /bin/deenurp
+
+# Install conda and hdbscan
+ENV PATH="/root/miniconda2/bin/:${PATH}"
+RUN cd /bin/deenurp && \
+	wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
+	bash Miniconda2-latest-Linux-x86_64.sh -b && \
+	conda install -c conda-forge hdbscan
+
+
+# Install python requirements
+RUN pip install -r /bin/deenurp/requirements.txt
+
+# Install deenurp
+RUN cd /bin/deenurp/bin/ && chmod +x bootstrap.sh && PYTHON=/usr/bin/python2.7 DEENURP=/bin/deenurp ./bootstrap.sh
+RUN cd /bin/deenurp/bin/ && /bin/bash -c "source bin-env/bin/activate" 
+
+# Add to path
+ENV PATH="/bin/deenurp/bin/bin-env/bin/:${PATH}"
+
+# Run tests
+RUN cd /bin/deenurp/tests && bash run.sh

README.rst

@@ -14,7 +14,7 @@ The Easy Way
   (on Ubuntu: ``sudo apt-get install gfortran libopenblas-dev liblapack-dev``)
 * Install Python 2.7
 * run `bin/bootstrap.sh`
-* run `source deenurp-env/bin/activate`
+* run `source bin-env/bin/activate`
 
 the `deenurp` executable should now be on your `$PATH`
 

requirements.txt

@@ -16,13 +16,13 @@ SQLAlchemy==1.0.12
 biopython==1.67
 decorator==4.0.9
 pandas==0.18.1
-cogent==1.5.3
+cogent==1.9
 futures==3.0.5
-git+https://github.com/cmccoy/peasel.git@b1d5783d8d6d56cb0274e7977d093583c9c5f968
+peasel==0.3.1
 retrying==1.3.3
 scipy==0.18.0
 scikit-learn==0.17.1
 hdbscan==0.8
-git+https://github.com/biocore/tax2tree.git@63b220f115633ceb028ad7c96b04f9f494cf6ef7
-git+https://github.com/fhcrc/taxtastic.git@v0.6.4
+t2t==0.1
+taxtastic==0.6.4
 wsgiref==0.1.2