Merge pull request #267 from dib-lab/misc

Updates and fixes for Docker config, preprequisites, and the README

.dockerignore

@@ -0,0 +1,2 @@
+scratch/
+notebook/

Dockerfile

@@ -1,13 +1,42 @@
-FROM ubuntu:16.04
+FROM debian:stable
 MAINTAINER Daniel Standage <daniel.standage@gmail.com>
 
-WORKDIR /src/
-COPY ./ /src/
+WORKDIR /workdir/
+COPY ./ /workdir/
 
-RUN apt-get update && apt-get install -y git build-essential libz-dev python-dev python-pip bwa
-RUN pip install --upgrade pip setuptools==32.0.0
-RUN pip install pysam==0.11.2.2 networkx==1.11 pandas==0.20.3
-RUN pip install git+https://github.com/dib-lab/khmer.git@6a1f3ec994299ceda4367d75e6aa441ebad12909
-RUN pip install .
+ENV PACKAGES locales git wget autoconf build-essential libcurl4-openssl-dev \
+             zlib1g-dev libbz2-dev libbz2-dev liblzma-dev libncurses5-dev \
+             python3-dev python3-pip python3-venv python3-wheel
+RUN apt-get update && apt-get install -y ${PACKAGES} && apt-get clean
+
+
+RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && locale-gen
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+
+RUN wget https://github.com/samtools/htslib/archive/1.8.tar.gz \
+    &&  tar -xzf 1.8.tar.gz && cd htslib-1.8/ \
+    && autoconf && autoheader && ./configure && make && make install \
+    && cd - && rm -r htslib-1.8/ 1.8.tar.gz
+RUN wget https://github.com/samtools/samtools/archive/1.8.tar.gz \
+    && tar -xzf 1.8.tar.gz && cd samtools-1.8/ \
+    && autoconf && autoheader && ./configure && make && make install \
+    && cd - && rm -r samtools-1.8/ 1.8.tar.gz
+RUN wget https://github.com/lh3/bwa/archive/v0.7.17.tar.gz \
+    && tar -xzf v0.7.17.tar.gz && cd bwa-0.7.17/ \
+    && make && cp bwa /usr/local/bin/bwa \
+    && cd - && rm -r bwa-0.7.17/ v0.7.17.tar.gz
+
+
+RUN pip3 install --upgrade pip 'setuptools>=32.0.0'
+RUN pip3 install cython==0.28.3 pysam==0.14.1 networkx==2.1 pandas==0.23.1 scipy==1.1.0 matplotlib==2.2.0
+RUN pip3 install git+https://github.com/dib-lab/khmer.git@6c893074ea005589c230fb7cb3712f0b258f42fc
+RUN pip3 install .
+
+
+RUN rm -r /workdir/*
 
 CMD bash

README.md

@@ -0,0 +1,66 @@
+[![kevlar build status][travisbadge]](https://travis-ci.org/dib-lab/kevlar)
+[![PyPI version][pypibadge]](https://pypi.python.org/pypi/biokevlar)
+[![Test coverage][codecovbadge]](https://codecov.io/github/dib-lab/kevlar)
+[![kevlar documentation][rtdbadge]](http://kevlar.readthedocs.io/en/latest/?badge=latest)
+[![Docker build status][dockerbadge]](https://quay.io/repository/dib-lab/kevlar)
+[![MIT licensed][licensebadge]](https://github.com/dib-lab/kevlar/blob/master/LICENSE)
+
+<img src="docs/_static/morpheus-kevlar.jpg" alt=" What if I told you we don't need alignments to find variants?" width="400px" />
+
+# kevlar
+
+Daniel Standage, 2016  
+https://kevlar.readthedocs.io
+
+Welcome to **kevlar**, software for predicting *de novo* genetic variants without mapping reads to a reference genome!
+kevlar's k-mer abundance based method calls single nucleotide variants (SNVs) as well as short, medium and long insertion/deletion variants (indels) simultaneously.
+This software is free for use under the MIT license.
+
+<details>
+  <summary>Where can I find kevlar online?</summary>
+  <ul>
+    <li>Source repository: https://github.com/dib-lab/kevlar</li>
+    <li>Documentation: https://kevlar.readthedocs.io</li>
+    <li>Stable releases: https://github.com/dib-lab/kevlar/releases</li>
+    <li>Issue tracker: https://github.com/dib-lab/kevlar/issues</li>
+  </ul>
+
+  If you have questions or need help with kevlar, the [GitHub issue tracker](https://github.com/dib-lab/kevlar) should be your first point of contact.
+</details>
+
+<details>
+  <summary>How do I install kevlar?</summary>
+
+  See [the kevlar documentation](http://kevlar.readthedocs.io/en/latest/install.html) for complete instructions, but the impatient can try the following.
+
+  ```
+  pip install git+https://github.com/dib-lab/khmer.git
+  pip install biokevlar
+  ```
+</details>
+
+<details>
+  <summary>How do I use kevlar?</summary>
+  <ul>
+    <li>Installation instructions: http://kevlar.readthedocs.io/en/latest/install.html</li>
+    <li>Quick start guide: http://kevlar.readthedocs.io/en/latest/quick-start.html</li>
+    <li>Tutorial: http://kevlar.readthedocs.io/en/latest/tutorial.html</li>
+  </ul>
+</details>
+
+<details>
+  <summary>How can I contribute?</summary>
+
+  We welcome contributions to the kevlar project from the community!
+  If you're interested in modifying kevlar or contributing to its ongoing development, feel free to send us a message or submit a pull request!
+
+  The kevlar software is a project of the [Lab for Data Intensive Biology](http://ivory.idyll.org/lab/) and the [Computational Genomics Lab](http://www.hormozdiarilab.org/) at UC Davis.
+</details>
+
+
+[travisbadge]: https://img.shields.io/travis/dib-lab/kevlar.svg
+[pypibadge]: https://img.shields.io/pypi/v/biokevlar.svg
+[codecovbadge]: https://img.shields.io/codecov/c/github/dib-lab/kevlar.svg
+[rtdbadge]: https://readthedocs.org/projects/kevlar/badge/?version=latest&maxAge=900
+[dockerbadge]: https://quay.io/repository/dib-lab/kevlar/status
+[licensebadge]: https://img.shields.io/badge/license-MIT-blue.svg

setup.py

@@ -29,6 +29,10 @@
     language='c',
 )
 
+dependencies = [
+    'pysam>=0.14', 'networkx>=2.0', 'pandas>=0.23', 'scipy>=1.1',
+    'matplotlib>=2.2'
+]
 
 setup(name='biokevlar',
       version=versioneer.get_version(),
@@ -45,8 +49,8 @@
       },
       include_package_data=True,
       ext_modules=[ksw2, fermilite],
-      setup_requires=['pysam', 'networkx>=2.0', 'pandas'],
-      install_requires=['pysam', 'networkx>=2.0', 'pandas'],
+      setup_requires=dependencies,
+      install_requires=dependencies,
       entry_points={
           'console_scripts': ['kevlar = kevlar.__main__:main']
       },