Merge pull request #274 from sanger-pathogens/rt660940_add_spades_to_…

…docker

RT 660940 - add spades to docker file

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Change Log
 
+[v2.14.2](https://github.com/sanger-pathogens/ariba/tree/v2.14.2) (2019-06-18)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.1...v2.14.2)
+
+**Fixed bugs:**
+
+- Added Spades assembler into Docker file - RT ticket 660940
+- Incremented release number
+- Added LICENSE file into release distribution - RT ticket 660890
+
 [v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.0...v2.14.1)
 

Dockerfile

@@ -4,6 +4,11 @@ ENV DEBIAN_FRONTEND=noninteractive
 
 MAINTAINER [email protected]
 
+# Software version numbers
+ARG BOWTIE2_VERSION=2.2.9
+ARG SPADES_VERSION=3.13.1
+ARG ARIBA_VERSION=2.14.2
+
 RUN apt-get -qq update && \
     apt-get install --no-install-recommends -y \
   build-essential \
@@ -22,19 +27,25 @@ RUN apt-get -qq update && \
   wget \
   zlib1g-dev
 
-RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip \
-  && unzip bowtie2-2.2.9-linux-x86_64.zip \
-  && rm -f bowtie2-2.2.9-linux-x86_64.zip
+RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip \
+  && unzip bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip \
+  && rm -f bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip
+
+RUN wget -q https://github.com/ablab/spades/releases/download/v${SPADES_VERSION}/SPAdes-${SPADES_VERSION}-Linux.tar.gz \
+  && tar -zxf SPAdes-${SPADES_VERSION}-Linux.tar.gz \
+  && rm -f SPAdes-${SPADES_VERSION}-Linux.tar.gz
 
 # Need MPLBACKEND="agg" to make matplotlib work without X11, otherwise get the error
 # _tkinter.TclError: no display name and no $DISPLAY environment variable
-ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg"
+ENV ARIBA_BOWTIE2=$PWD/bowtie2-${BOWTIE2_VERSION}/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg"
+ENV PATH=$PATH:$PWD/SPAdes-${SPADES_VERSION}-Linux/bin
 
 RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.14.1 \
+  && git checkout v${ARIBA_VERSION} \
+  && rm -rf .git \
   && python3 setup.py test \
   && python3 setup.py install
 

README.md

@@ -104,7 +104,7 @@ To use ARIBA use a command like this (substituting in your directories), where y
 
     docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba ariba -h
 
-When calling Ariba via Docker you'll also need to add **/data/** in front of all the passed in file or directory names (e.g. /data/my_output_folder) as that's where Ariba expects to find its data within the container.
+When calling Ariba via Docker (as above) you'll also need to add **/data/** in front of all the passed in file or directory names (e.g. /data/my_output_folder).
 
 
 ### Debian (testing)

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.1',
+    version='2.14.2',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},