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RT 660940 - add spades to docker file #274

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merged 3 commits into from
Jun 21, 2019
Merged

RT 660940 - add spades to docker file #274

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ec87112
Added Spades to docker file
kpepper Jun 18, 2019
4bb8144
Bumped Ariba version number
kpepper Jun 18, 2019
173ffbe
Moved software version numbers into ARGs
kpepper Jun 21, 2019
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9 changes: 9 additions & 0 deletions CHANGELOG.md
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@@ -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)

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21 changes: 16 additions & 5 deletions Dockerfile
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Expand Up @@ -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 \
Expand All @@ -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

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -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/*']},
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