From ec871128f9d4ba77464f6be7060335e5ed25a634 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= Date: Tue, 18 Jun 2019 15:25:52 +0100 Subject: [PATCH 1/3] Added Spades to docker file --- Dockerfile | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Dockerfile b/Dockerfile index c5602d73..86c6e4e0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,9 +26,14 @@ RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bo && unzip bowtie2-2.2.9-linux-x86_64.zip \ && rm -f bowtie2-2.2.9-linux-x86_64.zip +RUN wget -q https://github.com/ablab/spades/releases/download/v3.13.1/SPAdes-3.13.1-Linux.tar.gz \ + && tar -zxf SPAdes-3.13.1-Linux.tar.gz \ + && rm -f SPAdes-3.13.1-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 PATH=$PATH:$PWD/SPAdes-3.13.1-Linux/bin RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd From 4bb8144a9fb1f8a55996972c4940fe74548fb343 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= Date: Tue, 18 Jun 2019 15:26:40 +0100 Subject: [PATCH 2/3] Bumped Ariba version number --- CHANGELOG.md | 9 +++++++++ Dockerfile | 2 +- README.md | 2 +- setup.py | 2 +- 4 files changed, 12 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e29ef29..7951d3cc 100644 --- a/CHANGELOG.md +++ b/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) diff --git a/Dockerfile b/Dockerfile index 86c6e4e0..7a30aa1d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -39,7 +39,7 @@ 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 v2.14.2 \ && python3 setup.py test \ && python3 setup.py install diff --git a/README.md b/README.md index 6477b949..80a277f6 100644 --- a/README.md +++ b/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) diff --git a/setup.py b/setup.py index 016d7484..4bfad7c2 100644 --- a/setup.py +++ b/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/*']}, From 173ffbef8ea9138de245e37fa0ba80e1b7a66b35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= Date: Fri, 21 Jun 2019 12:10:20 +0100 Subject: [PATCH 3/3] Moved software version numbers into ARGs --- Dockerfile | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7a30aa1d..e10c83eb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,6 +4,11 @@ ENV DEBIAN_FRONTEND=noninteractive MAINTAINER ariba-help@sanger.ac.uk +# 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 \ @@ -22,24 +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/v3.13.1/SPAdes-3.13.1-Linux.tar.gz \ - && tar -zxf SPAdes-3.13.1-Linux.tar.gz \ - && rm -f SPAdes-3.13.1-Linux.tar.gz +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 PATH=$PATH:$PWD/SPAdes-3.13.1-Linux/bin +ENV ARIBA_BOWTIE2=$PWD/bowtie2-${BOWTIE2_VERSION}/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg" +ENV PATH=$PATH:$PWD/SPAdes-${SPADES_VERSION}-Linux/bin RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd RUN git clone https://github.com/sanger-pathogens/ariba.git \ && cd ariba \ - && git checkout v2.14.2 \ + && git checkout v${ARIBA_VERSION} \ + && rm -rf .git \ && python3 setup.py test \ && python3 setup.py install