From 3b7d0e942b54ff35302c808f62af8b85da2c565b Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Fri, 13 Mar 2020 18:16:11 +0000
Subject: [PATCH 1/3] new docker file

---
 Dockerfile | 116 +++++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 100 insertions(+), 16 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index fae2107..0413f1d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,26 +1,110 @@
 # This container will install IVA from master
 #
-FROM debian:testing
+FROM ubuntu:18.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+WORKDIR /tmp
+
+ENV INSTALL_DIRECTORY=/opt
+
 
 # Install required dependancies
-RUN apt-get -qq update && apt-get install -y openjdk-8-jdk python3-pip git wget unzip zlib1g-dev libncurses5-dev
+RUN apt-get update -y -qq \
+    && apt-get install -y -qq \
+      openjdk-8-jdk \
+      python3-pip \
+      git \
+      wget \
+      unzip \
+      zlib1g-dev \
+      libncurses5-dev \
+      pkg-config \ 
+      libcurl4-openssl-dev \
+      lbzip2 \
+      zlib1g \
+      libbz2-1.0 \
+      libncurses5 \
+      liblzma5 \
+      build-essential \
+      libncurses5-dev \
+      libbz2-dev \
+      liblzma-dev
+  
 ENV JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"
-RUN git clone https://github.com/sanger-pathogens/iva.git
-RUN cd iva && ./install_dependencies.sh
-ENV PATH /iva/build/kmc-2.3.0:/iva/build/samtools-1.3:/iva/build/smalt-0.7.6-bin:/iva/build/samtools-1.3:/iva/build/MUMmer3.23:/iva/build/SPAdes-3.7.1-Linux/bin:$PATH
-RUN export PATH
 
-# Install optional dependencies
-RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip && unzip Trimmomatic-0.38.zip
+ARG KMC_VERSION=3.0.0
+ARG MUMMER_VERSION=3.23
+ARG SAMTOOLS_VERSION=1.3
+ARG SMALT_VERSION=0.7.6
+ARG TRIMMOMATIC_VERSION=0.38
+ARG KRAKEN_VERSION=1.0
+ARG BLAST_VERSION=2.5.0
+
+# kmc
+RUN mkdir /opt/kmc-${KMC_VERSION} \
+    && cd /opt/kmc-${KMC_VERSION} \
+    && wget --progress=dot:giga https://github.com/refresh-bio/KMC/releases/download/v${KMC_VERSION}/KMC3.linux.tar.gz \
+    && tar xf KMC3.linux.tar.gz \
+    && rm KMC3.linux.tar.gz \
+    && chmod -R 755 /opt/kmc-${KMC_VERSION}
+ENV PATH=/opt/kmc-${KMC_VERSION}:$PATH
+
+# MUMmer
+RUN cd /opt \
+    && wget --progress=dot:giga "http://downloads.sourceforge.net/project/mummer/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz" \
+    && tar xf MUMmer${MUMMER_VERSION}.tar.gz \
+    && rm MUMmer${MUMMER_VERSION}.tar.gz \
+    && cd MUMmer${MUMMER_VERSION} \
+    && make
+ENV PATH=/opt/MUMmer${MUMMER_VERSION}:$PATH
+
+# samtools
+RUN cd /opt \
+    && wget --progress=dot:giga "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" \
+    && tar xf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+    && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+    && cd samtools-${SAMTOOLS_VERSION} \
+    && make
+ENV PATH=/opt/samtools-${SAMTOOLS_VERSION}:$PATH
+ 
+# smalt
+RUN cd /opt \
+    && wget --progress=dot:giga http://downloads.sourceforge.net/project/smalt/smalt-${SMALT_VERSION}-bin.tar.gz \
+    && tar xf smalt-${SMALT_VERSION}-bin.tar.gz \
+    && rm smalt-${SMALT_VERSION}-bin.tar.gz \
+    && cd smalt-${SMALT_VERSION}-bin \
+    && ln -fs smalt_x86_64 smalt
+ENV PATH=/opt/smalt-${SMALT_VERSION}-bin:$PATH
+    
+# Trimmomatic
+RUN cd / \
+    && wget --progress=dot:giga http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VERSION}.zip \
+    && unzip Trimmomatic-${TRIMMOMATIC_VERSION}.zip \
+    && rm Trimmomatic-${TRIMMOMATIC_VERSION}.zip
 
-RUN wget http://ccb.jhu.edu/software/kraken/dl/kraken-1.0.tgz && tar -xvzf kraken-1.0.tgz
-RUN cd kraken-1.0 && ./install_kraken.sh ../kraken_install
-ENV PATH /kraken_install/:$PATH
-RUN export PATH
+# Kraken
+RUN mkdir /tmp/KRAKEN \
+    && cd /tmp/KRAKEN \
+    && wget --progress=dot:giga http://ccb.jhu.edu/software/kraken/dl/kraken-${KRAKEN_VERSION}.tgz \
+    && tar -xvzf kraken-${KRAKEN_VERSION}.tgz \
+    && cd kraken-${KRAKEN_VERSION} \
+    && ./install_kraken.sh /opt/kraken-${KRAKEN_VERSION} \
+    && rm -rf /tmp/KRAKEN
+ENV PATH=/opt/kraken-${KRAKEN_VERSION}/:$PATH
 
-RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.5.0/ncbi-blast-2.5.0+-x64-linux.tar.gz && tar -xzvf ncbi-blast-2.5.0+-x64-linux.tar.gz
-ENV PATH /ncbi-blast-2.5.0+:$PATH
-RUN export PATH
+# ncbi blast
+RUN cd /opt \
+    && wget --progress=dot:giga ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz \
+    && tar -xf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz \
+    && rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
+ENV PATH=/opt/ncbi-blast-${BLAST_VERSION}+/bin:$PATH
 
 # Install IVA
-RUN cd iva && python3 setup.py install
\ No newline at end of file
+ARG BUILD_DIR=/tmp/IVA
+COPY . $BUILD_DIR
+RUN cd ${BUILD_DIR} \
+    && pip3 install cython \
+    && python3 setup.py test \
+    && python3 setup.py install \
+    && rm -rf ${BUILD_DIR}

From 8868302cd4c0c8c900b80bf12d92b7c7303130ae Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Fri, 13 Mar 2020 18:28:52 +0000
Subject: [PATCH 2/3] fix travis

---
 .travis.yml             | 5 ++++-
 install_dependencies.sh | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 5b82bb2..49114d9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,6 +5,9 @@ addons:
     - zlib1g-dev
     - libncurses5-dev
     - libncursesw5-dev
+    - pkg-config
+    - libcurl4-openssl-dev
+
 cache:
   directories:
   - build
@@ -33,4 +36,4 @@ before_script:
 script:
   - "coverage run setup.py test"
 after_success:
-  - codecov
\ No newline at end of file
+  - codecov
diff --git a/install_dependencies.sh b/install_dependencies.sh
index a688fd3..b3ae849 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -96,4 +96,4 @@ update_path ${mummer_dir}
 update_path ${samtools_dir}
 update_path ${smalt_dir}
 
-
+pip install cython

From 1dd70f2dfabb30c16956481b2d74661c860710fb Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Fri, 13 Mar 2020 18:55:41 +0000
Subject: [PATCH 3/3] Fix travis build and update docker file

---
 .travis.yml | 5 ++---
 Dockerfile  | 9 ---------
 2 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 49114d9..0a4f2a9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,9 +5,8 @@ addons:
     - zlib1g-dev
     - libncurses5-dev
     - libncursesw5-dev
-    - pkg-config
-    - libcurl4-openssl-dev
-
+    - libbz2-dev
+    - liblzma-dev
 cache:
   directories:
   - build
diff --git a/Dockerfile b/Dockerfile
index 0413f1d..8038355 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,15 +19,6 @@ RUN apt-get update -y -qq \
       unzip \
       zlib1g-dev \
       libncurses5-dev \
-      pkg-config \ 
-      libcurl4-openssl-dev \
-      lbzip2 \
-      zlib1g \
-      libbz2-1.0 \
-      libncurses5 \
-      liblzma5 \
-      build-essential \
-      libncurses5-dev \
       libbz2-dev \
       liblzma-dev