Merge Haploflow into master

.github/workflows/build-and-test.yml

@@ -16,6 +16,17 @@ jobs:
         with:
           go-version: '^1.15.6'
 
+      - name: Install Haploflow
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential git ronn
+          cd /opt/
+          git clone https://github.com/hzi-bifo/Haploflow
+          cd Haploflow
+          git checkout 9a5a0ff6c3a0435e723e41f98fe82ec2ad19cf50
+          sh build.sh
+          sudo ln -s /opt/Haploflow/build/haploflow ~/bin/haploflow
+
       - name: Install IVA assembler dependencies
         run: |
           sudo apt-get install -qq zlib1g-dev libncurses5-dev libncursesw5-dev mummer ncbi-blast+

Dockerfile

@@ -83,6 +83,16 @@ RUN apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev && \
     tar -xzf smalt-0.7.6-bin.tar.gz --no-same-owner && \
     ln -s /opt/smalt-0.7.6-bin/smalt_x86_64 /bin/smalt
 
+## Install Haploflow
+RUN apt-get update && \
+    apt-get install -y build-essential sudo git ronn cmake && \
+    cd /opt/ && \
+    git clone https://github.com/hzi-bifo/Haploflow && \
+    cd Haploflow && \
+    git checkout 9a5a0ff6c3a0435e723e41f98fe82ec2ad19cf50 && \
+    yes | sh build.sh && \
+    ln -s /opt/Haploflow/build/haploflow /bin/haploflow
+
 ## Install dependencies for genetracks/drawsvg
 RUN apt-get install -q -y libcairo2-dev
 

Singularity

@@ -1,6 +1,6 @@
 # Generate the Singularity container to run MiCall on Kive.
 Bootstrap: docker
-From: centos:7
+From: python:3.8
 
 %help
     MiCall maps all the reads from a sample against a set of reference
@@ -53,48 +53,28 @@ From: centos:7
 
 %post
     echo ===== Installing Prerequisites ===== >/dev/null
-    yum update -q -y
-
-    yum groupinstall -q -y 'development tools'
-    yum install -q -y epel-release
-    yum install -q -y unzip wget fontconfig bzip2-devel xz-devel openssl-devel \
-        libffi-devel sqlite-devel
-
-    echo ===== Installing Python ===== >/dev/null
-    wget -q https://www.python.org/ftp/python/3.8.3/Python-3.8.3.tar.xz
-    tar xJf Python*
-    rm Python*.xz
-    cd Python*
-    ./configure --enable-optimizations
-    make altinstall
-    cd ..
-    rm -rf Python*
-    ln -s /usr/local/bin/python3.8 /usr/local/bin/python3
+    apt-get update -q
+    apt-get install -q -y unzip wget
 
     echo ===== Installing blast ===== >/dev/null
-    cd /root
-    # Saved our own copy, because download was slow from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-1.x86_64.rpm
-    wget -q https://github.com/cfe-lab/MiCall/releases/download/v7.12.dev28/ncbi-blast-2.6.0+-1.x86_64.rpm
-    yum install -q -y ncbi-blast-2.6.0+-1.x86_64.rpm
-    rm ncbi-blast-2.6.0+-1.x86_64.rpm
-    python3 /opt/micall/micall/blast_db/make_blast_db.py
+    apt-get install -q -y ncbi-blast+
 
     echo ===== Installing Rust and merge-mates ===== >/dev/null
-    yum install -q -y rust cargo
+    wget -qO rustup.sh https://sh.rustup.rs
+    chmod +x /rustup.sh
+    /rustup.sh -y -q
+    . /root/.cargo/env
+    rm rustup.sh
     cargo install --quiet --root / --git https://github.com/jeff-k/merge-mates.git --rev 2fec61363f645e2008a4adff553d098beae21469
 
-    ## Miniconda (Python 2) (Don't use this)
-    #wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
-    #bash miniconda.sh -b -p /opt/miniconda
-
     echo ===== Installing bowtie2 ===== >/dev/null
     wget -q -O bowtie2.zip https://github.com/BenLangmead/bowtie2/releases/download/v2.2.8/bowtie2-2.2.8-linux-x86_64.zip
-    unzip -qq bowtie2.zip -d /opt/
+    unzip bowtie2.zip -d /opt/
     ln -s /opt/bowtie2-2.2.8/ /opt/bowtie2
     rm bowtie2.zip
 
     echo ===== Installing IVA dependencies ===== >/dev/null
-    yum install -q -y tcsh ncurses-devel zlib-devel
+    apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev
     cd /bin
     wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc
     wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc_dump
@@ -122,32 +102,23 @@ From: centos:7
     tar -xzf smalt-0.7.6-bin.tar.gz --no-same-owner
     ln -s /opt/smalt-0.7.6-bin/smalt_x86_64 /bin/smalt
 
+    echo ===== Installing Haploflow ===== >/dev/null
+    apt-get install -q -y libboost-all-dev build-essential sudo git ronn cmake
+    cd /opt/
+    git clone https://github.com/hzi-bifo/Haploflow
+    cd Haploflow
+    git checkout 9a5a0ff6c3a0435e723e41f98fe82ec2ad19cf50
+    yes | sh build.sh
+
     echo ===== Installing Python packages ===== >/dev/null
+    # Install dependencies for genetracks/drawsvg
+    apt-get install -q -y libcairo2-dev
     # Also trigger matplotlib to build its font cache.
-    wget -q https://bootstrap.pypa.io/get-pip.py
-    python3 get-pip.py
-    rm get-pip.py
     cd /opt
-    pip install --quiet -r /opt/micall/requirements.txt
-    ln -s /usr/local/bin/cutadapt /usr/local/bin/cutadapt-1.11
-    python3 -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
-
-    # Install dependencies for genetracks/drawsvg
-    yum install -q -y cairo-devel cairo cairo-tools zlib-devel
-
-    yum groupremove -q -y 'development tools'
-    yum remove -q -y epel-release wget unzip
-    yum autoremove -q -y
-    yum clean all
-
-    rm -rf /var/cache/yum
-
-    ## CAUTION! This changes the default python command to python3!
-    ## This breaks many things, including yum!
-    ## To switch back to python2, use this command:
-    # sudo alternatives --set python /usr/bin/python2
-    alternatives --install /usr/bin/python python /usr/bin/python2 50
-    alternatives --install /usr/bin/python python /usr/local/bin/python3 60
+    pip install --upgrade pip
+    pip install -r /opt/micall/requirements-basespace.txt
+    python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
+    python /opt/micall/micall/blast_db/make_blast_db.py
 
 %environment
     export PATH=/opt/bowtie2:/bin:/usr/local/bin