new vcf mix to deal with minos style

Pathogen-Genomics-Cymru · Sep 18, 2024 · f2b61d6 · f2b61d6
1 parent 690a443
commit f2b61d6
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Showing 4 changed files with 161 additions and 3 deletions.
diff --git a/bin/run-vcfmix.py b/bin/run-vcfmix.py
@@ -12,7 +12,7 @@ def go(vcf_file):
     v = lineageScan()
 
     # assuming postfix of ".minos.vcf"
-    sampleid = vcf_file.replace(".minos.vcf", "")
+    sampleid = vcf_file.replace("_allelic_depth.minos.vcf", "")
     print(sampleid)
 
     res = v.parse(vcffile=vcf_file, sample_id=sampleid)

diff --git a/config/containers.config b/config/containers.config
@@ -33,10 +33,10 @@ process {
     }
 
     withLabel:clockwork {
-        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.9"
+        container = "quay.io/pathogen-genomics-cymru/clockwork:0.9.9r1"
     }
 
     withLabel:vcfpredict {
-        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.9"
+        container = "quay.io/pathogen-genomics-cymru/vcfpredict:0.9.9r1"
     }
  }
diff --git a/docker/Dockerfile.clockwork-0.9.9r1 b/docker/Dockerfile.clockwork-0.9.9r1
@@ -0,0 +1,131 @@
+FROM ubuntu:focal
+
+
+LABEL maintainer="[email protected]" \
+about.summary="container for the clockwork workflow"
+
+ENV samtools_version=1.12 \
+htslib_version=1.12 \
+bcftools_version=1.12 \
+minimap2_version=2.17 \
+picard_version=2.18.16 \
+gramtools_version=8af53f6c8c0d72ef95223e89ab82119b717044f2 \
+vt_version=2187ff6347086e38f71bd9f8ca622cd7dcfbb40c \
+minos_version=0.11.0 \
+cortex_version=3a235272e4e0121be64527f01e73f9e066d378d3 \
+vcftools_version=0.1.15 \
+mccortex_version=97aba198d632ee98ac1aa496db33d1a7a8cb7e51 \
+stampy_version=1.0.32r3761 \
+python_version=3.6.5 \
+clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5 \
+gatk_version=4.6.0.0
+
+ENV PACKAGES="procps curl git build-essential wget zlib1g-dev pkg-config jq r-base-core rsync autoconf libncurses-dev libbz2-dev liblzma-dev libcurl4-openssl-dev cmake tabix libvcflib-tools libssl-dev software-properties-common perl locales locales-all" \
+PYTHON="python2.7 python-dev"
+
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
+RUN apt-get update \
+&& DEBIAN_FRONTEND=noninteractive apt-get install -y $PACKAGES $PYTHON \
+&& curl -fsSL https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz | tar -xz \
+&& cd Python-${python_version} \
+&& ./configure --enable-optimizations \
+&& make altinstall \
+&& cd .. \
+&& ln -s /usr/local/bin/python3.6 /usr/local/bin/python3 \
+&& ln -s /usr/local/bin/pip3.6 /usr/local/bin/pip3 \
+&& pip3 install --upgrade pip \
+&& pip3 install 'cluster_vcf_records==0.13.1' pysam setuptools  awscli \
+&& apt-get update
+
+#update jdk
+RUN wget https://download.java.net/java/GA/jdk18/43f95e8614114aeaa8e8a5fcf20a682d/36/GPL/openjdk-18_linux-x64_bin.tar.gz
+RUN tar -xvf openjdk-18_linux-x64_bin.tar.gz
+RUN mv jdk-18* /opt/
+ENV JAVA_HOME=/opt/jdk-18
+ENV PATH=$PATH:$JAVA_HOME/bin
+
+
+RUN curl -fsSL https://github.com/samtools/samtools/archive/${samtools_version}.tar.gz | tar -xz \
+&& curl -fsSL https://github.com/samtools/htslib/releases/download/${htslib_version}/htslib-${htslib_version}.tar.bz2 | tar -xj \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C samtools-${samtools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r samtools-${samtools_version} \
+&& curl -fsSL https://github.com/samtools/bcftools/archive/refs/tags/${bcftools_version}.tar.gz | tar -xz \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} \
+&& make -C bcftools-${bcftools_version} -j HTSDIR=../htslib-${htslib_version} prefix=/usr/local install \
+&& rm -r bcftools-${bcftools_version}
+
+
+RUN curl -fsSL minimap2-${minimap2_version}.tar.gz https://github.com/lh3/minimap2/archive/v${minimap2_version}.tar.gz | tar -xz \
+&& cd minimap2-${minimap2_version} \
+&& make \
+&& chmod +x minimap2 \
+&& mv minimap2 /usr/local/bin \
+&& cd .. \
+&& rm -r minimap2-${minimap2_version} \
+&& wget https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard.jar -O /usr/local/bin/picard.jar
+
+
+RUN git clone https://github.com/atks/vt.git vt-git \
+&& cd vt-git \
+&& git checkout ${vt_version} \
+&& make \
+&& cd .. \
+&& mv vt-git/vt /usr/local/bin \
+&& pip3 install tox "six>=1.14.0" \
+&& git clone https://github.com/iqbal-lab-org/gramtools \
+&& cd gramtools \
+&& git checkout ${gramtools_version} \
+&& pip3 install . \
+&& cd .. \
+&& pip3 install cython \
+&& pip3 install git+https://github.com/iqbal-lab-org/minos@v${minos_version}
+
+
+RUN git clone --recursive https://github.com/iqbal-lab/cortex.git \
+&& cd cortex \
+&& git checkout ${cortex_version} \
+&& bash install.sh \
+&& make NUM_COLS=1 cortex_var \
+&& make NUM_COLS=2 cortex_var \
+&& cd .. \
+&& mkdir bioinf-tools \
+&& cd bioinf-tools \
+&& curl -fsSL http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-${stampy_version}.tgz | tar -xz \
+&& make -C stampy-* \
+&& cp -s stampy-*/stampy.py . \
+&& curl -fsSL https://github.com/vcftools/vcftools/releases/download/v${vcftools_version}/vcftools-${vcftools_version}.tar.gz | tar -xz \
+&& cd vcftools-${vcftools_version} \
+&& ./configure --prefix $PWD/install \
+&& make && make install \
+&& ln -s src/perl/ . \
+&& cd .. \
+&& git clone --recursive https://github.com/mcveanlab/mccortex \
+&& cd mccortex \
+&& git checkout ${mccortex_version} \
+&& make all \
+&& cd .. \
+&& cp -s mccortex/bin/mccortex31 . \
+&& cd .. \
+&& git clone https://github.com/iqbal-lab-org/clockwork \
+&& cd clockwork \
+&& git checkout ${clockwork_version} \
+&& cd python \
+&& pip3 install . \
+&& chmod +x scripts/clockwork
+
+RUN wget https://github.com/broadinstitute/gatk/releases/download/${gatk_version}/gatk-${gatk_version}.zip -O /tmp/gatk-${gatk_version}.zip\
+	&& unzip /tmp/gatk-${gatk_version}.zip -d /opt/ \
+	&& rm /tmp/gatk-${gatk_version}.zip -f
+
+ENV CLOCKWORK_CORTEX_DIR=/cortex \
+PATH=${PATH}:/clockwork/python/scripts:/opt/gatk-${gatk_version} \
+PICARD_JAR=/usr/local/bin/picard.jar
+
+ENV LC_ALL en_US.UTF-8 \
+LANG en_US.UTF-8 \
+LANGUAGE en_US.UTF-8
+
+
diff --git a/docker/Dockerfile.vcfpredict-0.9.9r1 b/docker/Dockerfile.vcfpredict-0.9.9r1
@@ -0,0 +1,27 @@
+FROM ubuntu:20.04
+
+LABEL maintainer="[email protected]" \
+about.summary="container for the vcf predict workflow"
+
+#add run-vcf to container
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
+ENV PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq" \
+PYTHON="python3 python3-pip python3-dev"
+
+ENV vcfmix_version=d4693344bf612780723e39ce27c8ae3868f95417
+
+#apt updates
+RUN apt-get update \
+&& DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata \
+&& apt-get install -y $PACKAGES $PYTHON \
+&& apt-get install -y python3-packaging \
+&& git clone https://github.com/whalleyt/VCFMIX.git \
+&& cd VCFMIX \
+&& git checkout ${vcfmix_version} \
+&& pip3 install recursive_diff \
+&& pip3 install awscli \
+&& pip3 install . \
+&& cp -r data /usr/local/lib/python3.8/dist-packages \
+&& cd ..