iqbal-lab-org · evanbiederstedt · Nov 20, 2019
diff --git a/containers/clockwork/Dockerfile b/containers/clockwork/Dockerfile
@@ -0,0 +1,213 @@
+
+FROM ubuntu:18.04
+
+## need the following environment variable for automated installation of tzdata
+ENV DEBIAN_FRONTEND=noninteractive 
+
+
+LABEL authors="Martin Hunt (ebi.ac.uk), Evan Biederstedt ([email protected])" \
+    version.image="0.1.0" \
+    version.clockwork="v0.7.8" \
+    version.bcftools="1.3.1" \
+    version.bwa="v0.7.15" \
+    version.perl="5.24.1" \
+    version.enaBrowserTools="v1.4.1" \
+    version.fastqc="v0.11.5." \
+    version.picard="2.9.4" \
+    version.seqtk="v1.2" \
+    version.samtools="1.3.1" \
+    version.trimmomatic="0.36" 
+
+
+## from https://github.com/iqbal-lab-org/clockwork/blob/master/scripts/install_dependencies.sh
+
+# NOTE: needed to specify java version 8 (openjdk-8-jre) because
+# default is version 10 (from default-jre), which won't work with nextflow.
+
+
+## set Perl environment variables
+ENV PATH="/bioinf-tools/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools-1.4.1/python3:/clockwork/scripts/:$PATH"
+ENV PERL5LIB="/bioinf-tools/vcftools-0.1.15/install/share/perl/5.24.1/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB"
+ENV LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"
+
+
+
+RUN apt-get update
+RUN apt-get install -y software-properties-common
+RUN apt-add-repository universe
+RUN apt-get update
+
+RUN apt-get install -y \
+    build-essential \
+    cmake \
+    curl \
+    gawk \
+    git \
+    gnuplot \
+    graphviz \
+    openjdk-8-jre \
+    libarchive-dev \
+    liblzma-dev \
+    libbz2-dev \
+    libhts-dev \
+    libncurses5-dev \
+    libncursesw5-dev \
+    zlib1g-dev \
+    pkg-config \
+    python-dev \
+    python-pip \
+    python3-dev \
+    python3-pip \
+    python3-setuptools \
+    r-base-core \
+    rsync \
+    unzip \
+    wget --fix-missing
+
+
+#_________________________ bcftools _______________________#
+
+RUN wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 \
+    && tar xf bcftools-1.3.1.tar.bz2 \
+    && cd bcftools-1.3.1/ \
+    && make \ 
+    && cd .. \
+    && cp bcftools-1.3.1/bcftools /bin/bcftools
+
+
+#__________________________ BWA____________________________#
+RUN wget https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2 \
+    && tar xf bwa-0.7.15.tar.bz2 \
+    && cd bwa-0.7.15/ \
+    && make \
+    && cd .. \
+    && cp bwa-0.7.15/bwa /bin/bwa
+
+
+#_____________________ enaBrowserTools ____________________#
+RUN wget https://github.com/enasequence/enaBrowserTools/archive/v1.4.1.tar.gz \
+    && tar xf v1.4.1.tar.gz
+
+
+#_________________________ FASTQC ________________________#
+RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip \
+    && unzip fastqc_v0.11.5.zip \
+    && chmod 755 FastQC/fastqc \
+    && cp FastQC/fastqc /bin/fastqc
+
+#_________________________ qctools ________________________#
+RUN wget https://github.com/alastair-droop/fqtools/archive/986e451.tar.gz \
+    && tar xf 986e451.tar.gz \
+    && rm 986e451.tar.gz \
+    && cd fqtools-986e451/ \
+    && make \
+    && cd .. \
+    && cp fqtools-986e451/bin/fqtools /bin/fqtools
+
+#________________________ mccortex _______________________#
+RUN git clone --recursive https://github.com/mcveanlab/mccortex \
+    && cd mccortex \
+    && git checkout 97aba198d632ee98ac1aa496db33d1a7a8cb7e51 \
+    && make all \
+    && cd .. \
+    && cp mccortex/bin/mccortex31 /bin/mccortex31 
+
+
+#________________________ Mykrobe ________________________#
+RUN git clone https://github.com/Mykrobe-tools/mykrobe.git mykrobe \
+    && cd mykrobe \ 
+    && git checkout b47f6241cfb2d223bb53aafd90a3f91d97248052  \ 
+    && sed -i 's/help="build variant probes", aliases=.*$/help="build variant probes")/' src/mykrobe/cli.py \
+     # fix for python2: aliases is not an option so remove it
+    && wget -O mykrobe-data.tar.gz https://goo.gl/DXb9hN \ 
+    && tar -zxvf mykrobe-data.tar.gz && rm -fr src/mykrobe/data \ 
+    && mv mykrobe-data src/mykrobe/data \
+    && pip3 install .
+
+
+#________________________ nextflow _______________________#
+RUN wget -qO- get.nextflow.io | bash \
+    && chmod 755 nextflow
+
+#________________________ picard _________________________#
+RUN wget https://github.com/broadinstitute/picard/releases/download/2.9.4/picard.jar
+
+#________________________ seqtk __________________________#
+RUN wget https://github.com/lh3/seqtk/archive/v1.2.tar.gz \
+    && tar xf v1.2.tar.gz \
+    && rm v1.2.tar.gz \
+    && cd seqtk-1.2/ \
+    && make \
+    && cd .. \
+    && cp seqtk-1.2/seqtk /bin/seqtk
+
+#_________________________ samtools ______________________#
+RUN wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 \
+    && tar xf samtools-1.3.1.tar.bz2 \
+    && cd samtools-1.3.1/ \
+    && make \
+    && cd .. \
+    && cp samtools-1.3.1/samtools /bin/samtools \
+    && cp -rp samtools-1.3.1/misc/plot-bamstats /bin/plot-bamstats
+
+#________________________ stampy _________________________#
+RUN wget http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-latest.tgz \
+    && tar xf stampy-latest.tgz \
+    && rm stampy-latest.tgz \
+    && cd stampy-* \
+    && make \
+    && cd .. \
+    && cp stampy-*/stampy.py /bin/stampy.py
+
+#________________________ Trimmomatic ____________________#
+RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip \
+    && unzip Trimmomatic-0.36.zip
+
+#________________________ vcftools _______________________#
+RUN wget https://github.com/vcftools/vcftools/releases/download/v0.1.15/vcftools-0.1.15.tar.gz \
+    && tar xf vcftools-0.1.15.tar.gz \
+    && cd vcftools-0.1.15 \
+    && ./configure --prefix $PWD/install \
+    && make \
+    && make install
+
+# cortex needs the perl/ directory. It expects it to be in the vcftools root,
+# but somehwere between v0.1.9 and v0.1.15 it moved into src/.
+RUN ln -s src/perl/ .
+
+#________________________ cortex _________________________#
+RUN wget --no-check-certificate -O cortex.tar.gz https://github.com/iqbal-lab/cortex/archive/master.tar.gz \
+    && tar xf cortex.tar.gz \
+    && mv cortex-master cortex \
+    && cd cortex/ \
+    && bash install.sh \
+    && make NUM_COLS=1 cortex_var \
+    && make NUM_COLS=2 cortex_var
+
+# ___________________ python packages ___________________#
+# note: requests needs to be here instead of as part of
+# python setup.py install, because setup.py install
+# throws an error.  This way works.
+RUN pip3 install python-dateutil requests pysam pyfastaq pymysql numpy openpyxl pyflakes scipy XlsxWriter
+
+
+
+#________________________ gramtools _________________________#
+RUN pip3 install git+https://github.com/iqbal-lab-org/gramtools@4644135e162ff1ff333f970f1dafd919aa0fc279
+
+#________________________ mummer ____________________________#
+RUN wget https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz  \
+    && tar xf mummer-4.0.0beta2.tar.gz \
+    && cd mummer-4.0.0beta2 \
+    && ./configure \
+    && make \
+    && make install
+
+
+#________________________ minos _____________________________#
+RUN pip3 install bio-minos==0.9.1
+
+
+
+
+