Merge pull request #25 from ddesvillechabrol/add_medaka

add blast & medaka & prokka & quast

damona/software/blast/Singularity.blast_2.12.0

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+Bootstrap: docker
+From: debian:bookworm-slim
+
+%post
+  apt update && apt install -yq --no-install-recommends ncbi-blast+

damona/software/medaka/Singularity.medaka_1.7.3

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+Bootstrap: docker
+From: nvidia/cuda:11.2.2-cudnn8-runtime-ubuntu20.04
+
+
+%post
+  # Version recommended by nanoporetech
+  SAMTOOLS_VERSION=1.14
+  MINIMAP2_VERSION=2.17
+  MEDAKA_VERSION=1.7.3
+
+  # Install system package needed by medaka
+  apt update \
+  && DEBIAN_FRONTEND=noninteractive apt install -yq --no-install-recommends tzdata \
+  && apt install -yq --no-install-recommends \
+    bzip2 g++ gcc zlib1g-dev libbz2-dev liblzma-dev libffi-dev libncurses5-dev libncursesw5-dev \
+    ca-certificates libcurl4-gnutls-dev libssl-dev curl make cmake python3-all-dev python3-pip python3-setuptools \
+  && update-alternatives --install /usr/bin/python python /usr/bin/python3 10 \
+  && apt-clean && rm -rf /var/lib/apt/lists/*
+
+    # install samtools
+  curl -L https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 | tar -jxf - \
+    && cd samtools-${SAMTOOLS_VERSION} \
+    && ./configure && make all all-htslib && make install
+
+  # install minimap2
+  curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 | tar -jxf - minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 \
+    && mv ./minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2 /usr/local/bin
+
+  # install bcftools
+  curl -L https://github.com/samtools/bcftools/releases/download/${SAMTOOLS_VERSION}/bcftools-${SAMTOOLS_VERSION}.tar.bz2 | tar -jxf - \
+    && cd bcftools-${SAMTOOLS_VERSION} && ./configure --with-htslib=/samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION} && make && make install && cd -
+
+  # install medaka
+  pip install --upgrade pip
+  pip install medaka==${MEDAKA_VERSION}
+
+  rm -rf samtools-${SAMTOOLS_VERSION}
+  rm -rf minimap2-${MINIMAP2_VERSION}_x64-linux
+  apt purge -yq make cmake curl g++ gcc

damona/software/prokka/Singularity.prokka_1.14.6

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+Bootstrap: docker
+From: debian:bookworm-slim
+
+%post
+  PROKKA_VERSION=1.14.6
+  BEDTOOLS_VERSION=2.30.0
+  BARRNAP_VERSION=0.9
+  PRODIGAL_VERSION=2.6.3
+
+  # additional tools needed
+  apt update && apt install -yq --no-install-recommends ncbi-blast+ curl hmmer make cmake gcc g++ cpanminus \
+    libdatetime-perl libxml-simple-perl libdigest-md5-perl default-jre bioperl perl parallel libssl-dev libidn12 \
+    && apt autoclean && rm -rf /var/lib/apt/lists/*
+  cpanm --notest Bio::SearchIO::hmmer3
+
+  # little hack for libidn
+  ln -sf /usr/lib/x86_64-linux-gnu/libidn.so.12 /usr/lib/x86_64-linux-gnu/libidn.so.11
+
+  # install aragorn
+  curl -sSLO http://www.ansikte.se/ARAGORN/Downloads/aragorn1.2.41.c \
+    && gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.41.c \
+    && mv aragorn /usr/local/bin
+
+  # install prodigal
+  curl -sSL "https://github.com/hyattpd/Prodigal/archive/refs/tags/v${PRODIGAL_VERSION}.tar.gz" | tar zx \
+      && cd "Prodigal-${PRODIGAL_VERSION}" && make install && cd -
+  rm -rf "Prodigal-${PRODIGAL_VERSION}"
+
+  # install barrnap
+  curl -sSL "https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools.static.binary" -o bedtools \
+      && chmod 755 bedtools && mv bedtools /usr/local/bin
+  curl -sSL "https://github.com/tseemann/barrnap/archive/refs/tags/${BARRNAP_VERSION}.tar.gz" | tar zx \
+      && mv "barrnap-${BARRNAP_VERSION}" barrnap && cd barrnap && cd -
+
+  # install prokka
+  curl -sSL "https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz" | gunzip > tbl2asn \
+      && chmod 755 tbl2asn && mv tbl2asn /usr/local/bin/
+  curl -sSL "https://github.com/tseemann/prokka/archive/refs/tags/v${PROKKA_VERSION}.tar.gz" | tar zx && mv prokka-$PROKKA_VERSION prokka
+  /prokka/bin/prokka --setupdb
+
+  apt purge -y curl make cmake gcc g++
+
+%environment
+  export PATH=$PATH:/prokka/bin:/prokka/binaries/common:/prokka/binaries/linux:/barrnap/bin

damona/software/quast/Singularity.quast_5.2.0

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+Bootstrap: docker
+From: python:3.10-slim-bullseye
+
+%post
+  MINIMAP2_VERSION=2.24
+  QUAST_VERSION=5.2.0
+  SAMBAMBA_VERSION=0.8.2
+
+  apt update && apt install --no-install-recommends -yq pkg-config libfreetype6-dev libpng-dev bwa bedtools curl
+  pip install matplotlib
+
+  curl -L "https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2" | tar -jxf - --no-same-owner "minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2" \
+    && mv "./minimap2-${MINIMAP2_VERSION}_x64-linux/minimap2" /usr/local/bin
+
+  curl -sSL "https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba-${SAMBAMBA_VERSION}-linux-amd64-static.gz" \
+    | gunzip > sambamba  && chmod 755 sambamba && mv sambamba /usr/local/bin
+
+  curl -sSL "https://github.com/ablab/quast/releases/download/quast_${QUAST_VERSION}/quast-${QUAST_VERSION}.tar.gz" | tar zx \
+    && cd "quast-${QUAST_VERSION}" && pip install . && cd -
+
+  curl -sSL "http://ccb.jhu.edu/software/glimmerhmm/dl/GlimmerHMM-3.0.4.tar.gz" | tar -zxf - GlimmerHMM/bin \
+    && mv GlimmerHMM/bin/glimmerhmm_linux_x86_64 /usr/local/bin/glimmerhmm
+
+  # move gridss in dist-packages, it's a bit hacky but I do not want to install silva db with the quast full install
+  curl -sSL https://github.com/PapenfussLab/gridss/releases/download/v2.13.2/gridss-2.13.2-gridss-jar-with-dependencies.jar -o gridss-1.4.1.jar
+  mkdir -p "/usr/local/lib/python3.10/dist-packages/quast-${QUAST_VERSION}-py3.10.egg/quast_libs/gridss"
+  mv gridss-1.4.1.jar "/usr/local/lib/python3.10/dist-packages/quast-${QUAST_VERSION}-py3.10.egg/quast_libs/gridss"
+
+  apt purge -yq curl