lakinsm/summit-assembly:latest

$ singularity pull shub://lakinsm/summit-assembly:latest

Singularity Recipe

Bootstrap: docker
From: debian:jessie-slim


%post
    apt update \
    && apt install -y --no-install-recommends \
    build-essential \
    ca-certificates \
    git \
    gcc \
    make \
    automake \
    autoconf \
    openjdk-7-jre \
    wget \
    unzip \
    sed \
    && rm -rf /var/lib/apt/lists/*
    cd /opt
    git clone https://github.com/loneknightpy/idba \
    && cd idba \
    && sed -i 's/kMaxShortSequence = 128/kMaxShortSequence = 500/' src/sequence/short_sequence.h \
    && ./build.sh \
    && make
    cd /usr/local/bin
    ln -s /opt/idba/bin/idba_ud
    ln -s /opt/idba/bin/fq2fa
    cd /
    TRIMMOMATIC_SOURCE="Trimmomatic-0.36.zip" \
    TRIMMOMATIC_HOME="/opt/trimmomatic"
    wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip -O /opt/trimmomatic.zip && \
    unzip /opt/trimmomatic.zip -d /opt/ && \
    rm /opt/trimmomatic.zip
    cd /

    
%test
    which idba_ud

Collection


View on Datalad

Metrics

key value
id /containers/lakinsm-summit-assembly-latest
collection name lakinsm/summit-assembly
branch master
tag latest
commit deb5015e87d7c5a9e2e3a02536b858a43279d447
version (container hash) 3eb8581ceeaabd872c2b81bdad16eb6f
build date 2018-08-28T03:21:34.065Z
size (MB) 604
size (bytes) 214450207
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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