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
- Name: lakinsm/summit-assembly
- License: None
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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