cfljam/Pop-Genomics-Workshop2019:latest

$ singularity pull shub://cfljam/Pop-Genomics-Workshop2019:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu
%labels
MAINTAINER John McCallum cfljam@users.noreply.github.com
%post

## A Docker Image for MAPGD + htslib + Samtools


DEBIAN_FRONTEND=noninteractive
apt-get update && \
apt-get -y install \
build-essential \
curl \
gcc \
git \
gettext \
libgsl-dev \
libcurl4-openssl-dev \
libgettextpo-dev \
libbz2-dev \
libncurses5-dev \
libsqlite3-dev \
liblzma-dev \
nano \
sqlite3 \
unzip \
zlib1g \
zlib1g-dev \
zip \
wget && \
rm -rf /var/lib/apt/lists/*

###############################
## Install Samtools + htlslib##
###############################

export SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2"

wget $SAMTOOLS_URL  -O samtools.tar.bz2 && \
tar -xjvf samtools.tar.bz2 && \
cd samtools-* && \
./configure && \
make && \
make prefix=/usr/local install &&\
cd htslib-* && \
./configure && \
make && \
sudo make install && \
make test

LD_LIBRARY_PATH='/samtools-1.9/htslib-1.9/'

###########
# MAPGD ###
###########

MAPGD_URL="https://github.com/LynchLab/MAPGD/archive/master.zip"
wget -O MAPGD.zip $MAPGD_URL  && \
unzip MAPGD.zip   && \
cd MAPGD-* && \
./configure && \
make && \
make install  # && \
#make test

%environment
export DEBIAN_FRONTEND=noninteractive
export LD_LIBRARY_PATH='/samtools-1.9/htslib-1.9/'
%runscript
exec /bin/bash "$@"

Collection

• Name: cfljam/Pop-Genomics-Workshop2019
• License: None

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