motroy/singularity-roary-piggy:latest

$ singularity pull shub://motroy/singularity-roary-piggy:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%environment
export PATH="/Software/roary/sanger-pathogens-Roary-db170bf/:/Software/roary/sanger-pathogens-Roary-db170bf/bin:/Software/piggy/scripts_piggy:/Software/piggy/:/Software/piggy/bin:/Databases/:$PATH"

%post
apt update && apt install -y git curl wget less locate unzip build-essential perl libexpat1-dev expat bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree
cpanm --force --notest Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File Bio::Roary
mkdir -p /Software/ && cd /Software/
mkdir roary && cd roary
wget https://github.com/sanger-pathogens/Roary/tarball/master/sanger-pathogens-Roary-v3.12.0-17-gdb170bf.tar.gz
tar zxvf sanger-pathogens-Roary-v3.12.0-17-gdb170bf.tar.gz
cd /Software
git clone https://github.com/harry-thorpe/piggy
mkdir -p /Databases/ && cd /Databases
export PATH="/Software/roary/sanger-pathogens-Roary-db170bf/:/Software/roary/sanger-pathogens-Roary-db170bf/bin:/Software/piggy/scripts_piggy:/Software/piggy/:/Software/piggy/bin:/Databases/:$PATH"

Collection

• Name: motroy/singularity-roary-piggy
• License: MIT License

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