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Singularity_recipev5.Shannon
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Singularity_recipev5.Shannon
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BootStrap: shub
From: shub://elisadonnard/singularity:r3.5
%labels
AUTHOR Elisa Donnard
Version v5.0
%post
# singularity image with all CRISPRCasFinder.pl-v4.2's dependencies installed
# same version than CRISPRCasFinder.pl, here 4.2.19
#
# modified by Elisa Donnard in 09/30/2019
# authors: David Couvin, Fabrice Leclerc, Claire Toffano-Nioche
# installations
apt-get -y update
apt-get -y upgrade
#important packages
apt-get -y install wget
apt-get -y install curl
apt-get -y install git
apt-get -y install default-jre
apt-get -y install python
apt-get -y install parallel
apt-get -y install cpanminus
#"bioinfo" packages
apt-get -y install hmmer
apt-get -y install emboss
apt-get -y install emboss-lib
apt-get -y install ncbi-blast+
apt-get -y install bioperl
apt-get -y install bioperl-run
apt-get -y install libdatetime-perl
apt-get -y install libxml-simple-perl
apt-get -y install libdigest-md5-perl
apt-get -y install clustalw
cpanm Try::Tiny
cpanm Test::Most
cpanm JSON::Parse
cpanm Class::Struct
cpanm Bio::DB::Fasta
cpanm File::Copy
cpanm Bio::Seq Bio::SeqIO
cpanm Bio::Tools::Run::Alignment::Clustalw
cpanm -f Bio::Tools::Run::Alignment::Muscle
#install muscle
apt-get -y install muscle
#install prodigal
apt-get -y install prodigal