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Singularity
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Bootstrap: docker
From: bioperl/bioperl
Stage: devel
%labels
author Stefano Ghignone
maintainer sghignone
name RNNOTATOR
version 3.5(released YY-MM-DD)
%environment
export PATH=/usr/local/bin:$PATH
%post
apt update && apt -y full-upgrade && apt -y install build-essential wget git
export LC_ALL="C.UTF-8"
export LANG="C.UTF-8"
echo 'export LC_ALL=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
echo 'export LANG=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
curl -L http://cpanmin.us | perl - --sudo App::cpanminus
cpanm --quiet --notest Statistics::Descriptive Parallel::ForkManager Tree
#Install BLAT
wget -c http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P /usr/local/bin
chmod +x /usr/local/bin/blat
#Move to install DIR
cd /opt
#Installing VELVET
git clone https://github.com/dzerbino/velvet.git
cd velvet && make
chmod +x velvet?
cd ..
#Installing OASES
git clone --recursive https://github.com/dzerbino/oases
cd oases && make
chmod +x oases
cd ..
#Installing BWA
wget -c https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 -P /opt
tar -xf bwa-0.7.17.tar.bz2 -C /opt
cd bwa-0.7.17 && make
cd ..
rm bwa-0.7.17.tar.bz2
#Installing MUMMER
wget -c https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz -P /opt
tar -xzf MUMmer3.23.tar.gz -C /opt
cd MUMmer3.23 && make install
cd ..
rm MUMmer3.23.tar.gz
ln -s /opt/MUMmer3.23/nucmer /usr/bin/.
ln -s /opt/MUMmer3.23/show-coords /usr/bin/.
ln -s /opt/MUMmer3.23/delta-filter /usr/bin/.
#Installing VMATCH
wget -c http://www.vmatch.de/distributions/vmatch-2.3.1-Linux_x86_64-64bit.tar.gz -P /opt
tar -xzf vmatch-2.3.1-Linux_x86_64-64bit.tar.gz -C /opt
rm vmatch-2.3.1-Linux_x86_64-64bit.tar.gz
%environment
export PATH=/opt/velvet:/opt/velvet/contrib/AssemblyAssembler1.3:/opt/oases:/opt/bwa-0.7.17:/opt/MUMmer3.23:/opt/MUMmer3.23/scripts:/opt/vmatch-2.3.1-Linux_x86_64-64bit:$PATH
export LD_LIBRARY_PATH=/opt/vmatch-2.3.1-Linux_x86_64-64bit/SELECT:$PATH
%post
#Installing AMOS
wget -c https://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz -P /opt
tar -xzf amos-3.1.0.tar.gz -C /opt
# cd amos-3.1.0 && ./configure CXXFLAGS="-g -O2 -Wno-narrowing"
#The solution is to editsrc/Align/find-tandem.ccFile, add at the beginning#include <getopt.h>
sed -i '1s/^/#include <getopt.h>\n/' amos-3.1.0/src/Align/find-tandem.cc
cd amos-3.1.0 && ./configure && make && make install
cd ..
rm amos-3.1.0.tar.gz
%environment
export PATH=/opt/amos-3.1.0/bin:$PATH