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MIDAS-mod.def
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Bootstrap: docker
From: ubuntu:16.04
%help
This is a container for MIDAS
/~https://github.com/snayfach/MIDAS
Based on a the Dockerfile from
/~https://github.com/FredHutch/docker-midas
%labels
Author Charles Peterson <cpeterson@oarc.ucla.edu>
%files
./midas_mod.tar.gz /usr/midas/midas_mod.tar.gz
%post
export DEBIAN_FRONTEND=noninteractive
export APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1
export SINGULARITY_SHELL=/bin/bash
apt update
apt-get install -y libncurses5-dev libncursesw5-dev build-essential wget unzip python2.7 python-dev git python-pip bats awscli curl zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl1.0.0 libssl-dev libtbb-dev g++ hmmer
cd /tmp
cat << EOF1 > requirements.txt
pandas==0.20.3
biopython==1.70
numpy==1.13.1
scipy==0.19.1
awscli==1.11.146
boto3==1.4.7
pysam==0.13
EOF1
pip install -r /tmp/requirements.txt
mkdir -pv /usr/midas
cd /usr/midas
#INSTALLING MIDAS
tar -xvf midas_mod.tar.gz
cd software
python MIDAS_mod/setup.py install
rm /usr/midas/software/MIDAS_mod/bin/Linux/samtools
rm -r /usr/midas/software/MIDAS_mod/bin/Linux/bowtie2*
#INSTALLING SAMTOOLS
cd /usr/midas
wget /~https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2
tar xf samtools-1.2.tar.bz2
cd samtools-1.2
make ; make install
rm /usr/local/bin/samtools
ln -s /usr/midas/samtools-1.2/samtools /usr/midas/software/MIDAS_mod/bin/Linux/
ln -s /usr/midas/samtools-1.2/samtools /usr/local/bin/
rm /usr/midas/samtools-1.2.tar.bz2
#INSTALLING BOWTIE2
cd /usr/midas
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip
unzip bowtie2-2.2.9-linux-x86_64.zip
rm bowtie2-2.2.9-linux-x86_64.zip
cd bowtie2-2.2.9
ln -s /usr/midas/bowtie2-2.2.9/bowtie2* /usr/midas/software/MIDAS_mod/bin/Linux/
ln -s /usr/midas/bowtie2-2.2.9/bowtie2* /usr/local/bin/
#INSTALLING SRA TOOLKIT
cd /usr/local/bin
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz
tar xzf sratoolkit.2.8.2-ubuntu64.tar.gz
ln -s /usr/local/bin/sratoolkit.2.8.2-ubuntu64/bin/* /usr/local/bin/
rm sratoolkit.2.8.2-ubuntu64.tar.gz
#INSTALLING VSEARCH
cd /usr/local
mkdir vsearch
cd vsearch
wget /~https://github.com/torognes/vsearch/releases/download/v2.14.2/vsearch-2.14.2-linux-x86_64.tar.gz
tar xzvf vsearch-2.14.2-linux-x86_64.tar.gz
cp vsearch-2.14.2-linux-x86_64/bin/vsearch /usr/local/bin/
%environment
export PYTHONPATH="/usr/midas/software/MIDAS_mod:${PYTHONPATH}"
export PATH="/usr/midas/software/MIDAS_mod/scripts:${PATH}"