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Singularity.2.0
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Singularity.2.0
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Bootstrap: docker
From: conda/miniconda3
%environment
PATH=/opt/bedtools2/bin:/usr/local/envs/py36/bin:/opt/souporcell:/opt/souporcell/troublet/target/release:/usr/local/condabin:/opt/minimap2-2.7:/root/.cargo/bin:/opt/vartrix-v1.1.3-x86_64-linux/:/opt:$PATH
%post -c /bin/bash
apt update
yes | apt-get install wget
yes | apt-get install build-essential
yes | apt-get install curl
echo blah
yes | /usr/local/bin/conda create -n py36 python=3.6
. /opt/conda/bin/activate py36
yes | apt-get install libncurses5-dev
yes | apt-get install zlib1g-dev
yes | apt-get install libbz2-dev
yes | apt-get install liblzma-dev
cd /opt
wget https://github.com/lh3/minimap2/archive/v2.7.tar.gz
tar -xzvf v2.7.tar.gz
cd minimap2-2.7
make
cd ..
wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
tar -zxvf bedtools-2.28.0.tar.gz
cd bedtools2
make
cd ..
CARGO_HOME=/opt/.cargo RUSTUP_HOME=/opt/.cargo bash -c 'curl https://sh.rustup.rs -sSf | sh -s -- -y'
source /opt/.cargo/env
which cargo
rustup default stable
yes | apt-get install git
cd /opt
git clone https://github.com/wheaton5/souporcell.git
cd souporcell/troublet
cargo build --release
cd /opt/souporcell/souporcell
cargo build --release
cd /opt
yes | /usr/local/envs/py36/bin/pip install pysam
/usr/local/envs/py36/bin/pip install pyvcf
/usr/local/envs/py36/bin/pip install numpy
/usr/local/envs/py36/bin/pip install scipy
/usr/local/envs/py36/bin/pip install pystan==2.17.1.0
/usr/local/envs/py36/bin/pip install pyfaidx
cd /opt
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
tar xvfj htslib-1.9.tar.bz2
cd htslib-1.9
./configure
make
make install
cd ..
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar xvfj samtools-1.9.tar.bz2
rm samtools-1.9.tar.bz2
cd samtools-1.9
./configure
make
make install
cd ..
wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
tar xvfj bcftools-1.9.tar.bz2
rm bcftools-1.9.tar.bz2
cd bcftools-1.9
./configure
make
make install
cd /opt
wget https://github.com/ekg/freebayes/releases/download/v1.3.1/freebayes-v1.3.1
mv freebayes-v1.3.1 freebayes
chmod 777 freebayes
wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.16/vartrix_linux
mv vartrix_linux vartrix
chmod 777 vartrix