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Singularity.Demuxafy_update
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Bootstrap: docker
From: drneavin/demuxafy:v2.0.1
%labels
Author = Drew Neavin
Image_version = 2.1.0
%environment
export PATH=/opt:/usr/games:/opt/samtools-1.16.1:/opt/bcftools-1.16:/opt/conda/envs/py37/bin:/opt/conda/bin:/opt/Demultiplexing_Doublet_Detecting_Docs/scripts:opt/Demultiplexing_Doublet_Detecting_Docs/mods:/opt/bedtools2/bin:opt/vcflib/bin:/opt/vcflib/scripts:/opt/souporcell:/opt/souporcell/troublet/target/release:/opt/minimap2-2.7:/root/.cargo/bin:/opt/freebayes/scripts:/opt/popscle/bin/:/opt/conda/envs/py37/lib/python3.7/site-packages/scSplit/:/opt/Drop-seq_tools-2.5.4/:$PATH
export PYTHONPATH=/opt/conda/envs/py37/lib/python3.7/site-packages/
export LC_ALL=C
%post
### Add in demuxalot and dropulation tools
## demuxalot
/opt/conda/envs/py37/bin/pip install demuxalot
## dropulation
cd opt
wget https://github.com/broadinstitute/Drop-seq/releases/download/v2.5.4/Drop-seq_tools-2.5.4.zip
unzip Drop-seq_tools-2.5.4.zip
## Install java (for dropulation)
# apt-get install libc6-i386 libc6-x32 libxi6 libxtst6 -y
# wget https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.deb
# dpkg -i jdk-20_linux-x64_bin.deb
# apt-get update
# apt-get install -y openjdk-11-jdk
## dependency: libasound2
apt-get install -y libasound2
wget https://download.bell-sw.com/java/11.0.20+8/bellsoft-jdk11.0.20+8-linux-amd64.deb
dpkg -i bellsoft-jdk11.0.20+8-linux-amd64.deb
### Install biopython to handle gzipped fasta files in souporcell
/opt/conda/envs/py36/bin/pip install biopython==1.78
### Install biopython to handle gzipped fasta files for other methods
/opt/conda/envs/py36/bin/pip install biopython
### Remove and reisntall Demuxafy
rm -rf /opt/Demultiplexing_Doublet_Detecting_Docs
### Get the github repo with scripts for workflow ###
cd /opt
git clone --branch v2.1.0 https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
# git clone --branch main https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
cd Demultiplexing_Doublet_Detecting_Docs
rm -rf references ## Only hosting on github for people to download if they want, no need to take up extra space in the image
rm -rf docs ## doc files, dont need in image
### Make scripts executable ###
chmod 777 -R /opt/Demultiplexing_Doublet_Detecting_Docs/scripts