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Singularity
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Singularity
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Bootstrap:docker
From:continuumio/miniconda3:4.6.14
%labels
MAINTAINER Max Emil Schön <[email protected]>
DESCRIPTION Singularity image containing all requirements for the PhyloMagnet pipeline
VERSION 0.7
%environment
PATH=/opt/conda/envs/PhyloMagnet-0.7/bin:$PATH
export PATH
%files
environment.yml /
%post
apt-get update
apt-get install -y procps libxtst6
apt-get clean -y
####### parapa #########
cd /usr/local/bin
wget https://cme.h-its.org/exelixis/resource/download/software/papara_nt-2.5-static_x86_64.tar.gz
tar -xvf papara_nt-2.5-static_x86_64.tar.gz
rm papara_nt-2.5-static_x86_64.tar.gz
mv papara_static_x86_64 papara
/opt/conda/bin/conda env create -f /environment.yml
/opt/conda/bin/conda clean -a
%test
VERSION="0.7"
/opt/conda/envs/PhyloMagnet-$VERSION/opt/megan-6.12.3/tools/daa-meganizer -h
/opt/conda/envs/PhyloMagnet-$VERSION/opt/megan-6.12.3/tools/gc-assembler -h
/opt/conda/envs/PhyloMagnet-$VERSION/bin/trimal --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/mafft --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/diamond version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/fastq-dump --version
which /opt/conda/envs/PhyloMagnet-$VERSION/bin/FastTree
/opt/conda/envs/PhyloMagnet-$VERSION/bin/iqtree -h
/opt/conda/envs/PhyloMagnet-$VERSION/bin/python3 --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/raxml-ng -version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/epa-ng --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/gappa --help
/opt/conda/envs/PhyloMagnet-$VERSION/bin/prank -version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/python3 -c "import ete3"
/usr/local/bin/papara