maxemil/PhyloMagnet:latest

$ singularity pull shub://maxemil/PhyloMagnet:latest

Singularity Recipe

Bootstrap:docker
From:continuumio/miniconda3:4.6.14

%labels
    MAINTAINER Max Emil Schön <max-emil.schon@icm.uu.se>
    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

Collection


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Metrics

key value
id /containers/maxemil-PhyloMagnet-latest
collection name maxemil/PhyloMagnet
branch master
tag latest
commit c742de49e22fb820924d6b32311b501f6ab47d27
version (container hash) 33bf1df183c46c2464fa00cfdd8b2fde
build date 2021-04-07T12:42:12.051Z
size (MB) 3042.0
size (bytes) 974110751
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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