QuentinLetourneur/Let-it-bin:binsanity

$ singularity pull shub://QuentinLetourneur/Let-it-bin:binsanity

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%setup
    export LC_ALL=C

%post
    mkdir /pasteur
    apt -y update
    apt -y install wget subread python python-pip camlp4-extra gawk libgsl0-dev libgsl0-dev \
    sqlite3 libsqlite3-dev libz-dev m4 ocaml patch ocaml-native-compilers opam zip
    pip install biopython scipy scikit-learn pandas
    
	cd /home
    wget  http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
    tar -xzf hmmer-3.1b2-linux-intel-x86_64.tar.gz
    rm hmmer-3.1b2-linux-intel-x86_64.tar.gz
    cd hmmer-3.1b2-linux-intel-x86_64
    ./configure
    make
    make install
    cd easel
    make install
    
	cd /home
    wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz
    tar -xzf v2.6.3.tar.gz
    rm v2.6.3.tar.gz
    cd Prodigal-2.6.3
    make install
    
	cd /home
    wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha18/pplacer-linux-v1.1.alpha18-2-gcb55169.zip
    unzip pplacer-linux-v1.1.alpha18-2-gcb55169.zip
    rm pplacer-linux-v1.1.alpha18-2-gcb55169.zip
    cd pplacer-Linux-v1.1.alpha18-2-gcb55169
    mv guppy pplacer rppr /usr/local/bin
    
	cd /home
    pip install pysam matplotlib dendropy screamingbackpack
    wget https://github.com/Ecogenomics/CheckM/archive/v1.0.7.tar.gz
    tar -xzf v1.0.7.tar.gz
    rm v1.0.7.tar.gz
    cd CheckM-1.0.7
    python setup.py install
    wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
    tar -xzf checkm_data_2015_01_16.tar.gz
    rm checkm_data_2015_01_16.tar.gz
    
	# directly modify the file because cannot be done dynamicly with checkm setRoot
    sed -i 's/"dataRoot": ""/"dataRoot": "\/home\/CheckM-1.0.7\/"/' /usr/local/lib/python2.7/dist-packages/checkm/DATA_CONFIG
    
	cd /home
    wget https://github.com/edgraham/BinSanity/archive/v0.2.6.1.tar.gz
    tar -xzf v0.2.6.1.tar.gz
    cd BinSanity-0.2.6.1
    sed -i 's/README.rst/README.md/' setup.py
    python setup.py install

Collection


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Metrics

key value
id /containers/QuentinLetourneur-Let-it-bin-binsanity
collection name QuentinLetourneur/Let-it-bin
branch master
tag binsanity
commit 647c7b5e55f98b734d8bcb0be2bbc1953b9bb875
version (container hash) d72f799eb63cbe93110b703d0811ddd7
build date 2018-09-02T17:27:42.144Z
size (MB) 2878
size (bytes) 854093855
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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