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VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

Project webpage

Here is an example of one very demanding installation with plenty of third party software requirements. Since the environment originally is provided by conda, here we will use From: continuumio/miniconda3.

Third party software dependency.

Program Version URL
BLAST 2.2.30+ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
DendroPy 4.0 https://pythonhosted.org/DendroPy/#installing
MetAL 1.1 http://kumiho.smith.man.ac.uk/blog/whelanlab/?page_id=396
MrBayes 3.2.3 http://mrbayes.sourceforge.net/
MUSCLE 3.8.21 http://www.drive5.com/muscle/downloads.htm
NoRMD 1.3 ftp://ftp-igbmc.u-strasbg.fr/pub/NORMD/
PAML 4.4e http://abacus.gene.ucl.ac.uk/software/paml.html
ProtTest3 3.4 https://github.com/ddarriba/prottest3

Warning

It also requires Python 2.7!

  1. Clone the original repository - there are some binaries that needs to copyed in the container (lines 8 and 9 in the definition file).
    Download manually the third party software packages. 
    $ git clone https://github.com/aewebb80/VESPA.git
$ wget -O VESPA.tar.gz https://github.com/aewebb80/VESPA/archive/refs/tags/1.0.1.tar.gz
$ wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.3/mrbayes-3.2.3.tar.gz
$ wget https://github.com/ddarriba/prottest3/releases/download/3.4.2-release/prottest-3.4.2-20160508.tar.gz
$ wget http://www.bork.embl.de/Docu/AQUA/latest/norMD1_3.tar.gz
  2. Here is the Singularity definition file 
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    Bootstrap: docker
From: continuumio/miniconda3

%files
  VESPA.tar.gz /
  mrbayes-3.2.3.tar.gz /
  prottest-3.4.2-20160508.tar.gz /
  VESPA/executables/Linux/normd /usr/local/bin
  VESPA/executables/Linux/metal /usr/local/bin
  vespa.yaml /

%environment
  export LC_ALL=C
  export PROTTEST_HOME=/opt/prottest-3.4.2


%post
  export LC_ALL=C
  export PROTTEST_HOME=/opt/prottest-3.4.2
  export DEBIAN_FRONTEND=noninteractive

  mkdir -p /tmp/apt
  echo 'Dir::Cache /tmp/apt;'  > /etc/apt/apt.conf.d/singularity-cache.conf

  apt-get update; apt-get -y dist-upgrade && apt-get install -y wget git ant perl build-essential cmake openjdk-11-jdk autoconf

  # VESPA -----------------------------------------------
  cd /opt ; tar -xvf /VESPA.tar.gz 
  cd VESPA-1.0.1; chmod +x vespa.py ; cp vespa.py /usr/local/bin
  chmod +x *Codeml*.pl ; cp *Codeml*.pl /usr/local/bin ; cp -a CodemlWrapper/ /usr/share/perl/5.32


  # Beagle ----------------------------------------------
  cd /opt
  #export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
  git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
  cd beagle-lib && mkdir build; cd build 
  cmake ..
  make install

  # MrBayes ---------------------------------------------
  cd /opt ; tar -xvf /mrbayes-3.2.3.tar.gz
  cd mrbayes_3.2.3/src && autoconf && ./configure LDFLAGS="-Wl,--allow-multiple-definition" && make install 

  # prottest3 ------------------------------------------
  cd /opt
  tar -xvf /prottest-3.4.2-20160508.tar.gz 

  # Conda ----------------------------------------------
  conda update -n base -c defaults conda
  #conda install -c conda-forge pip mamba

  conda env create -f /vespa.yaml -n VESPA
  echo "conda activate VESPA" >> /opt/conda/etc/profile.d/conda.sh

  conda clean --all --yes
  rm /*.tar.gz

%runscript
   params="$@"
  /bin/bash --rcfile /opt/conda/etc/profile.d/conda.sh -ic "vespa.py $params"
    and the adapted vespa.yaml conda enviroment file. 
    name: vespa27
channels:
  - defaults
dependencies:
  - conda-forge::python=2.7
  - conda-forge::numba
  - conda-forge::h5py
  - bioconda::blast=2.2.31
  - bioconda::dendropy=4.2.0
  - bioconda::muscle=3.8.31
  - bioconda::paml

Note, how conda environment VESPA is activated (first line 54, then line 61) to run the tool within the environment.