installMetaErg.sh

#!/usr/bin/env bash
# Author: Lukas Jansen
# Licensed under the Academic Free License version 3.0
set -e


tmhmm="tmhmm-2.0c.Linux.tar.gz"
signalp="signalp-5.0b.Linux.tar.gz"


if (( $# != 1 )); then
    echo "Only one parameter allowed!"
    echo "installMetaErg.sh <installdir>"
    exit 1
fi

targetdir=$1
tmhmm32bit=true
swissknife="https://sourceforge.net/projects/swissknife/files/swissknife/1.78/swissknife_1.78.tar.gz/download"
minpath="https://omics.informatics.indiana.edu/mg/get.php?justdoit=yes&software=minpath1.4.tar.gz"

mkdir -p ~/.cpanm

cat << 'EOF' > metaerg.yml
name: metaerg
channels:
  - bioconda
  - conda-forge
dependencies:
  - perl-archive-extract
  - perl-bioperl
  - perl-bio-eutilities
  - perl-dbd-sqlite
  - perl-dbi
  - perl-file-copy-recursive
  - perl-lwp-protocol-https
  - aragorn
  - blast
  - diamond
  - hmmer
  - minced
  - prodigal
  - perl-app-cpanminus
  - wget
  - python=2.7
  - git
  - patch
EOF
conda env create -f "metaerg.yml" -p "$targetdir"
rm "metaerg.yml"
tar xzf "$tmhmm" -C "$targetdir"
tar xzf "$signalp" -C "$targetdir"
olddir="$(pwd)"
cd "$targetdir"
source activate ./
cpanm "$swissknife" -n


#
# MinPath
#
wget -qO- "$minpath" | tar -xzf - 

cat << 'EOF' > etc/conda/activate.d/minpath-activate.sh
export MinPath_CONDA_BACKUP=${MINPATH:-}
export MinPath=$CONDA_PREFIX/MinPath
EOF

cat << 'EOF' > etc/conda/deactivate.d/minpath-deactivate.sh
export MinPath=$MinPath_CONDA_BACKUP
unset MinPath_CONDA_BACKUP
if [ -z $MinPath ]; then
    unset MinPath
fi
EOF

ln -sr $(echo "MinPath/MinPath?.?.py") "bin/MinPath.py"


shebangfix='1 s,^.*$,#!/usr/bin/env perl,'
unamefix="s/\`uname -m\`/'i386'/"

#
# TMHMM
#
mv tmhmm-?.??/bin/* bin/
mv tmhmm-?.??/lib/* lib/

sed -i "$shebangfix" bin/tmhmm
sed -i "$shebangfix" bin/tmhmmformat.pl

if [ "$tmhmm32bit" = true ] ; then
   sed -i "$unamefix" bin/tmhmm
fi

#
# Signalp
#

mv signalp-?.??/bin/* bin/
mv signalp-?.??/lib/* lib/

#
# Metaerg
#
git clone https://github.com/xiaoli-dong/metaerg.git metaerg

ln -sr metaerg/bin/*.pl bin/

check_tools.pl

cd $olddir

echo 
echo "Finished! You can now just activate the conda env (source activate $targetdir) and run the MetaErg scripts. You probably still have to download or build the database."
echo "Download:"
echo "wget http://ebg.ucalgary.ca/metaerg/db.tar.gz"
echo "(After activation) Build into the metaerg default folder:"
echo "setup_db.pl -o $targetdir/metaerg -v 132 # SILVA version"