antismash.build

. tools.config

set -e

if [ ! -f ${PREFIX}/bin/diamond ]; then
  bash -x diamond.build
fi

if [ ! -f ${PREFIX}/bin/prodigal ]; then
  bash -x prodigal.build
fi

if [ ! -f ${PREFIX}/bin/blastp ]; then
  bash -x blast.build
fi

if [ ! -f ${PREFIX}/bin/hmmpfam2 ]; then
  bash -x hmmer2.build
fi

if [ ! -f ${PREFIX}/bin/hmmscan ]; then
  bash -x hmmer3.build
fi

if [ ! -f ${PREFIX}/bin/muscle ]; then
  bash -x muscle.build
fi

if [ ! -f ${PREFIX}/bin/FastTree ]; then
  bash -x fasttree.build
fi

if [ ! -f ${PREFIX}/bin/glimmerhmm ]; then
  bash -x glimmerhmm.build
fi

if [ ! -f ${PREFIX}/bin/meme ]; then
  bash -x meme.build
fi

if [ ! -f ${PREFIX}/bin/python3 ]; then
  bash -x python3.build
fi

python -m venv ${PREFIX}/lib/venvs/antismash
source ${PREFIX}/lib/venvs/antismash/bin/activate


VERSION=5.1.2

wget -q https://github.com/antismash/antismash/archive/5-1-2.tar.gz
tar xzf 5-1-2.tar.gz
cd antismash-5-1-2

# pfam 32.0 update
wget -q -O - https://github.com/antismash/antismash/commit/210228d7920a23775d1defea0531c9ca786a9660.patch \
  | patch -p1

# pfam2go update
wget -q -O - https://github.com/antismash/antismash/commit/e88a9601c36998d7812a8f21c0042f7e03b6eb92.patch \
  | patch -p1

# Improve thioamide-NRP rules
wget -q -O - https://github.com/antismash/antismash/commit/d9593343f05e82dc30646dd5cd83f0fda66bf966.patch \
  | patch -p1

# find more transAT-PKS clusters
wget -q -O - https://github.com/antismash/antismash/commit/e78eef4aa07af4b6dfdc72611bbb299a7dc04431.patch \
  | patch -p1

# clusterfinder: fix subregions being added twice
wget -q -O - https://github.com/antismash/antismash/commit/aa8968e6d7bc8c220af1e0256a2949873866bf0f.patch \
  | patch -p1


pip3 install helperlibs
pip3 install numpy
pip3 install matplotlib
pip3 install jinja2
pip3 install bcbio-gff
pip3 install pyScss
pip3 install pysvg-py3

python3 setup.py install 

cd ..
rm -rf 5-1-2.tar.gz antismash-5-1-2


ln -sf ${PREFIX}/lib/venvs/antismash/bin/antismash ${PREFIX}/bin/
ln -sf ${PREFIX}/lib/venvs/antismash/bin/download-antismash-databases ${PREFIX}/bin/
chgrp -h ${GROUP} ${PREFIX}/bin/{antismash,download-antismash-databases}