trying to get funannotate to work

setup_funannotate

# trying to follow the sparse/incomplete instructions here:
# https://funannotate.readthedocs.io/en/latest/conda.html#conda
# also guided by running funannotate check --show-versions
# should look like https://funannotate.readthedocs.io/en/latest/dependencies.html

module load miniconda

conda create -yn funannotate -c bioconda -c conda-forge biopython \
                                                        matplotlib \
                                                        natsort \
                                                        numpy \
                                                        pandas \
                                                        psutil \
                                                        python=2.7 \
                                                        requests \
                                                        scikit-learn \
                                                        scipy \
                                                        seaborn \
source activate funannotate

conda install -yc bioconda -c conda-forge 'augustus=3.2.3' \
                                          'repeatmasker=4.0.*' \
                                          'repeatmodeler=1.0.*' \
                                          'trinity=2.5.*' \
                                          bedtools \
                                          blast \
                                          blat \
                                          bowtie2 \
                                          codingquarry \
                                          diamond \
                                          eggnog-mapper \
                                          exonerate \
                                          fisher \
                                          gcc_impl_linux-64 \
                                          gcc_linux-64 \
                                          gfortran_impl_linux-64 \
                                          gfortran_linux-64 \
                                          gmap \
                                          goatools \
                                          hisat2 \
                                          hmmer \
                                          infernal \
                                          kallisto \
                                          minimap2 \
                                          mummer \
                                          perl-bioperl \
                                          perl-carp \
                                          perl-clone \
                                          perl-data-dumper \
                                          perl-db-file \
                                          perl-dbd-mysql \
                                          perl-dbd-sqlite \
                                          perl-file-which \
                                          perl-getopt-long \
                                          perl-hash-merge \
                                          perl-json \
                                          perl-parallel-forkmanager \
                                          perl-pod-usage \
                                          perl-scalar-util-numeric \
                                          raxml \
                                          rmblast \
                                          samtools \
                                          stringtie \
                                          tbl2asn \
                                          trimal \
                                          trnascan-se \
                                          ucsc-pslcdnafilter
conda install -yc etetoolkit ete3 ete_toolchain
conda remove -y --force mafft

for bin in ${CONDA_PREFIX}/bin/x86_64-conda_cos6-linux-gnu-* ;
do
    ln -s $bin ${bin/x86_64-conda_cos6-linux-gnu-/}
done

cpanm Logger::Simple \
      Thread::Queue \
      threads \
      threads::shared

export DEPS_DIR="${CONDA_PREFIX}/funannotate_deps"
mkdir -p $DEPS_DIR

# MAFFT
cd $DEPS_DIR
wget https://mafft.cbrc.jp/alignment/software/mafft-7.450-linux.tgz && \
  tar xf mafft-7.450-linux.tgz && rm mafft-7.450-linux.tgz

# FASTA36
cd $DEPS_DIR
wget https://github.com/wrpearson/fasta36/releases/download/fasta-v36.3.8g/fasta-36.3.8g-linux64.tar.gz && \
  tar xf fasta-36.3.8g-linux64.tar.gz && rm fasta-36.3.8g-linux64.tar.gz && \
  mv fasta-36.3.8g fasta-36
cd $DEPS_DIR/fasta-36
for prog in ./*36
do
    ln -s $prog ${prog/36/}
done


# GeneMark-ES/ET
# go get gm_et_linux_64.tar.gz and gm_key_64.gz
cd $DEPS_DIR
tar xf gm_et_linux_64.tar.gz  --strip-components=1
gunzip -c gm_key_64.gz > gmes_petap/gm_key_64

# EVidence modeler
cd $DEPS_DIR
wget https://github.com/nextgenusfs/EVidenceModeler/archive/0.1.3.tar.gz && \
  tar xf 0.1.3.tar.gz && rm 0.1.3.tar.gz && \
  mv EVidenceModeler-0.1.3 evidencemodeler

# PASA
cd $DEPS_DIR
wget https://github.com/PASApipeline/PASApipeline/archive/pasa-v2.3.3.tar.gz && \
  tar xf pasa-v2.3.3.tar.gz && rm pasa-v2.3.3.tar.gz && \
  mv PASApipeline-pasa-v2.3.3 PASApipeline && cd PASApipeline && make clean && make

# RepeatMasker
cd $CONDA_PREFIX/share/RepeatMasker && tar xf /gpfs/ysm/datasets/db/RepBaseRepeatMaskerEdition-20170127.tar && \
  ./configure
# rmblast? prfix is /gpfs/ysm/project/NETID/conda_envs/funannotate/bin


# funannotate
cd $CONDA_PREFIX
git clone -b 1.5.1 https://github.com/nextgenusfs/funannotate.git

cat << EOF > $CONDA_PREFIX/etc/conda/activate.d/00-funnanotate_activate.sh
export PRE_FUN_PATH=$PATH
export PATH=$CONDA_PREFIX/funannotate:$DEPS_DIR/mafft-linux64:$DEPS_DIR/mafft-linux64/bin:$DEPS_DIR/fasta-36/bin:$DEPS_DIR/PASApipeline:$DEPS_DIR/gmes_petap:$DEPS_DIR/evidencemodeler:$CONDA_PREFIX/bin/ete3_apps/bin:$PATH
export GENEMARK_PATH=$DEPS_DIR/gmes_petap
export PASAHOME=$DEPS_DIR/PASApipeline
export EVM_HOME=$DEPS_DIR/evidencemodeler
export BAMTOOLS_PATH=$CONDA_PREFIX/bin
export TRINITYHOME=$CONDA_PREFIX/opt/trinity-2.5.1
export GENEMARK_PATH=$DEPS_DIR/gmes_petap
EOF

cat << EOF > $CONDA_PREFIX/etc/conda/deactivate.d/00-funnanotate_deactitvate.sh
PATH=$PRE_FUN_PATH
unset GENEMARK_PATH
unset PASAHOME
unset EVM_HOME
unset BAMTOOLS_PATH
unset TRINITYHOME
unset GENEMARK_PATH
EOF

chmod +x $CONDA_PREFIX/etc/conda/activate.d/00-funnanotate_activate.sh $CONDA_PREFIX/etc/conda/deactivate.d/00-funnanotate_deactitvate.sh