adapt mantis changes in runscripts/binny_tmux.sh

runscripts/binny_tmux.sh

@@ -114,11 +114,16 @@ elif [ "$INITIAL" = true ]; then
  eval $LOADING_MODULES
  eval $CONDA_START
  echo 'Getting MANTIS'
- # mkdir -r ${DIR}/workflow/bin/mantis
- # git clone https://github.com/PedroMTQ/mantis.git ${DIR}/workflow/bin/mantis
- curl -L https://github.com/PedroMTQ/mantis/archive/master.zip --output $DIR/workflow/bin/mantis.zip
- unzip -q $DIR/workflow/bin/mantis.zip -d $DIR/workflow/bin/ && mv $DIR/workflow/bin/mantis-master $DIR/workflow/bin/mantis && rm $DIR/workflow/bin/mantis.zip
- snakemake $SNAKEMAKE_EXTRA_ARGUMENTS --verbose --cores 1 -s $DIR/Snakefile --conda-create-envs-only --use-conda --conda-prefix $DIR/conda --local-cores 1 --configfile $CONFIGFILE
+ curl -L https://github.com/PedroMTQ/mantis/archive/refs/tags/1.3.zip --output $DIR/workflow/bin/mantis.zip
+ unzip -q $DIR/workflow/bin/mantis.zip -d $DIR/workflow/bin/ && mv $DIR/workflow/bin/mantis-1.3 $DIR/workflow/bin/mantis \
+ && rm $DIR/workflow/bin/mantis.zip
+ echo 'Getting UniFunc'
+ # Get UniFunc release 1.1
+ curl -L https://github.com/PedroMTQ/UniFunc/archive/refs/tags/1.1.zip --output $DIR/workflow/bin/unifunc.zip
+ unzip -q $DIR/workflow/bin/unifunc.zip -d $DIR/workflow/bin/ && mv $DIR/workflow/bin/UniFunc-1.1 \
+ $DIR/workflow/bin/mantis/Resources/UniFunc && rm $DIR/workflow/bin/unifunc.zip
+ snakemake $SNAKEMAKE_EXTRA_ARGUMENTS --verbose --cores 1 -s $DIR/Snakefile --conda-create-envs-only --use-conda \
+ --conda-prefix $DIR/conda --local-cores 1 --configfile $CONFIGFILE
  DB_PATH=`grep "db_path:" $CONFIGFILE | cut -f 2 -d " "`
  temp="${DB_PATH%\"}"
  DB_PATH="${temp#\"}"
@@ -127,13 +132,14 @@ elif [ "$INITIAL" = true ]; then
  then
  DB_PATH=${DIR}/$DB_PATH
  fi
- sed -i -e "s|\#nog_hmm_folder\=|nog_hmm_folder=NA|g" \
-  -e "s|\#pfam_hmm_folder\=|pfam_hmm_folder=NA|g" \
- -e "s|\#kofam_hmm_folder\=|kofam_hmm_folder=NA|g" \
- -e "s|\#tigrfam_hmm_folder\=|tigrfam_hmm_folder=NA|g" \
- -e "s|\#ncbi_hmm_folder\=|ncbi_hmm_folder=NA|g" \
+ echo "Initializing conda environments."
+ sed -i -e "s|\#nog_ref_folder\=|nog_ref_folder=NA|g" \
+ -e "s|\#pfam_ref_folder\=|pfam_ref_folder=NA|g" \
+ -e "s|\#kofam_ref_folder\=|kofam_ref_folder=NA|g" \
+ -e "s|\#ncbi_ref_folder\=|ncbi_ref_folder=NA|g" \
  -e "s|\#ncbi_dmp_path_folder\=|ncbi_dmp_path_folder=NA|g" \
- -e "s|\#custom_ref\=path\/to\/hmm/custom1\.hmm|custom_ref=${DIR}/database/hmms/checkm_tf/checkm_filtered_tf.hmm\ncheckm_filtered_tf_weight=0.5\ncustom_ref=${DIR}/database/hmms/checkm_pf/checkm_filtered_pf.hmm\ncheckm_filtered_pf_weight=1|g" \
+ -e "s|\#tcdb_ref_folder\=|tcdb_ref_folder=NA|g" \
+ -e "s|\#custom_ref\=path\/to\/hmm/custom1\.hmm|custom_ref=${DIR}/database/hmms/checkm_tf/checkm_filtered_tf.hmm\ncheckm_filtered_tf_weight=0.5\ncustom_ref=${DIR}/database/hmms/checkm_pf/checkm_filtered_pf.hmm\ncheckm_filtered_pf_weight=1|g" \
  ${DIR}/workflow/bin/mantis/MANTIS.config
  for i in ${DIR}/conda/*.yaml; do
  env_name=$(head -n 1 ${i} | cut -d' ' -f2)