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database-setup.sh
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#!/bin/bash
VERSION=1.0
help_message () {
echo""
echo "MuDoGeR database script v=$VERSION"
echo "Usage: bash -i database-setup.sh --dbs [module] -o output_folder_for_dbs"
echo ""
echo " --dbs all download and install the necessaries databases for all MuDoGeR modules [default]"
echo " --dbs prokaryotes download and install the necessaries databases for prokaryotes module"
echo " --dbs viruses download and install the necessaries databases for viruses module"
echo " --dbs eukaryotes download and install the necessaries databases for eukaryotes module"
echo " -o path/folder/to/save/dbs output folder where you want to save the downloaded databases"
echo " --help | -h show this help message"
echo " --version | -v show mudoger version"
echo "";}
active_module="all"
while true; do
case "$1" in
--dbs) active_module=$2; shift 2;;
-o) database_location=$2; shift 2;;
-h | --help) help_message; exit 1; shift 1;;
-v | --version) echo "$VERSION"; exit 1; shift 1;;
--) help_message; exit 1; shift; break ;;
*) break;;
esac
done
mkdir -p "$database_location"
conda activate mudoger_env
config_file="$(which config.sh)"
source "$config_file"
echo DATABASES_LOCATION="$database_location" > ${config_file/config/database}
if [ "$active_module" = "all" ]; then
############################################### PROKARYOTES ###############################################
### CheckM
mkdir -p "$database_location"/checkm
cd "$database_location"/checkm
if [ ! -f selected_marker_sets.tsv ]; then
echo 'installing checkm database ...'
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xf checkm_data_2015_01_16.tar.gz
rm -fr checkm_data_2015_01_16.tar.gz
CHECKM_DB="$database_location"/checkm #Fixed? we need to test
echo CHECKM_DB="$CHECKM_DB" >> "$config_path"
else echo "-> your CheckM database is ready"
fi
### GTDB-tk
mkdir -p "$database_location"/"gtdbtk"
cd "$database_location"/"gtdbtk"
if [ ! -d release* ]; then
#https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz
#wget https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_v2_data.tar.gz
wget https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz
#tar xzf gtdbtk_data.tar.gz
#rm -fr gtdbtk_data.tar.gz
# Extract the contents (assuming a tar archive)
tar xzf gtdbtk_data.*
# Remove the downloaded file
rm -fr gtdbtk_data.*
else echo "-> your GTDBtk database is ready"
fi
############################################### VIRUSES ###############################################
## VIBRANT
VIBRANT_DB_DIR=$database_location/vibrant
if [ ! -f $VIBRANT_DB_DIR/Pfam-A_v32.HMM.h3p ] ;
then
#echo 'let us download '$VIBRANT_DB_DIR
conda activate $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
pip install pickle-mixin --quiet
if [ ! -f $VIBRANT_DB_DIR/vog.hmm.tar.gz ] ; then
wget http://fileshare.csb.univie.ac.at/vog/vog94/vog.hmm.tar.gz -P $VIBRANT_DB_DIR
else :; fi
if [ ! -f $VIBRANT_DB_DIR/Pfam-A.hmm.gz ]; then
wget https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz -P $VIBRANT_DB_DIR
else :; fi
if [ ! -f $VIBRANT_DB_DIR/profiles.tar.gz ]; then
wget https://www.genome.jp/ftp/db/kofam/archives/2023-08-01/profiles.tar.gz -P $VIBRANT_DB_DIR
else :; fi
#echo 'downloaded'
tar -xzf $VIBRANT_DB_DIR/vog.hmm.tar.gz -C $VIBRANT_DB_DIR
gunzip $VIBRANT_DB_DIR/Pfam-A.hmm.gz -d $VIBRANT_DB_DIR
tar -xzf $VIBRANT_DB_DIR/profiles.tar.gz -C $VIBRANT_DB_DIR
#echo 'decompressed'
for v in $VIBRANT_DB_DIR/VOG*.hmm;
do cat $v >> $VIBRANT_DB_DIR/vog_temp.HMM;
done
for k in $VIBRANT_DB_DIR/profiles/K*.hmm;
do cat $k >> $VIBRANT_DB_DIR/kegg_temp.HMM;
done
#echo 'concatenated'
rm -f $VIBRANT_DB_DIR/VOG0*.hmm
rm -f $VIBRANT_DB_DIR/VOG1*.hmm
rm -f $VIBRANT_DB_DIR/VOG2*.hmm
rm -rf $VIBRANT_DB_DIR/profiles
#echo 'clean'
prof_names="${CONDA_PREFIX}/share/vibrant-1.2.1/db/databases/profile_names"
cp -r $prof_names $VIBRANT_DB_DIR
hmmfetch -o $VIBRANT_DB_DIR/VOGDB94_phage.HMM -f $VIBRANT_DB_DIR/vog_temp.HMM $VIBRANT_DB_DIR/profile_names/VIBRANT_vog_profiles.txt
hmmfetch -o $VIBRANT_DB_DIR/KEGG_profiles_prokaryotes.HMM -f $VIBRANT_DB_DIR/kegg_temp.HMM $VIBRANT_DB_DIR/profile_names/VIBRANT_kegg_profiles.txt
mv $VIBRANT_DB_DIR/Pfam-A.hmm $VIBRANT_DB_DIR/Pfam-A_v32.HMM
rm -rf $VIBRANT_DB_DIR/vog_temp.HMM $VIBRANT_DB_DIR/kegg_temp.HMM $VIBRANT_DB_DIR/vog.hmm.tar.gz $VIBRANT_DB_DIR/profiles.tar.gz
hmmpress $VIBRANT_DB_DIR/VOGDB94_phage.HMM
hmmpress $VIBRANT_DB_DIR/KEGG_profiles_prokaryotes.HMM
hmmpress $VIBRANT_DB_DIR/Pfam-A_v32.HMM
echo '---> hmmfetch and hmmpressed'
yes | cp -r $VIBRANT_DB_DIR files $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
conda deactivate
echo '-> your VIBRANT database is now ready'
else echo '-> your VIBRANT database is ready'
fi
# WISH
WISH_DB_DIR=$database_location/wish
if [ ! -f $database_location/.wish_db_finished ];
then
mkdir -p $WISH_DB_DIR
wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz" -P $WISH_DB_DIR
#old links
#wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz" -P $WISH_DB_DIR
#wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.3.1.genomic.fna.gz" -P $WISH_DB_DIR
#wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.4.1.genomic.fna.gz" -P $WISH_DB_DIR
gunzip $WISH_DB_DIR/*
cat $WISH_DB_DIR/* > $WISH_DB_DIR/viral_refseq.fna
python3 $MUDOGER_DEPENDENCIES_PATH/split-all-seq.py $WISH_DB_DIR/viral_refseq.fna $WISH_DB_DIR/viruses
for d in $WISH_DB_DIR/viruses-*fa;
do
if grep -q phage "$d";
then :;
else
rm -f "$d";
fi;
done
mv $WISH_DB_DIR/viruses* $WISH_DB_DIR/phages
rm -rf $WISH_DB_DIR/viral.1.1.genomic.fna #$WISH_DB_DIR/viral.2.1.genomic.fna $WISH_DB_DIR/viral.3.1.genomic.fna $WISH_DB_DIR/viral.4.1.genomic.fna $WISH_DB_DIR/viral_refseq.fna
touch $database_location/.wish_db_finished
else
echo "-> your Wish database is ready"
fi
### CheckV
mkdir -p "$database_location"/checkv
cd "$database_location"/checkv
if [ ! -d checkv-db-v1.0 ]; then
wget https://portal.nersc.gov/CheckV/checkv-db-v1.0.tar.gz
tar -zxf checkv-db-v1.0.tar.gz
rm -fr checkv-db-v1.0.tar.gz
else echo "-> your CheckV database is ready"
fi
############################################### EUKARYOTES ###############################################
### EukCC
mkdir -p "$database_location"/eukccdb
cd "$database_location"/eukccdb
if [ ! -d "$database_location"/eukccdb/db_base ]; then
wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_1.1.tar.gz
tar -xzf eukcc2_db_ver_1.1.tar.gz
rm -fr eukcc2_db_ver_1.1.tar.gz
mv eukcc2_db_ver_1.1/* ./
rm -fr eukcc2_db_ver_1.1/
else echo "-> your EUKCC database is ready"
fi
### BUSCO eukaryotes database
mkdir -p "$database_location"/buscodbs
cd "$database_location"/buscodbs
if [ ! -d "$database_location"/buscodbs/lineages/eukaryota_odb10 ]; then
conda activate "$MUDOGER_DEPENDENCIES_ENVS_PATH"/busco_env
busco --download_path "$database_location"/buscodbs --download "eukaryota"
else echo "-> your BUSCO eukaryotes database is ready"
fi
elif [ "$active_module" = "prokaryotes" ]; then
############################################### PROKARYOTES ###############################################
### CheckM
mkdir -p "$database_location"/checkm
cd "$database_location"/checkm
if [ ! -f selected_marker_sets.tsv ]; then
echo 'installing checkm database ...'
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xf checkm_data_2015_01_16.tar.gz
rm -fr checkm_data_2015_01_16.tar.gz
CHECKM_DB="$database_location"/checkm #Fixed? we need to test
echo CHECKM_DB="$CHECKM_DB" >> "$config_path"
else echo "-> your CheckM database is ready"
fi
### GTDB-tk
mkdir -p "$database_location"/"gtdbtk"
cd "$database_location"/"gtdbtk"
if [ ! -d release* ]; then
#https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz
#wget https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_v2_data.tar.gz
#tar -xzf gtdbtk_v2_data.tar.gz
#rm -fr gtdbtk_v2_data.tar.gz
wget https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz
# Extract the contents (assuming a tar archive)
tar xzf gtdbtk_data.*
# Remove the downloaded file
rm -fr gtdbtk_data.*
else echo "-> your GTDBtk database is ready"
fi
elif [ "$active_module" = "viruses" ]; then
############################################### VIRUSES ###############################################
## VIBRANT
conda activate $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
pip install pickle-mixin --quiet
VIBRANT_DB_DIR=$database_location/vibrant
if [ ! -f $VIBRANT_DB_DIR/Pfam-A_v32.HMM.h3p ] ;
then
#echo 'let us download '$VIBRANT_DB_DIR
if [ ! -f $VIBRANT_DB_DIR/vog.hmm.tar.gz ] ; then
wget http://fileshare.csb.univie.ac.at/vog/vog94/vog.hmm.tar.gz -P $VIBRANT_DB_DIR
else :; fi
if [ ! -f $VIBRANT_DB_DIR/Pfam-A.hmm.gz ]; then
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz -P $VIBRANT_DB_DIR
else :; fi
if [ ! -f $VIBRANT_DB_DIR/profiles.tar.gz ]; then
wget ftp://ftp.genome.jp/pub/db/kofam/archives/2019-08-10/profiles.tar.gz -P $VIBRANT_DB_DIR
else :; fi
#echo 'downloaded'
tar -xzf $VIBRANT_DB_DIR/vog.hmm.tar.gz -C $VIBRANT_DB_DIR
gunzip $VIBRANT_DB_DIR/Pfam-A.hmm.gz -d $VIBRANT_DB_DIR
tar -xzf $VIBRANT_DB_DIR/profiles.tar.gz -C $VIBRANT_DB_DIR
#echo 'decompressed'
for v in $VIBRANT_DB_DIR/VOG*.hmm;
do cat $v >> $VIBRANT_DB_DIR/vog_temp.HMM;
done
for k in $VIBRANT_DB_DIR/profiles/K*.hmm;
do cat $k >> $VIBRANT_DB_DIR/kegg_temp.HMM;
done
#echo 'concatenated'
rm -f $VIBRANT_DB_DIR/VOG0*.hmm
rm -f $VIBRANT_DB_DIR/VOG1*.hmm
rm -f $VIBRANT_DB_DIR/VOG2*.hmm
rm -rf $VIBRANT_DB_DIR/profiles
#echo 'clean'
prof_names="$(echo $PATH | sed "s/:/\n/g" | grep vibrant | sed "s/bin/share\/vibrant-1.2.0\/databases\/profile_names/g")"
cp -r $prof_names $VIBRANT_DB_DIR
hmmfetch -o $VIBRANT_DB_DIR/VOGDB94_phage.HMM -f $VIBRANT_DB_DIR/vog_temp.HMM $VIBRANT_DB_DIR/profile_names/VIBRANT_vog_profiles.txt
hmmfetch -o $VIBRANT_DB_DIR/KEGG_profiles_prokaryotes.HMM -f $VIBRANT_DB_DIR/kegg_temp.HMM $VIBRANT_DB_DIR/profile_names/VIBRANT_kegg_profiles.txt
mv $VIBRANT_DB_DIR/Pfam-A.hmm $VIBRANT_DB_DIR/Pfam-A_v32.HMM
rm -rf $VIBRANT_DB_DIR/vog_temp.HMM $VIBRANT_DB_DIR/kegg_temp.HMM $VIBRANT_DB_DIR/vog.hmm.tar.gz $VIBRANT_DB_DIR/profiles.tar.gz
hmmpress $VIBRANT_DB_DIR/VOGDB94_phage.HMM
hmmpress $VIBRANT_DB_DIR/KEGG_profiles_prokaryotes.HMM
hmmpress $VIBRANT_DB_DIR/Pfam-A_v32.HMM
#echo 'hmmfetch and hmmpressed'
chmod +x $MUDOGER_CLONED_TOOLS_PATH/VIBRANT/scripts/*
cp -rf $MUDOGER_CLONED_TOOLS_PATH/VIBRANT/scripts $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
chmod +x $MUDOGER_CLONED_TOOLS_PATH/VIBRANT/VIBRANT_run.py
cp $MUDOGER_CLONED_TOOLS_PATH/VIBRANT/VIBRANT_run.py $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
cp -r $VIBRANT_DB_DIR files $MUDOGER_DEPENDENCIES_ENVS_PATH/vibrant_env
conda deactivate
echo '-> your VIBRANT database is now ready'
else echo '-> your VIBRANT database is ready'
fi
# WISH
WISH_DB_DIR=$database_location/wish
if [ ! -f $database_location/.wish_db_finished ];
then
mkdir -p $WISH_DB_DIR
wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz" -P $WISH_DB_DIR
wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz" -P $WISH_DB_DIR
wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.3.1.genomic.fna.gz" -P $WISH_DB_DIR
wget "https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.4.1.genomic.fna.gz" -P $WISH_DB_DIR
gunzip $WISH_DB_DIR/*
cat $WISH_DB_DIR/* > $WISH_DB_DIR/viral_refseq.fna
python3 $MUDOGER_DEPENDENCIES_PATH/split-all-seq.py $WISH_DB_DIR/viral_refseq.fna $WISH_DB_DIR/viruses
for d in $WISH_DB_DIR/viruses-*fa;
do
if grep -q phage "$d";
then :;
else
rm -f "$d";
fi;
done
mv $WISH_DB_DIR/viruses* $WISH_DB_DIR/phages
rm -rf $WISH_DB_DIR/viral.1.1.genomic.fna $WISH_DB_DIR/viral.2.1.genomic.fna $WISH_DB_DIR/viral.3.1.genomic.fna $WISH_DB_DIR/viral.4.1.genomic.fna $WISH_DB_DIR/viral_refseq.fna
touch $database_location/.wish_db_finished
else
echo "-> your Wish database is ready"
fi
### CheckV
mkdir -p "$database_location"/checkv
cd "$database_location"/checkv
if [ ! -d checkv-db-v1.0 ]; then
wget https://portal.nersc.gov/CheckV/checkv-db-v1.0.tar.gz
tar -zxf checkv-db-v1.0.tar.gz
rm -fr checkv-db-v1.0.tar.gz
else echo "-> your CheckV database is ready"
fi
elif [ "$active_module" = "eukaryotes" ]; then
############################################### EUKARYOTES ###############################################
### EukCC
mkdir -p "$database_location"/eukccdb
cd "$database_location"/eukccdb
if [ ! -d "$database_location"/eukccdb/db_base ]; then
wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_1.1.tar.gz
tar -xzf eukcc2_db_ver_1.1.tar.gz
rm -fr eukcc2_db_ver_1.1.tar.gz
mv eukcc2_db_ver_1.1/* ./
rm -fr eukcc2_db_ver_1.1/
else echo "-> your EUKCC database is ready"
fi
### BUSCO eukaryotes database
mkdir -p "$database_location"/buscodbs
cd "$database_location"/buscodbs
if [ ! -d "$database_location"/buscodbs/lineages/eukaryota_odb10 ]; then
conda activate "$MUDOGER_DEPENDENCIES_ENVS_PATH"/busco_env
busco --download_path "$database_location"/buscodbs --download "eukaryota"
else echo "-> your BUSCO eukaryotes database is ready"
fi
else
comm "Please select a proper parameter."
help_message
exit 1
fi