From 10d266aac4d8015dc03284f44054397b06d1b419 Mon Sep 17 00:00:00 2001 From: akrinos Date: Thu, 31 Mar 2022 09:19:14 -0400 Subject: [PATCH] Update download_database.sh --- scripts/download_database.sh | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/scripts/download_database.sh b/scripts/download_database.sh index e554df3..f39c2ed 100644 --- a/scripts/download_database.sh +++ b/scripts/download_database.sh @@ -14,27 +14,27 @@ mkdir -p $REFERENCE_DIR/$DATABASE if [[ $DATABASE == "marmmetsp" ]]; then # Download MMETSP reference FASTA - wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA $REF_FASTA_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA "$REF_FASTA_URL" ALLEXITS=$(($ALLEXITS + $?)) # Download MMETSP reference taxonomy table - wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE $REF_TABLE_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE "$REF_TABLE_URL" ALLEXITS=$(($ALLEXITS + $?)) echo "All reference files for MarRef-MMETSP downloaded to $REFERENCE_DIR/$DATABASE" elif [[ $DATABASE == "mmetsp" ]]; then # Download MMETSP reference FASTA - wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA $REF_FASTA_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA "$REF_FASTA_URL" ALLEXITS=$(($ALLEXITS + $?)) # Download MMETSP reference taxonomy table - wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE $REF_TABLE_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE "$REF_TABLE_URL" ALLEXITS=$(($ALLEXITS + $?)) echo "All reference files for MMETSP downloaded to $REFERENCE_DIR/$DATABASE" elif [[ $DATABASE == "eukprot" ]]; then # Download tar of all EukProt files - wget -O $REFERENCE_DIR/$DATABASE/$DATABASE.tgz $REF_FASTA_URL + wget -O $REFERENCE_DIR/$DATABASE/$DATABASE.tgz "$REF_FASTA_URL" ALLEXITS=$(($ALLEXITS + $?)) # Unzip to proteins folder @@ -42,7 +42,7 @@ elif [[ $DATABASE == "eukprot" ]]; then ALLEXITS=$(($ALLEXITS + $?)) # Download EukProt taxonomy file - wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE $REF_TABLE_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE "$REF_TABLE_URL" ALLEXITS=$(($ALLEXITS + $?)) ALLFILES="" @@ -60,14 +60,14 @@ elif [[ $DATABASE == "eukprot" ]]; then echo "All reference files for EukProt downloaded to ${PWD}/$DATABASE" elif [[ $DATABASE == "phylodb" ]]; then # Download PhyloDB reference FASTA - wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA.gz $REF_FASTA_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_FASTA.gz "$REF_FASTA_URL" gunzip -f $REFERENCE_DIR/$DATABASE/$REF_FASTA.gz #sed -i -e 's/>* .*$//' $REFERENCE_DIR/$DATABASE/$REF_FASTA #sed -i $'s/\t/ /g' $REFERENCE_DIR/$DATABASE/$REF_FASTA ALLEXITS=$(($ALLEXITS + $?)) # Download PhyloDB reference taxonomy table - wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE.gz $REF_TABLE_URL + wget -O $REFERENCE_DIR/$DATABASE/$REF_TABLE.gz "$REF_TABLE_URL" gunzip -f $REFERENCE_DIR/$DATABASE/$REF_TABLE.gz ALLEXITS=$(($ALLEXITS + $?)) @@ -89,4 +89,4 @@ elif [[ $DATABASE == "eukzoo" ]]; then else echo "Specified database not found." exit 1 -fi \ No newline at end of file +fi