Merge branch 'master' of github.com:AlexanderLabWHOI/EUKulele

AlexanderLabWHOI · Apr 4, 2022 · 747e7e7 · 747e7e7
2 parents 1475a5e + 668f3a1
commit 747e7e7
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 10 deletions.
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -27,7 +27,6 @@ requirements:
     - python-coveralls
     - pytest-cov
     - pytest-xdist 
-
     - blast 
 #    - busco==4.1.4
     - diamond 

diff --git a/scripts/download_database.sh b/scripts/download_database.sh
@@ -14,35 +14,35 @@ 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
     tar zxvf $REFERENCE_DIR/$DATABASE/$DATABASE.tgz -C $REFERENCE_DIR/$DATABASE
     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
+fi